Proteopedia - User contributions [en]

The Structure of PI3K

2021-04-22T18:55:31Z

Hannah Campbell:

==Structure of PI3K==
Class I [[PI3K|PI3Ks]], which are tightly regulated by tyrosine kinases, are composed of an 85kDa regulatory/adapter subunit (p85) and a 110kDa catalytic subunit (p110). <ref name="Flip"> PMID: 10525402</ref>
 

==Adapter Subunit==
<StructureSection load='1dq8' size='450' side='right' scene='User:David_Canner/Sandbox_P/Full/4' caption='Structure of PI3K p110, ([[3hhm]])'>
===The p85 Adapter Subunit===
Class IA PI3Ks are tightly associated with a 85 kDa regulatory subunit called p85.<ref name="Wymann"/> P85 contains a Src homology 3 (SH3) domain, a breakpoint-cluster region homology (BH) domain between two proline-rich regions, and two C-terminal SH2 domains separated by an inter-SH2 (iSH2) region, which tightly binds p85 to the catalytic subunit.<ref>PMID:1707345</ref> Since PI3K has multiple protein-interaction domains, p85 is able to interact with several signaling molecules simultaneously, allowing for significant fine tuning of PI3K activity. <ref name="Wymann"> PMID: 9838078</ref>

====Src Homology 3 (SH3) Domain====
<scene name='User:David_Canner/Sandbox_P/Sh3_network_open/1'>The SH3 domain of PI3K</scene> has homologues found in many intracellular signaling proteins. <ref name="Batra">PMID:19919182</ref> It mediates protein-protein interactions by binding to proline-rich motifs in target proteins forming multimeric signaling complexes. <ref>PMID:1708916</ref> Of note, the SH3 domain interacts with Src (Src homology 2/α-collagen-related), CDC42GAP (Cdc42 GTPase-activating protein) and the [[oncogene|proto-oncogene]] product Cbl. SH3 binds to proline rich ligands via a network of hydrophobic and hydrogen bond interactions, <scene name='User:David_Canner/Sandbox_P/Sh3_network/3'>particularly with the conserved residues Trp 55, Pro 70, and Tyr 73</scene> ([[3i5r]]).<ref name="Batra"/>
 

====Proline-Rich Regions====
The proline rich regions which flank the BH domain are ideal ligands for various SH3 containing non-receptor protein tyrosine kinases like [[Src]], Lyn & Fyn, often with the product of the proteo-oncogene product Cbl as a docking site. <ref>PMID:9160881</ref>
 

====Src Homology 2 (SH2) Domains====
<scene name='User:David_Canner/Sandbox_P/Sh2_open/1'>PI3K has two SH2 domains</scene>, an N-terminal (nSH2) domain and a C-terminal (CSH2) domain. <ref name="Flip"/> Both domains recognize similar consensus phosphorylated tyrosine motifs with the pattern: pY-V-X-M in activated receptors and adaptor proteins like PDGF, erbB3, c-Kit and CSF-1 receptors. <ref name="Weber">PMID:11123912</ref> It is upon the interaction of receptor and SH2 domain that the heterodimeric PI3K complex is activated. <ref name="Miled"> PMID: 17626883</ref> The <scene name='User:David_Canner/Sandbox_P/Sh2/2'>docking site for receptor in NSH2 is defined by the conserved residues Arg 340, Arg 358, and Thr 371</scene> ([[2iui]]), all of which coordinate the phosphorylated tyrosoine phosphate group.<ref name="Nolte"> PMID:8599763</ref> nSH2 was found to interact with the catalytic subunit directly, forming a broad-based scaffold for p110α and coordinates communication between the interacting domains. (Discussed Below). <ref name="Amzel"/>
 

====BH Domain====
The BH domain specifically interacts with the Rho family proteins, Cdc42 and Rac1. Although no crystal structure of the BH domain has been solved to date, mutagenesis experiments have verified that the conserved residues Arg 151, Lys 187 and Pro 270 play important roles in the interaction with Rac1 and Cdc42. <ref name="Wymann"/>
 

====Inter-SH2 (iSH2) Region====
The <scene name='User:David_Canner/Sandbox_P/Ish2/2'>iSH2, two long coiled alpha helices</scene> ([[2v1y]]), is flanked by the two <scene name='User:David_Canner/Sandbox_P/Sh2_flanked_ish2/1'>SH2 domains</scene>. The primary purpose of the iSH2 is to <scene name='User:David_Canner/Sandbox_P/Abd/3'>tightly bind the adaptor-binding domain (ABD) on the catalytic p110 subunit</scene> ([[3hhm]]), effectively holding the PI3K heterodimer together. In fact, disruption of this interaction via antibodies prevents the formation of the PI3K heterodimer completely. <ref name="Wymann"/> It is further believed that binding of phosphopetide by the SH2 domains causes conformational strains which is <scene name='User:David_Canner/Sandbox_P/Ish2_propagation/2'>propagated to the catalytic subunit directly and via the iSH2</scene><ref name="Wymann"/>
 

==Regulation of Class IA PI3K via p85 Phosphorylation==
All PI3K catalytic subunits possess intrinsic protein serine kinase activity. PI3K regulatory subunits can be phophorylated by the catalytic subunit (p110) at specific sites. For example, phophorylation of Ser 608, a residue located in an area of the iSH2 domain that is critical for PIP2 presentation to the catalytic subunit, results in a dramatic reduction in PI3K lipid kinase activity.<ref>PMID: 8313897</ref> Additionally, tyrosines 580 and 607 can be phosphorylated upon stimulation with insulin and growth factor along with <scene name='User:David_Canner/Sandbox_P/Tyr_508/1'>Tyr 508 upon PDGF receptor mediation</scene>. <ref name="Wymann"/> Phosphorylation of Tyr 688 in the CSH2 domain by Abl and Lck results in reduced affinity for phosphopeptides and subsequent activation of the catalytic domain. <ref>PMID:9461588 </ref>
 

==The Catalytic Subunit==

===The Catalytic Subunit (P110) of Class 1 PI3Ks===
The catalytic subunit, P110 has several isoforms that associate with different classes of PI3Ks. P110α, β, and δ associate with Class IA PI3Ks while p110γ associates with Class 1B PI3ks. <ref name="Wymann"/> The <scene name='User:David_Canner/Sandbox_P/Full/1'>p110α subunit contains several domains including</scene> an N-terminal adaptor-binding domain (ABD), a Ras binding domain (RBD) a C2 domain that likely binds to the cellular membrane, a helical domain (HD) with unknown function, and the actual catalytic kinase domain. <ref name="Amzel"> PMID: 19805105 </ref> The actions of these domains are coordinated by the nSH2 communicating domain in p85.
<html5media height="360" width="640">https://vimeo.com/540290912</html5media>

The video above depicts the ATP binding pocket of PI3K.
 

===Communication between nSH2 & The Catalytic Subunit Domains===
<scene name='User:David_Canner/Sandbox_P/Nsh2_full/1'>The alpha-A helix of NSH2 </scene> (residues 340-345) is anchored into <scene name='User:David_Canner/Sandbox_P/Nsh2_pocket/2'> a cavity created by the C2 and Kinase domain interface.</scene> Helix α11K of the <scene name='User:David_Canner/Sandbox_P/Kinase_domain_out/2'>Kinase domain</scene> (residues 1017-1024) <scene name='User:David_Canner/Sandbox_P/Nsh2_kianse/1'>interacts with the alpha-A helix of nSH2.</scene> nSH2 interacts with the <scene name='User:David_Canner/Sandbox_P/C2_out/3'>C2 domain</scene> through a network of charge-charge interactions involving two loops on nSH2 (Residues 374-377 & 350-354) and C2 residues 364-371, a strong <scene name='User:David_Canner/Sandbox_P/Nsh2_charge_charge/3'>salt bridge between NSH2 Glu 349 and C2 residue Arg 357, and hydrogen bonds between NSH2 Glu 348 and C2 Glu 453 and Asp 454.</scene> <ref name="Amzel"/>
 

The <scene name='User:David_Canner/Sandbox_P/Helical_overview/2'>helical domain in p110</scene>, whose function isn’t thoroughly understood, interacts with nSH2 via charge interactions. The HD residue, <scene name='User:David_Canner/Sandbox_P/Helical_domain/1'>Glu 542 forms a salt bridge with Arg 358 on NSH2 while Glu 545 interacts with NSH2 Lys 379</scene>. These residues are known hotspot mutations which are associated with various types of cancer. <ref name="Amzel"/> This loop in <scene name='User:David_Canner/Sandbox_P/Nsh2__and_helical_ligand_out/2'>the helical domain </scene> which contains the hotspots (residues 542-546) is located precisely where <scene name='User:David_Canner/Sandbox_P/Nsh2_ligand_just_ligand_full/1'> the phosphopeptide of NSH2 ligands, like PDGFR, bind to NSH2.</scene> The salt bridge formed between <scene name='User:David_Canner/Sandbox_P/Nsh2_disruption_of_salt/1'>Glu 542 and nSH2 is disrupted upon binding phosphorylated peptides</scene> like PDGFR, eliminating nSH2-mediated inhibition of p110α and activating the enzyme to phosphorylate PIP2 into PIP3. The hotspot mutation at Glu 542 accomplishes the same thing by eliminating the salt bridge and uninhibiting p110α. It is the <scene name='User:David_Canner/Sandbox_P/Kinase_with_atp_full/2'>kinase domain </scene> which <scene name='User:David_Canner/Sandbox_P/Kinase_with_atp_zoomed/3'>binds ATP to provide the phosphate group</scene> used to convert PIP2 into PIP3. <ref name="Amzel"/>

===Model for Catalysis===
Although no <scene name='User:David_Canner/Sandbox_P/Inhibitor_main/4'>crystal structure of PI3K</scene> with bound substate analog has been solved, a model for PIP2 phosphorylation has been developed and is generally supported. <ref name="Walker2">PMID:10580505</ref> In this model, the headgroup of PIP2 is <scene name='User:David_Canner/Sandbox_P/Catalytic_cavity/2'>positioned in a cavity</scene> between the <scene name='User:David_Canner/Sandbox_P/Catalytic_site/1'>C-terminal helix 12 of the kinase domain, the “activation” loop, and the “catalytic” loop</scene>. This puts the 5-phosphate of PIP2 near Lys 973 and the <scene name='User:David_Canner/Sandbox_P/Catalytic_site_atp_lys/1'>I-phosphate of ATP near Lys 807 and Lys 808</scene>. The <scene name='User:David_Canner/Sandbox_P/Catalytic_site_pip2/1'>basic residues Arg 947</scene> and Lys 973 can bind the 4-Phosphate of PIP2 and help provide the Class I PI3Ks with their specificity for PIP2. Once PIP2 and ATP are bound, it is believed <scene name='User:David_Canner/Sandbox_P/Catalytic_site_his/1'>His 948 rotates to interact with PIP2</scene>, deprotonating it at the C-3 Hydroxyl position creating a nucleophile. This nucleophile subsequently attacks the gamma phosphate of ATP producing PIP3. <ref name="Walker2"/>
</StructureSection>

==Additional Resources==
* See [[Phosphoinositide 3-Kinases]] for the main page or [[PI3K Activation, Inhibition, & Medical Implications]] for PI3Ks medical importance.
* See [[Cancer]] for additional information.
* See [[Diabetes]] for additional information.

==References==
<references/>
__NOTOC__
__NOEDITSECTION__

The Structure of PI3K

2021-04-22T18:54:50Z

Hannah Campbell:

==Structure of PI3K==
Class I [[PI3K|PI3Ks]], which are tightly regulated by tyrosine kinases, are composed of an 85kDa regulatory/adapter subunit (p85) and a 110kDa catalytic subunit (p110). <ref name="Flip"> PMID: 10525402</ref>
 

==Adapter Subunit==
<StructureSection load='1dq8' size='450' side='right' scene='User:David_Canner/Sandbox_P/Full/4' caption='Structure of PI3K p110, ([[3hhm]])'>
===The p85 Adapter Subunit===
Class IA PI3Ks are tightly associated with a 85 kDa regulatory subunit called p85.<ref name="Wymann"/> P85 contains a Src homology 3 (SH3) domain, a breakpoint-cluster region homology (BH) domain between two proline-rich regions, and two C-terminal SH2 domains separated by an inter-SH2 (iSH2) region, which tightly binds p85 to the catalytic subunit.<ref>PMID:1707345</ref> Since PI3K has multiple protein-interaction domains, p85 is able to interact with several signaling molecules simultaneously, allowing for significant fine tuning of PI3K activity. <ref name="Wymann"> PMID: 9838078</ref>

====Src Homology 3 (SH3) Domain====
<scene name='User:David_Canner/Sandbox_P/Sh3_network_open/1'>The SH3 domain of PI3K</scene> has homologues found in many intracellular signaling proteins. <ref name="Batra">PMID:19919182</ref> It mediates protein-protein interactions by binding to proline-rich motifs in target proteins forming multimeric signaling complexes. <ref>PMID:1708916</ref> Of note, the SH3 domain interacts with Src (Src homology 2/α-collagen-related), CDC42GAP (Cdc42 GTPase-activating protein) and the [[oncogene|proto-oncogene]] product Cbl. SH3 binds to proline rich ligands via a network of hydrophobic and hydrogen bond interactions, <scene name='User:David_Canner/Sandbox_P/Sh3_network/3'>particularly with the conserved residues Trp 55, Pro 70, and Tyr 73</scene> ([[3i5r]]).<ref name="Batra"/>
 

====Proline-Rich Regions====
The proline rich regions which flank the BH domain are ideal ligands for various SH3 containing non-receptor protein tyrosine kinases like [[Src]], Lyn & Fyn, often with the product of the proteo-oncogene product Cbl as a docking site. <ref>PMID:9160881</ref>
 

====Src Homology 2 (SH2) Domains====
<scene name='User:David_Canner/Sandbox_P/Sh2_open/1'>PI3K has two SH2 domains</scene>, an N-terminal (nSH2) domain and a C-terminal (CSH2) domain. <ref name="Flip"/> Both domains recognize similar consensus phosphorylated tyrosine motifs with the pattern: pY-V-X-M in activated receptors and adaptor proteins like PDGF, erbB3, c-Kit and CSF-1 receptors. <ref name="Weber">PMID:11123912</ref> It is upon the interaction of receptor and SH2 domain that the heterodimeric PI3K complex is activated. <ref name="Miled"> PMID: 17626883</ref> The <scene name='User:David_Canner/Sandbox_P/Sh2/2'>docking site for receptor in NSH2 is defined by the conserved residues Arg 340, Arg 358, and Thr 371</scene> ([[2iui]]), all of which coordinate the phosphorylated tyrosoine phosphate group.<ref name="Nolte"> PMID:8599763</ref> nSH2 was found to interact with the catalytic subunit directly, forming a broad-based scaffold for p110α and coordinates communication between the interacting domains. (Discussed Below). <ref name="Amzel"/>
 

====BH Domain====
The BH domain specifically interacts with the Rho family proteins, Cdc42 and Rac1. Although no crystal structure of the BH domain has been solved to date, mutagenesis experiments have verified that the conserved residues Arg 151, Lys 187 and Pro 270 play important roles in the interaction with Rac1 and Cdc42. <ref name="Wymann"/>
 

====Inter-SH2 (iSH2) Region====
The <scene name='User:David_Canner/Sandbox_P/Ish2/2'>iSH2, two long coiled alpha helices</scene> ([[2v1y]]), is flanked by the two <scene name='User:David_Canner/Sandbox_P/Sh2_flanked_ish2/1'>SH2 domains</scene>. The primary purpose of the iSH2 is to <scene name='User:David_Canner/Sandbox_P/Abd/3'>tightly bind the adaptor-binding domain (ABD) on the catalytic p110 subunit</scene> ([[3hhm]]), effectively holding the PI3K heterodimer together. In fact, disruption of this interaction via antibodies prevents the formation of the PI3K heterodimer completely. <ref name="Wymann"/> It is further believed that binding of phosphopetide by the SH2 domains causes conformational strains which is <scene name='User:David_Canner/Sandbox_P/Ish2_propagation/2'>propagated to the catalytic subunit directly and via the iSH2</scene><ref name="Wymann"/>
 

==Regulation of Class IA PI3K via p85 Phosphorylation==
All PI3K catalytic subunits possess intrinsic protein serine kinase activity. PI3K regulatory subunits can be phophorylated by the catalytic subunit (p110) at specific sites. For example, phophorylation of Ser 608, a residue located in an area of the iSH2 domain that is critical for PIP2 presentation to the catalytic subunit, results in a dramatic reduction in PI3K lipid kinase activity.<ref>PMID: 8313897</ref> Additionally, tyrosines 580 and 607 can be phosphorylated upon stimulation with insulin and growth factor along with <scene name='User:David_Canner/Sandbox_P/Tyr_508/1'>Tyr 508 upon PDGF receptor mediation</scene>. <ref name="Wymann"/> Phosphorylation of Tyr 688 in the CSH2 domain by Abl and Lck results in reduced affinity for phosphopeptides and subsequent activation of the catalytic domain. <ref>PMID:9461588 </ref>
 

==The Catalytic Subunit==

===The Catalytic Subunit (P110) of Class 1 PI3Ks===
The catalytic subunit, P110 has several isoforms that associate with different classes of PI3Ks. P110α, β, and δ associate with Class IA PI3Ks while p110γ associates with Class 1B PI3ks. <ref name="Wymann"/> The <scene name='User:David_Canner/Sandbox_P/Full/1'>p110α subunit contains several domains including</scene> an N-terminal adaptor-binding domain (ABD), a Ras binding domain (RBD) a C2 domain that likely binds to the cellular membrane, a helical domain (HD) with unknown function, and the actual catalytic kinase domain. <ref name="Amzel"> PMID: 19805105 </ref> The actions of these domains are coordinated by the nSH2 communicating domain in p85.
<html5media height="360" width="640">https://vimeo.com/540290912</html5media>
The video above depicts the ATP binding pocket of PI3K.
 

===Communication between nSH2 & The Catalytic Subunit Domains===
<scene name='User:David_Canner/Sandbox_P/Nsh2_full/1'>The alpha-A helix of NSH2 </scene> (residues 340-345) is anchored into <scene name='User:David_Canner/Sandbox_P/Nsh2_pocket/2'> a cavity created by the C2 and Kinase domain interface.</scene> Helix α11K of the <scene name='User:David_Canner/Sandbox_P/Kinase_domain_out/2'>Kinase domain</scene> (residues 1017-1024) <scene name='User:David_Canner/Sandbox_P/Nsh2_kianse/1'>interacts with the alpha-A helix of nSH2.</scene> nSH2 interacts with the <scene name='User:David_Canner/Sandbox_P/C2_out/3'>C2 domain</scene> through a network of charge-charge interactions involving two loops on nSH2 (Residues 374-377 & 350-354) and C2 residues 364-371, a strong <scene name='User:David_Canner/Sandbox_P/Nsh2_charge_charge/3'>salt bridge between NSH2 Glu 349 and C2 residue Arg 357, and hydrogen bonds between NSH2 Glu 348 and C2 Glu 453 and Asp 454.</scene> <ref name="Amzel"/>
 

The <scene name='User:David_Canner/Sandbox_P/Helical_overview/2'>helical domain in p110</scene>, whose function isn’t thoroughly understood, interacts with nSH2 via charge interactions. The HD residue, <scene name='User:David_Canner/Sandbox_P/Helical_domain/1'>Glu 542 forms a salt bridge with Arg 358 on NSH2 while Glu 545 interacts with NSH2 Lys 379</scene>. These residues are known hotspot mutations which are associated with various types of cancer. <ref name="Amzel"/> This loop in <scene name='User:David_Canner/Sandbox_P/Nsh2__and_helical_ligand_out/2'>the helical domain </scene> which contains the hotspots (residues 542-546) is located precisely where <scene name='User:David_Canner/Sandbox_P/Nsh2_ligand_just_ligand_full/1'> the phosphopeptide of NSH2 ligands, like PDGFR, bind to NSH2.</scene> The salt bridge formed between <scene name='User:David_Canner/Sandbox_P/Nsh2_disruption_of_salt/1'>Glu 542 and nSH2 is disrupted upon binding phosphorylated peptides</scene> like PDGFR, eliminating nSH2-mediated inhibition of p110α and activating the enzyme to phosphorylate PIP2 into PIP3. The hotspot mutation at Glu 542 accomplishes the same thing by eliminating the salt bridge and uninhibiting p110α. It is the <scene name='User:David_Canner/Sandbox_P/Kinase_with_atp_full/2'>kinase domain </scene> which <scene name='User:David_Canner/Sandbox_P/Kinase_with_atp_zoomed/3'>binds ATP to provide the phosphate group</scene> used to convert PIP2 into PIP3. <ref name="Amzel"/>

===Model for Catalysis===
Although no <scene name='User:David_Canner/Sandbox_P/Inhibitor_main/4'>crystal structure of PI3K</scene> with bound substate analog has been solved, a model for PIP2 phosphorylation has been developed and is generally supported. <ref name="Walker2">PMID:10580505</ref> In this model, the headgroup of PIP2 is <scene name='User:David_Canner/Sandbox_P/Catalytic_cavity/2'>positioned in a cavity</scene> between the <scene name='User:David_Canner/Sandbox_P/Catalytic_site/1'>C-terminal helix 12 of the kinase domain, the “activation” loop, and the “catalytic” loop</scene>. This puts the 5-phosphate of PIP2 near Lys 973 and the <scene name='User:David_Canner/Sandbox_P/Catalytic_site_atp_lys/1'>I-phosphate of ATP near Lys 807 and Lys 808</scene>. The <scene name='User:David_Canner/Sandbox_P/Catalytic_site_pip2/1'>basic residues Arg 947</scene> and Lys 973 can bind the 4-Phosphate of PIP2 and help provide the Class I PI3Ks with their specificity for PIP2. Once PIP2 and ATP are bound, it is believed <scene name='User:David_Canner/Sandbox_P/Catalytic_site_his/1'>His 948 rotates to interact with PIP2</scene>, deprotonating it at the C-3 Hydroxyl position creating a nucleophile. This nucleophile subsequently attacks the gamma phosphate of ATP producing PIP3. <ref name="Walker2"/>
</StructureSection>

==Additional Resources==
* See [[Phosphoinositide 3-Kinases]] for the main page or [[PI3K Activation, Inhibition, & Medical Implications]] for PI3Ks medical importance.
* See [[Cancer]] for additional information.
* See [[Diabetes]] for additional information.

==References==
<references/>
__NOTOC__
__NOEDITSECTION__

Phosphoinositide 3-Kinases

2021-04-22T18:49:44Z

Hannah Campbell:

{{BAMBED
|DATE=November 15, 2010
|OLDID=1144475
|BAMBEDDOI=10.1002/bmb.20540
}}
<StructureSection load='3hhm' size='350' side='right' scene='' caption='PI3K (grey) complex with NISH2 P85α and wortmannin (PDB code [[3hhm]]) '>

[[Image: PI3KOpener.PNG|250px|left|thumb| PI3K p110α Subunit, [[3hhm]]]]
{{Clear}}
__TOC__
== Function ==
[[Phosphoinositide 3-Kinases]] or '''phosphatidylinositol 3-kinase''' (PI3K) are a family of ubiquitously distributed lipid kinases, that play a critical role in the regulation of numerous cellular processes including cellular growth and morphology, programmed cell death, cell motility and adhesion, mitogenesis and glucose uptake. <ref name="Driscoll"> PMID: 12151228</ref> PI3K generates important second messengers by catalyzing the transfer of the γ-phosphate group of ATP to the D3 position of phosphoinositides. <ref name="Wymann"> PMID: 9838078</ref> The PI3K preferred substrate is Phosphatidylinositol-4,5-bisphosphate (PIP2), which is converted into phosphatidylinositol-3,4,5-triphosphate (PIP3) upon phosphorylation at the cell membrane. The importance of PI3K is evident in knockout mice studies in which those mice with disruptions of critical PI3K components have significant deficiencies in immune and inflammatory response <ref name="Fubar"> PMID:10972292</ref> sometimes resulting in embryonic death.<ref>PMID:10196176</ref> Aberrations in PIP3 levels, either through activation of PI3ks or through inactivation of lipid phosphatase [[PTEN]], occur frequently in numerous forms of cancer, making PI3K an exciting new target to treat [[Cancer|cancer]] among other human diseases.<ref name="Miled"> PMID: 17626883</ref> For additional details see 
* [[PI3K Activation, Inhibition, & Medical Implications]] 
* [[Human PI3K p110alpha/p85alpha]] 
* [[The Structure of PI3K]] 
* [[Diabetes & Hypoglycemia]].

==The Classes of PI3Ks==
[[Image:PI3KTransduction.PNG|250px|left|thumb| Signal Transduction Pathway. PI3K Highlighted in Red. Click to Expand]]
{{Clear}}
PI3Ks can be grouped into three distinct classes, Class I-III. Class I PI3Ks, the most well understood and thoroughly explored PI3K class, are composed of a 110kDa <scene name='Phosphoinositide_3-Kinases/Model_cat/2'>catalytic subunit</scene> and a 50-100 kDa <scene name='Phosphoinositide_3-Kinases/Model_ada/1'>adaptor subunit</scene>. Activation of Class I PI3Ks is controlled by extracellular signaling via receptors with intrinsic tyrosine kinase activity, G protein-linked receptors, or receptors coupled to [[SRC]] like protein tyrosine kinases. <ref>PMID:1851250</ref> Class II PI3Ks are relatively poorly understood but are 170-210 kDa and have in vitro substrate specificity toward PtdIns 4-P. Class III PI3Ks depend on Vps15p protein Ser/Thr kinases, which recruits the phosphatidylinositol kinase to late Golgi Compartments. <ref name="Wymann"/>
===Class I Subclasses===
PI3Ks are activated by extracellular agonists via the translocation of PI3Ks to the plasma membrane for easy access to lipid substrates. Depending on the adaptor proteins involved in the process, Class I PI3Ks are segregated into two subgroups. Those that associate with p85 will be directed to phosphorylated tyrosine motifs (Class IA), '''Phosphatidylinositol-4, 5-bisphosphate 3-kinase''' (PI3Kγ) catalyzes the conversion of 1-phosphatidyl-1D-myo-inositol-4, 5-bisphosphate and ATP to 1-phosphatidyl-1D-myo-inositol-4, 5-trisphosphate. PI3Kγ interacts with trimeric G proteins and the p101 protein (Class IB) <ref name="Wymann"/>
==Structure of PI3K==
For Full Article, See: [[The Structure of PI3K]] 

Class I PI3Ks, which are tightly regulated by tyrosine kinases, are composed of an 85kDa regulatory/adapter subunit (p85) and a 110kDa catalytic subunit (p110). <ref name="Flip"> PMID: 10525402</ref>
 

==PI3K Activation, Inhibition, and Medical Implications==
For Full Article, See: [[PI3K Activation, Inhibition, & Medical Implications]] 

A number of inhibitors for PI3K have been developed to understand how PI3K is activated and functions. These analysis have massive medical implications for the treatment of [[Cancer]] and [[Diabetes]]. Inhibitors of Type I PI3K p110γ and Type I PI3K p110δ are tested as therapeutic drugs against inflammatory etiologists <ref>PMID:19876783</ref>.
 

== 3D Structures of PI3K==
[[Phosphoinositide 3-kinase 3D structures]]

</StructureSection>

==Additional Resources==
* See: [[Cancer]] For Additional Proteins involved in the disease. 
* See: [[Oncogenes]] for Additional examples of oncogenes and tumor suppressor genes.
 

==References==
<references />

[[Category:Topic Page]]
[[Category:Featured in BAMBED]]

__NOEDITSECTION__

WWP2

2021-04-22T18:48:07Z

Hannah Campbell:

<StructureSection load='5TJ7' size='350' side='right' caption="WWP2 Ubiquitin Ligase Chimeric Structure (PDB entry [[5TJ7]]). The 2,3-linker (red) connects the WW2 domain (yellow) to the WW3 domain. The hinge (magenta) connects the C-terminal lobe (green) and N-terminal lobe (silver) of the HECT domain." scene="84/848928/Overallcolored/14">
__TOC__
==Introduction==
'''WWP2''' (WW domain-containing protein 2) is a type of [[ubiquitin protein ligase]]. Ubiquitination can serve as a signal for degradation, lead to translocation within the cell, and result in altered activity and altered protein-protein interactions. The ubiquitination pathway comprises of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-ligating (E3) enzymes. WWP2 is a member of the HECT ('''H'''omologous to the '''E'''6-AP '''C'''arboxyl '''T'''erminus) E3 Ligase class of enzymes. HECT E3 Ligases accept a [[ubiquitin]] molecule from E2 enzymes and transfer the ubiquitin to a Lysine residue in the target signaling molecule or transcription factor <ref>PMID:15021885</ref>.

The thioester bond formation between an active site Cystine on HECT E3 Ligases and the ubiquitin ligand differentiates the HECT family of enzymes from the more abundant RING ('''R'''eally '''I'''nteresting '''N'''ew '''G'''ene) family of ubiquitin ligases which mediate ubiquitin transfer through non-covalent interactions. Within HECT E3 Ligases, WWP2 falls into the NEDD 4 family (named after the instance in which the first member was discovered: a study of developmentally down-regulated proteins in neuronal embryonic mouse cells) which generally target proteins with a PPxY motif. NEDD4 E3 Ligases consist of an amino-terminal C2 domain, between two and four WW domains, and a carboxy-terminal HECT domain. Two conformational states (a ground state inverse T shape and catalytically active L shape) have been observed.

==Structure==
[[Image:WWP2 Scheme from paper fig 1A top.png|300px|right|thumb| WWP2 Scheme without C2 Domain]]
[[Image:WWP2 Scheme from paper D3.png|300px|right|thumb| WWP2 Scheme WW2-2,3-linker-HECT]]
Full-length WWP2 consists of an amino-terminal C2 domain, four WW domains (labeled WW1-WW4), and a carboxy-terminal HECT domain. WW domains are one of the smallest studied protein modules, consisting of less than 40 amino acids, fold into three-stranded beta-sheets. They are characterized by two highly conserved <scene name='84/848928/Trpsinww2/2'>Trp residues</scene> positioned 20-22 amino acids apart and a high affinity for proline-rich motifs. Linkers of varying length and secondary structure connect the C2 domain to WW1, WW1 to WW2, WW2 to WW3, WW3 to WW4, and WW4 to the HECT domain. A chimeric <scene name='84/848928/Overallcolored/12'>structure</scene> of WWP2 consisting of the <scene name='84/848928/Ww2_domain/8'>WW2 domain</scene>, the WW2-WW3 linker (<scene name='84/848928/Linkeronly/1'>2,3-linker</scene>), and the HECT domain is shown on the right.

The HECT domain is divided into two lobes (labeled N and C). The N-lobe serves as a binding site for the E2-ubiquitin complex and includes an exosite for non-covalent ubiquitin binding relevant to autoinhibition while the C-lobe contains an active site with a catalytic Cys residue to which the substrate ubiquitin molecule can covalently attach. The <scene name='84/848928/Hinge_zoomed/7'>hinge</scene> (magenta) connects the N and C lobes of the HECT domain and allows for flexible movement of the lobes as ubiquitin is transferred from the E2-ubiquitin complex docked on the N-lobe to the ubiquitin binding site in the C-lobe. A transthiolation reaction in this active site results in a thioester bond between the ubiquitin and a Cys residue. The HECT domain is in an inverse T shape when inactive (autoinhibited) and takes on an L shape when active. WW2 interaction with HECT is mediated by the six C terminal residues.
<html5media height="360" width="640">https://vimeo.com/540291073</html5media>

The video above shows the protein WWP2, with emphasis on the hinge loop shown in magenta.

The alpha-helical 2,3-linker is subject to tyrosine phosphorylation at either end of the linker at residues <scene name='84/848928/Tyr392tyr369/2'>Tyr369 and Tyr392</scene>. Chen et. al. have shown that the phosphorylation of Tyr369 allows for allosteric activation by ubiquitination at the exosite in the N-lobe, while phosphorylation of Tyr392 residue leads to a destabilization of the T conformation of the HECT domain.

== Function ==
Studies suggest that the C2 domain, with calcium ion and phospholipid binding properties, is required for membrane binding while the WW domains play a critical role in substrate specificity. Genetic deletions of WW domains and linkers have shown increased autoubiquitination activity. The WW domains and linkers play a role in altering protein conformation, with the 2,3-linker playing the greatest role.

This linker plays an autoinhibitory role. The ground state conformation of the protein has the 2,3-linker close to the N-lobe, while WW1 and WW2 domains block the N lobe’s ubiquitin-binding site. Upon phosphorylation the 2,3-linker changes conformation, moving further from the N lobe, allowing the protein to bind ubiquitin in the E2 and N lobe binding sites. This binding will further open the protein up to bind possible substrates, like PTEN.
Interactions between the hinge and the 2,3-linker appear to restrict flexibility of the C-lobe which is necessary for ubiquitin transferase activity. This interaction further locks the protein into the T position. A current model of WWP2 activation by Chen et. al. proposes the following: (1) autoinhibited WWP2 gets phosphorylated at the 2,3-linker, (2) loosening of the 2,3-linker interactions with the hinge and ubiquitin binding exosite allow ubiquitin to bind in the C-lobe, (3) the target substrate protein binds with specifity towards the WW domains, (4) the substrate protein gets ubiquitinated, and (5) the 2,3-linker gets dephosphorylated, allowing WWP2 to return to the autoinhibited ground state conformation. <ref>PMID:28475870</ref>

== Relevance ==
Mutations in the NEDD4 family of proteins have been associated with several cancers and immune disorders. Many of these mutations occur in the 2,3-linker/HECT autoinhibited domains and the modified activity of the E3 Ligases as a result of these mutations can lead to an increase in the growth of tumor cells. WWP2 may play a role in the regulation of oncogenic signaling pathways through interactions with its substrate [[PTEN]], a tumor suppressor in the [[PI3K]] pathway. The downregulation of voltage-gated sodium channels by WWP2 and other members of the NEDD4 family is an active area of research. Other known targets of WWP2 include SMADs, OCT4, EGR2, and TIRF. <ref>PMID:25216927</ref>
</StructureSection>

== References ==
<references/>

WWP2

2021-04-22T18:47:36Z

Hannah Campbell:

<StructureSection load='5TJ7' size='350' side='right' caption="WWP2 Ubiquitin Ligase Chimeric Structure (PDB entry [[5TJ7]]). The 2,3-linker (red) connects the WW2 domain (yellow) to the WW3 domain. The hinge (magenta) connects the C-terminal lobe (green) and N-terminal lobe (silver) of the HECT domain." scene="84/848928/Overallcolored/14">
__TOC__
==Introduction==
'''WWP2''' (WW domain-containing protein 2) is a type of [[ubiquitin protein ligase]]. Ubiquitination can serve as a signal for degradation, lead to translocation within the cell, and result in altered activity and altered protein-protein interactions. The ubiquitination pathway comprises of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-ligating (E3) enzymes. WWP2 is a member of the HECT ('''H'''omologous to the '''E'''6-AP '''C'''arboxyl '''T'''erminus) E3 Ligase class of enzymes. HECT E3 Ligases accept a [[ubiquitin]] molecule from E2 enzymes and transfer the ubiquitin to a Lysine residue in the target signaling molecule or transcription factor <ref>PMID:15021885</ref>.

The thioester bond formation between an active site Cystine on HECT E3 Ligases and the ubiquitin ligand differentiates the HECT family of enzymes from the more abundant RING ('''R'''eally '''I'''nteresting '''N'''ew '''G'''ene) family of ubiquitin ligases which mediate ubiquitin transfer through non-covalent interactions. Within HECT E3 Ligases, WWP2 falls into the NEDD 4 family (named after the instance in which the first member was discovered: a study of developmentally down-regulated proteins in neuronal embryonic mouse cells) which generally target proteins with a PPxY motif. NEDD4 E3 Ligases consist of an amino-terminal C2 domain, between two and four WW domains, and a carboxy-terminal HECT domain. Two conformational states (a ground state inverse T shape and catalytically active L shape) have been observed.

==Structure==
[[Image:WWP2 Scheme from paper fig 1A top.png|300px|right|thumb| WWP2 Scheme without C2 Domain]]
[[Image:WWP2 Scheme from paper D3.png|300px|right|thumb| WWP2 Scheme WW2-2,3-linker-HECT]]
Full-length WWP2 consists of an amino-terminal C2 domain, four WW domains (labeled WW1-WW4), and a carboxy-terminal HECT domain. WW domains are one of the smallest studied protein modules, consisting of less than 40 amino acids, fold into three-stranded beta-sheets. They are characterized by two highly conserved <scene name='84/848928/Trpsinww2/2'>Trp residues</scene> positioned 20-22 amino acids apart and a high affinity for proline-rich motifs. Linkers of varying length and secondary structure connect the C2 domain to WW1, WW1 to WW2, WW2 to WW3, WW3 to WW4, and WW4 to the HECT domain. A chimeric <scene name='84/848928/Overallcolored/12'>structure</scene> of WWP2 consisting of the <scene name='84/848928/Ww2_domain/8'>WW2 domain</scene>, the WW2-WW3 linker (<scene name='84/848928/Linkeronly/1'>2,3-linker</scene>), and the HECT domain is shown on the right.

The HECT domain is divided into two lobes (labeled N and C). The N-lobe serves as a binding site for the E2-ubiquitin complex and includes an exosite for non-covalent ubiquitin binding relevant to autoinhibition while the C-lobe contains an active site with a catalytic Cys residue to which the substrate ubiquitin molecule can covalently attach. The <scene name='84/848928/Hinge_zoomed/7'>hinge</scene> (magenta) connects the N and C lobes of the HECT domain and allows for flexible movement of the lobes as ubiquitin is transferred from the E2-ubiquitin complex docked on the N-lobe to the ubiquitin binding site in the C-lobe. A transthiolation reaction in this active site results in a thioester bond between the ubiquitin and a Cys residue. The HECT domain is in an inverse T shape when inactive (autoinhibited) and takes on an L shape when active. WW2 interaction with HECT is mediated by the six C terminal residues.
<html5media height="360" width="360">https://vimeo.com/540291073</html5media>

The video above shows the protein WWP2, with emphasis on the hinge loop shown in magenta.

The alpha-helical 2,3-linker is subject to tyrosine phosphorylation at either end of the linker at residues <scene name='84/848928/Tyr392tyr369/2'>Tyr369 and Tyr392</scene>. Chen et. al. have shown that the phosphorylation of Tyr369 allows for allosteric activation by ubiquitination at the exosite in the N-lobe, while phosphorylation of Tyr392 residue leads to a destabilization of the T conformation of the HECT domain.

== Function ==
Studies suggest that the C2 domain, with calcium ion and phospholipid binding properties, is required for membrane binding while the WW domains play a critical role in substrate specificity. Genetic deletions of WW domains and linkers have shown increased autoubiquitination activity. The WW domains and linkers play a role in altering protein conformation, with the 2,3-linker playing the greatest role.

This linker plays an autoinhibitory role. The ground state conformation of the protein has the 2,3-linker close to the N-lobe, while WW1 and WW2 domains block the N lobe’s ubiquitin-binding site. Upon phosphorylation the 2,3-linker changes conformation, moving further from the N lobe, allowing the protein to bind ubiquitin in the E2 and N lobe binding sites. This binding will further open the protein up to bind possible substrates, like PTEN.
Interactions between the hinge and the 2,3-linker appear to restrict flexibility of the C-lobe which is necessary for ubiquitin transferase activity. This interaction further locks the protein into the T position. A current model of WWP2 activation by Chen et. al. proposes the following: (1) autoinhibited WWP2 gets phosphorylated at the 2,3-linker, (2) loosening of the 2,3-linker interactions with the hinge and ubiquitin binding exosite allow ubiquitin to bind in the C-lobe, (3) the target substrate protein binds with specifity towards the WW domains, (4) the substrate protein gets ubiquitinated, and (5) the 2,3-linker gets dephosphorylated, allowing WWP2 to return to the autoinhibited ground state conformation. <ref>PMID:28475870</ref>

== Relevance ==
Mutations in the NEDD4 family of proteins have been associated with several cancers and immune disorders. Many of these mutations occur in the 2,3-linker/HECT autoinhibited domains and the modified activity of the E3 Ligases as a result of these mutations can lead to an increase in the growth of tumor cells. WWP2 may play a role in the regulation of oncogenic signaling pathways through interactions with its substrate [[PTEN]], a tumor suppressor in the [[PI3K]] pathway. The downregulation of voltage-gated sodium channels by WWP2 and other members of the NEDD4 family is an active area of research. Other known targets of WWP2 include SMADs, OCT4, EGR2, and TIRF. <ref>PMID:25216927</ref>
</StructureSection>

== References ==
<references/>

Major Histocompatibility Complex Class I

2021-04-22T18:45:32Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC I (HLA A2:01) by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers discovered that neoantigen p53R175H is displayed by HLA:A2 on the cell surface at very low density. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are easier to graft into different therapuetic formats and are an off the shelf ready to use therapy. Specifically, researchers developed a bispecific antibody constructed from H2 and an antiCD3 antibody, (H2- scDb) that can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC I can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/540292892</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/540291923</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-04-22T18:43:29Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC I (HLA A2:01) by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers discovered that neoantigen p53R175H is displayed by HLA:A2 on the cell surface at very low density. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are easier to graft into different therapuetic formats and are an off the shelf ready to use therapy. Specifically, researchers developed a bispecific antibody constructed from H2 and an antiCD3 antibody, (H2- scDb) that can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC I can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/540292892</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Farnesyl diphosphate synthase

2021-04-22T18:41:56Z

Hannah Campbell:

== Introduction ==
<StructureSection load='2opm' size='350' side='right' scene='48/485622/Cv/15' caption='Human farnesyl diphosphate synthase complex with lipophylic bisphosphonate inhibitor and Mg+2 ions (green) (PDB code [[2opm]]) '>
__TOC__
'''Farnesyl pyrophosphate synthase''' (FPPS) is a chain elongation enzyme that catalyzes carbon-carbon formation in two consecutive condensation reactions that convert one equivalent of dimethylallyl diphosphate (DMAPP) and two equivalents of isopentyl diphosphates (IPP) into one equivalent of Farnesyl pyrophosphate (FPP). <ref>PMID:11152452</ref>In the first step, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second step, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). It is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FFPS has been studied in conjunction with different parasites. Bisphosphonates have been shown to inhibit FPPS and are currently being used for osteoporosis and the treatment of various bone diseases. Inhibition of FPPS in parasites such Trypanosoma cruzi (Tc), Trypanosoma brucei (Tb), Toxoplasma gondii and Leishmania major (Lm) displays antiparasitic activity which is being evaluated as putative therapeutics. <ref> PMID: 24598749</ref> <ref> PMID: 30926449</ref> <ref> PMID: 16835450</ref> <ref> PMID: 12089677</ref> <ref> PMID: 31296439 </ref> <ref>DOI: 10.1016/j.ijantimicag.2003.07.020</ref> <ref>DOI: 10.1074/jbc.M103950200</ref> <ref> DOI: 10.1128/AAC.46.3.929-931.2002</ref> <ref> DOI:10.1021/jm040132t</ref> <ref>DOI: 10.1021/jm0002578</ref> <ref>DOI:10.1021/jm0102809 </ref> <ref> DOI: 10.1128/AAC.01873-15</ref>

== Function ==
In the first condensation reaction, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second condensation reaction, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). FPP is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FPPS has been studied in conjunction with different parasites. TcFPPS refers to FPPS in the Typanosoma cruzi parasite while LmFPPS refers to FPPS in the Leishmania major parasite. Bisphosphonates have been shown to inhibit FPPS and are currently being used as antiparasitic drugs as well as a treatment for various bone diseases.

[[Image:FPPSynthesisDiagram.png|700x750px]]

== Structure ==

FPPS exists as a homodimer, with each monomer having an active site. The monomers have the characteristic FPPS fold of a ten-helix bundle and four other helices that run perpendicular to the bundle. There are two substrate sites, one is allylic and the other is homoallylic. GPP and DMAPP bind to the allylic site, while IPP binds to the homoallylic site. These two sites are connected to the top of the bundle and exist as part of a cavity<ref>PMID:24598749</ref>. Another characteristic feature of all FPPS enzymes are two highly conserved aspartate rich motifs. These motifs are called <scene name='48/485622/Lmfpps_rbs/5'>First Aspartate Rich Motif (FARM) and Second Aspartate Rich Motif (SARM)</scene>, and have sequences of DDXX(XX)D and DDXXD respectively. FARM and SARM are found on opposite sides on the active site cavity facing one another<ref>DOI: 10.1021/acs.biochem.0c00432</ref>.

When FPPS interacts with bisphosphonates, the bisphosphonates bind in the homoallylic binding sites and are coordinated by three divalent cations (Ca2+ or Mg2+). The identity of the bisphosphonate influences which divalent cations bind, as well as whether IPP binds. In the <scene name='48/485622/Lmfpps_rbs/6'>structure</scene> of LmFPPS with 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium, three Ca 2+ ions and IPP are present.
FPS <scene name='48/485622/Cv/12'>active site</scene> contains <scene name='48/485622/Cv/13'>Mg+2 ions coordination sites</scene> and binds <scene name='48/485622/Cv/11'>bisphosphonate inhibitors</scene>; see also <scene name='48/485622/Cv/14'>phosphates coordination sites</scene>, (PDB code [[2opm]])<ref>PMID:19309137</ref>, water molecules are shown as red spheres.

== Relevance ==

FPS bisphosphonate inhibitors (like zoledronic acid) are used as drugs for treatment of bone resorption diseases<ref>PMID:24369118</ref>. FPS inhibitor [[Alendronate]] or Fosamax is used in treatment of osteoporosis<ref>PMID:9116385</ref>. Bisphosphonates have been explored as antiparasitic drugs with FPPS because current treatments are expensive, have low efficacy, and have dangerous side effects. FPPS is important in the lengthening of hydrophobic chains and determination of their specificity.

==Published 3D structures of FPPS==
[[Farnesyl diphosphate synthase 3D structures]]

</StructureSection>

== References ==
<references/>

[[Category:Topic Page]]

Farnesyl diphosphate synthase

2021-04-22T18:38:57Z

Hannah Campbell:

== Introduction ==
<StructureSection load='2opm' size='350' side='right' scene='48/485622/Cv/15' caption='Human farnesyl diphosphate synthase complex with lipophylic bisphosphonate inhibitor and Mg+2 ions (green) (PDB code [[2opm]]) '>
__TOC__
'''Farnesyl pyrophosphate synthase''' (FPPS) is a chain elongation enzyme that catalyzes carbon-carbon formation in two consecutive condensation reactions that convert one equivalent of dimethylallyl diphosphate (DMAPP) and two equivalents of isopentyl diphosphates (IPP) into one equivalent of Farnesyl pyrophosphate (FPP). <ref>PMID:11152452</ref>In the first step, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second step, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). It is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FFPS has been studied in conjunction with different parasites. Bisphosphonates have been shown to inhibit FPPS and are currently being used for osteoporosis and the treatment of various bone diseases. Inhibition of FPPS in parasites such Trypanosoma cruzi (Tc), Trypanosoma brucei (Tb), Toxoplasma gondii and Leishmania major (Lm) displays antiparasitic activity which is being evaluated as putative therapeutics. <ref> PMID: 24598749</ref> <ref> PMID: 30926449</ref> <ref> PMID: 16835450</ref> <ref> PMID: 12089677</ref> <ref> PMID: 31296439 </ref> <ref>DOI: 10.1016/j.ijantimicag.2003.07.020</ref> <ref>DOI: 10.1074/jbc.M103950200</ref> <ref> DOI: 10.1128/AAC.46.3.929-931.2002</ref> <ref> DOI:10.1021/jm040132t</ref> <ref>DOI: 10.1021/jm0002578</ref> <ref>DOI:10.1021/jm0102809 </ref> <ref> DOI: 10.1128/AAC.01873-15</ref>

== Function ==
In the first condensation reaction, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second condensation reaction, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). FPP is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FPPS has been studied in conjunction with different parasites. TcFPPS refers to FPPS in the Typanosoma cruzi parasite while LmFPPS refers to FPPS in the Leishmania major parasite. Bisphosphonates have been shown to inhibit FPPS and are currently being used as antiparasitic drugs as well as a treatment for various bone diseases.

[[Image:FPPSynthesisDiagram.png|700x750px]]

== Structure ==

FPPS exists as a homodimer, with each monomer having an active site. The monomers have the characteristic FPPS fold of a ten-helix bundle and four other helices that run perpendicular to the bundle. There are two substrate sites, one is allylic and the other is homoallylic. GPP and DMAPP bind to the allylic site, while IPP binds to the homoallylic site. These two sites are connected to the top of the bundle and exist as part of a cavity<ref>PMID:24598749</ref>. Another characteristic feature of all FPPS enzymes are two highly conserved aspartate rich motifs. These motifs are called <scene name='48/485622/Lmfpps_rbs/5'>First Aspartate Rich Motif (FARM) and Second Aspartate Rich Motif (SARM)</scene>, and have sequences of DDXX(XX)D and DDXXD respectively. FARM and SARM are found on opposite sides on the active site cavity facing one another<ref>DOI: 10.1021/acs.biochem.0c00432</ref>.

When FPPS interacts with bisphosphonates, the bisphosphonates bind in the homoallylic binding sites and are coordinated by three divalent cations (Ca2+ or Mg2+). The identity of the bisphosphonate influences which divalent cations bind, as well as whether IPP binds. In the <scene name='48/485622/Lmfpps_rbs/6'>structure</scene> of LmFPPS with 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium, three Ca 2+ ions and IPP are present.
FPS <scene name='48/485622/Cv/12'>active site</scene> contains <scene name='48/485622/Cv/13'>Mg+2 ions coordination sites</scene> and binds <scene name='48/485622/Cv/11'>bisphosphonate inhibitors</scene>; see also <scene name='48/485622/Cv/14'>phosphates coordination sites</scene>, (PDB code [[2opm]])<ref>PMID:19309137</ref>, water molecules are shown as red spheres.

== Relevance ==

FPS bisphosphonate inhibitors (like zoledronic acid) are used as drugs for treatment of bone resorption diseases<ref>PMID:24369118</ref>. FPS inhibitor [[Alendronate]] or Fosamax is used in treatment of osteoporosis<ref>PMID:9116385</ref>. Bisphosphonates have been explored as antiparasitic drugs with FPPS because current treatments are expensive, have low efficacy, and have dangerous side effects. FPPS is important in the lengthening of hydrophobic chains and determination of their specificity.

<html5media height="360" width="640">https://vimeo.com/540292892</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. In light green there are nine amino acids sandwiched in between alpha helices of HLA that are part of p53R175H.

==Published 3D structures of FPPS==
[[Farnesyl diphosphate synthase 3D structures]]

</StructureSection>

== References ==
<references/>

[[Category:Topic Page]]

Farnesyl diphosphate synthase

2021-04-22T18:38:18Z

Hannah Campbell:

== Introduction ==
<StructureSection load='2opm' size='350' side='right' scene='48/485622/Cv/15' caption='Human farnesyl diphosphate synthase complex with lipophylic bisphosphonate inhibitor and Mg+2 ions (green) (PDB code [[2opm]]) '>
__TOC__
'''Farnesyl pyrophosphate synthase''' (FPPS) is a chain elongation enzyme that catalyzes carbon-carbon formation in two consecutive condensation reactions that convert one equivalent of dimethylallyl diphosphate (DMAPP) and two equivalents of isopentyl diphosphates (IPP) into one equivalent of Farnesyl pyrophosphate (FPP). <ref>PMID:11152452</ref>In the first step, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second step, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). It is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FFPS has been studied in conjunction with different parasites. Bisphosphonates have been shown to inhibit FPPS and are currently being used for osteoporosis and the treatment of various bone diseases. Inhibition of FPPS in parasites such Trypanosoma cruzi (Tc), Trypanosoma brucei (Tb), Toxoplasma gondii and Leishmania major (Lm) displays antiparasitic activity which is being evaluated as putative therapeutics. <ref> PMID: 24598749</ref> <ref> PMID: 30926449</ref> <ref> PMID: 16835450</ref> <ref> PMID: 12089677</ref> <ref> PMID: 31296439 </ref> <ref>DOI: 10.1016/j.ijantimicag.2003.07.020</ref> <ref>DOI: 10.1074/jbc.M103950200</ref> <ref> DOI: 10.1128/AAC.46.3.929-931.2002</ref> <ref> DOI:10.1021/jm040132t</ref> <ref>DOI: 10.1021/jm0002578</ref> <ref>DOI:10.1021/jm0102809 </ref> <ref> DOI: 10.1128/AAC.01873-15</ref>

== Function ==
In the first condensation reaction, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second condensation reaction, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). FPP is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FPPS has been studied in conjunction with different parasites. TcFPPS refers to FPPS in the Typanosoma cruzi parasite while LmFPPS refers to FPPS in the Leishmania major parasite. Bisphosphonates have been shown to inhibit FPPS and are currently being used as antiparasitic drugs as well as a treatment for various bone diseases.

[[Image:FPPSynthesisDiagram.png|700x750px]]

== Structure ==

FPPS exists as a homodimer, with each monomer having an active site. The monomers have the characteristic FPPS fold of a ten-helix bundle and four other helices that run perpendicular to the bundle. There are two substrate sites, one is allylic and the other is homoallylic. GPP and DMAPP bind to the allylic site, while IPP binds to the homoallylic site. These two sites are connected to the top of the bundle and exist as part of a cavity<ref>PMID:24598749</ref>. Another characteristic feature of all FPPS enzymes are two highly conserved aspartate rich motifs. These motifs are called <scene name='48/485622/Lmfpps_rbs/5'>First Aspartate Rich Motif (FARM) and Second Aspartate Rich Motif (SARM)</scene>, and have sequences of DDXX(XX)D and DDXXD respectively. FARM and SARM are found on opposite sides on the active site cavity facing one another<ref>DOI: 10.1021/acs.biochem.0c00432</ref>.

When FPPS interacts with bisphosphonates, the bisphosphonates bind in the homoallylic binding sites and are coordinated by three divalent cations (Ca2+ or Mg2+). The identity of the bisphosphonate influences which divalent cations bind, as well as whether IPP binds. In the <scene name='48/485622/Lmfpps_rbs/6'>structure</scene> of LmFPPS with 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium, three Ca 2+ ions and IPP are present.
FPS <scene name='48/485622/Cv/12'>active site</scene> contains <scene name='48/485622/Cv/13'>Mg+2 ions coordination sites</scene> and binds <scene name='48/485622/Cv/11'>bisphosphonate inhibitors</scene>; see also <scene name='48/485622/Cv/14'>phosphates coordination sites</scene>, (PDB code [[2opm]])<ref>PMID:19309137</ref>, water molecules are shown as red spheres.

== Relevance ==

FPS bisphosphonate inhibitors (like zoledronic acid) are used as drugs for treatment of bone resorption diseases<ref>PMID:24369118</ref>. FPS inhibitor [[Alendronate]] or Fosamax is used in treatment of osteoporosis<ref>PMID:9116385</ref>. Bisphosphonates have been explored as antiparasitic drugs with FPPS because current treatments are expensive, have low efficacy, and have dangerous side effects. FPPS is important in the lengthening of hydrophobic chains and determination of their specificity.

<html5media height="360" width="640">https://vimeo.com/540292892></html5media>

<html5media height="360" width="640">https://vimeo.com/540292892</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. In light green there are nine amino acids sandwiched in between alpha helices of HLA that are part of p53R175H.

==Published 3D structures of FPPS==
[[Farnesyl diphosphate synthase 3D structures]]

</StructureSection>

== References ==
<references/>

[[Category:Topic Page]]

Farnesyl diphosphate synthase

2021-04-22T18:36:19Z

Hannah Campbell:

== Introduction ==
<StructureSection load='2opm' size='350' side='right' scene='48/485622/Cv/15' caption='Human farnesyl diphosphate synthase complex with lipophylic bisphosphonate inhibitor and Mg+2 ions (green) (PDB code [[2opm]]) '>
__TOC__
'''Farnesyl pyrophosphate synthase''' (FPPS) is a chain elongation enzyme that catalyzes carbon-carbon formation in two consecutive condensation reactions that convert one equivalent of dimethylallyl diphosphate (DMAPP) and two equivalents of isopentyl diphosphates (IPP) into one equivalent of Farnesyl pyrophosphate (FPP). <ref>PMID:11152452</ref>In the first step, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second step, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). It is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FFPS has been studied in conjunction with different parasites. Bisphosphonates have been shown to inhibit FPPS and are currently being used for osteoporosis and the treatment of various bone diseases. Inhibition of FPPS in parasites such Trypanosoma cruzi (Tc), Trypanosoma brucei (Tb), Toxoplasma gondii and Leishmania major (Lm) displays antiparasitic activity which is being evaluated as putative therapeutics. <ref> PMID: 24598749</ref> <ref> PMID: 30926449</ref> <ref> PMID: 16835450</ref> <ref> PMID: 12089677</ref> <ref> PMID: 31296439 </ref> <ref>DOI: 10.1016/j.ijantimicag.2003.07.020</ref> <ref>DOI: 10.1074/jbc.M103950200</ref> <ref> DOI: 10.1128/AAC.46.3.929-931.2002</ref> <ref> DOI:10.1021/jm040132t</ref> <ref>DOI: 10.1021/jm0002578</ref> <ref>DOI:10.1021/jm0102809 </ref> <ref> DOI: 10.1128/AAC.01873-15</ref>

== Function ==
In the first condensation reaction, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second condensation reaction, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). FPP is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FPPS has been studied in conjunction with different parasites. TcFPPS refers to FPPS in the Typanosoma cruzi parasite while LmFPPS refers to FPPS in the Leishmania major parasite. Bisphosphonates have been shown to inhibit FPPS and are currently being used as antiparasitic drugs as well as a treatment for various bone diseases.

[[Image:FPPSynthesisDiagram.png|700x750px]]

== Structure ==

FPPS exists as a homodimer, with each monomer having an active site. The monomers have the characteristic FPPS fold of a ten-helix bundle and four other helices that run perpendicular to the bundle. There are two substrate sites, one is allylic and the other is homoallylic. GPP and DMAPP bind to the allylic site, while IPP binds to the homoallylic site. These two sites are connected to the top of the bundle and exist as part of a cavity<ref>PMID:24598749</ref>. Another characteristic feature of all FPPS enzymes are two highly conserved aspartate rich motifs. These motifs are called <scene name='48/485622/Lmfpps_rbs/5'>First Aspartate Rich Motif (FARM) and Second Aspartate Rich Motif (SARM)</scene>, and have sequences of DDXX(XX)D and DDXXD respectively. FARM and SARM are found on opposite sides on the active site cavity facing one another<ref>DOI: 10.1021/acs.biochem.0c00432</ref>.

When FPPS interacts with bisphosphonates, the bisphosphonates bind in the homoallylic binding sites and are coordinated by three divalent cations (Ca2+ or Mg2+). The identity of the bisphosphonate influences which divalent cations bind, as well as whether IPP binds. In the <scene name='48/485622/Lmfpps_rbs/6'>structure</scene> of LmFPPS with 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium, three Ca 2+ ions and IPP are present.
FPS <scene name='48/485622/Cv/12'>active site</scene> contains <scene name='48/485622/Cv/13'>Mg+2 ions coordination sites</scene> and binds <scene name='48/485622/Cv/11'>bisphosphonate inhibitors</scene>; see also <scene name='48/485622/Cv/14'>phosphates coordination sites</scene>, (PDB code [[2opm]])<ref>PMID:19309137</ref>, water molecules are shown as red spheres.

== Relevance ==

FPS bisphosphonate inhibitors (like zoledronic acid) are used as drugs for treatment of bone resorption diseases<ref>PMID:24369118</ref>. FPS inhibitor [[Alendronate]] or Fosamax is used in treatment of osteoporosis<ref>PMID:9116385</ref>. Bisphosphonates have been explored as antiparasitic drugs with FPPS because current treatments are expensive, have low efficacy, and have dangerous side effects. FPPS is important in the lengthening of hydrophobic chains and determination of their specificity.

<html5media height="360" width="640">https://vimeo.com/540292892></html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. In light green there are nine amino acids sandwiched in between alpha helices of HLA that are part of p53R175H.

==Published 3D structures of FPPS==
[[Farnesyl diphosphate synthase 3D structures]]

</StructureSection>

== References ==
<references/>

[[Category:Topic Page]]

Farnesyl diphosphate synthase

2021-04-22T18:34:02Z

Hannah Campbell:

== Introduction ==
<StructureSection load='2opm' size='350' side='right' scene='48/485622/Cv/15' caption='Human farnesyl diphosphate synthase complex with lipophylic bisphosphonate inhibitor and Mg+2 ions (green) (PDB code [[2opm]]) '>
__TOC__
'''Farnesyl pyrophosphate synthase''' (FPPS) is a chain elongation enzyme that catalyzes carbon-carbon formation in two consecutive condensation reactions that convert one equivalent of dimethylallyl diphosphate (DMAPP) and two equivalents of isopentyl diphosphates (IPP) into one equivalent of Farnesyl pyrophosphate (FPP). <ref>PMID:11152452</ref>In the first step, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second step, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). It is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FFPS has been studied in conjunction with different parasites. Bisphosphonates have been shown to inhibit FPPS and are currently being used for osteoporosis and the treatment of various bone diseases. Inhibition of FPPS in parasites such Trypanosoma cruzi (Tc), Trypanosoma brucei (Tb), Toxoplasma gondii and Leishmania major (Lm) displays antiparasitic activity which is being evaluated as putative therapeutics. <ref> PMID: 24598749</ref> <ref> PMID: 30926449</ref> <ref> PMID: 16835450</ref> <ref> PMID: 12089677</ref> <ref> PMID: 31296439 </ref> <ref>DOI: 10.1016/j.ijantimicag.2003.07.020</ref> <ref>DOI: 10.1074/jbc.M103950200</ref> <ref> DOI: 10.1128/AAC.46.3.929-931.2002</ref> <ref> DOI:10.1021/jm040132t</ref> <ref>DOI: 10.1021/jm0002578</ref> <ref>DOI:10.1021/jm0102809 </ref> <ref> DOI: 10.1128/AAC.01873-15</ref>

== Function ==
In the first condensation reaction, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second condensation reaction, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). FPP is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FPPS has been studied in conjunction with different parasites. TcFPPS refers to FPPS in the Typanosoma cruzi parasite while LmFPPS refers to FPPS in the Leishmania major parasite. Bisphosphonates have been shown to inhibit FPPS and are currently being used as antiparasitic drugs as well as a treatment for various bone diseases.

[[Image:FPPSynthesisDiagram.png|700x750px]]

== Structure ==

FPPS exists as a homodimer, with each monomer having an active site. The monomers have the characteristic FPPS fold of a ten-helix bundle and four other helices that run perpendicular to the bundle. There are two substrate sites, one is allylic and the other is homoallylic. GPP and DMAPP bind to the allylic site, while IPP binds to the homoallylic site. These two sites are connected to the top of the bundle and exist as part of a cavity<ref>PMID:24598749</ref>. Another characteristic feature of all FPPS enzymes are two highly conserved aspartate rich motifs. These motifs are called <scene name='48/485622/Lmfpps_rbs/5'>First Aspartate Rich Motif (FARM) and Second Aspartate Rich Motif (SARM)</scene>, and have sequences of DDXX(XX)D and DDXXD respectively. FARM and SARM are found on opposite sides on the active site cavity facing one another<ref>DOI: 10.1021/acs.biochem.0c00432</ref>.

When FPPS interacts with bisphosphonates, the bisphosphonates bind in the homoallylic binding sites and are coordinated by three divalent cations (Ca2+ or Mg2+). The identity of the bisphosphonate influences which divalent cations bind, as well as whether IPP binds. In the <scene name='48/485622/Lmfpps_rbs/6'>structure</scene> of LmFPPS with 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium, three Ca 2+ ions and IPP are present.
FPS <scene name='48/485622/Cv/12'>active site</scene> contains <scene name='48/485622/Cv/13'>Mg+2 ions coordination sites</scene> and binds <scene name='48/485622/Cv/11'>bisphosphonate inhibitors</scene>; see also <scene name='48/485622/Cv/14'>phosphates coordination sites</scene>, (PDB code [[2opm]])<ref>PMID:19309137</ref>, water molecules are shown as red spheres.

== Relevance ==

FPS bisphosphonate inhibitors (like zoledronic acid) are used as drugs for treatment of bone resorption diseases<ref>PMID:24369118</ref>. FPS inhibitor [[Alendronate]] or Fosamax is used in treatment of osteoporosis<ref>PMID:9116385</ref>. Bisphosphonates have been explored as antiparasitic drugs with FPPS because current treatments are expensive, have low efficacy, and have dangerous side effects. FPPS is important in the lengthening of hydrophobic chains and determination of their specificity.

<html5media height="640" width="640">https://vimeo.com/540292892>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. In light green there are nine amino acids sandwiched in between alpha helices of HLA that are part of p53R175H.

==Published 3D structures of FPPS==
[[Farnesyl diphosphate synthase 3D structures]]

</StructureSection>

== References ==
<references/>

[[Category:Topic Page]]

Farnesyl diphosphate synthase

2021-04-22T18:32:56Z

Hannah Campbell:

== Introduction ==
<StructureSection load='2opm' size='350' side='right' scene='48/485622/Cv/15' caption='Human farnesyl diphosphate synthase complex with lipophylic bisphosphonate inhibitor and Mg+2 ions (green) (PDB code [[2opm]]) '>
__TOC__
'''Farnesyl pyrophosphate synthase''' (FPPS) is a chain elongation enzyme that catalyzes carbon-carbon formation in two consecutive condensation reactions that convert one equivalent of dimethylallyl diphosphate (DMAPP) and two equivalents of isopentyl diphosphates (IPP) into one equivalent of Farnesyl pyrophosphate (FPP). <ref>PMID:11152452</ref>In the first step, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second step, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). It is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FFPS has been studied in conjunction with different parasites. Bisphosphonates have been shown to inhibit FPPS and are currently being used for osteoporosis and the treatment of various bone diseases. Inhibition of FPPS in parasites such Trypanosoma cruzi (Tc), Trypanosoma brucei (Tb), Toxoplasma gondii and Leishmania major (Lm) displays antiparasitic activity which is being evaluated as putative therapeutics. <ref> PMID: 24598749</ref> <ref> PMID: 30926449</ref> <ref> PMID: 16835450</ref> <ref> PMID: 12089677</ref> <ref> PMID: 31296439 </ref> <ref>DOI: 10.1016/j.ijantimicag.2003.07.020</ref> <ref>DOI: 10.1074/jbc.M103950200</ref> <ref> DOI: 10.1128/AAC.46.3.929-931.2002</ref> <ref> DOI:10.1021/jm040132t</ref> <ref>DOI: 10.1021/jm0002578</ref> <ref>DOI:10.1021/jm0102809 </ref> <ref> DOI: 10.1128/AAC.01873-15</ref>

== Function ==
In the first condensation reaction, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second condensation reaction, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). FPP is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FPPS has been studied in conjunction with different parasites. TcFPPS refers to FPPS in the Typanosoma cruzi parasite while LmFPPS refers to FPPS in the Leishmania major parasite. Bisphosphonates have been shown to inhibit FPPS and are currently being used as antiparasitic drugs as well as a treatment for various bone diseases.

[[Image:FPPSynthesisDiagram.png|700x750px]]

== Structure ==

FPPS exists as a homodimer, with each monomer having an active site. The monomers have the characteristic FPPS fold of a ten-helix bundle and four other helices that run perpendicular to the bundle. There are two substrate sites, one is allylic and the other is homoallylic. GPP and DMAPP bind to the allylic site, while IPP binds to the homoallylic site. These two sites are connected to the top of the bundle and exist as part of a cavity<ref>PMID:24598749</ref>. Another characteristic feature of all FPPS enzymes are two highly conserved aspartate rich motifs. These motifs are called <scene name='48/485622/Lmfpps_rbs/5'>First Aspartate Rich Motif (FARM) and Second Aspartate Rich Motif (SARM)</scene>, and have sequences of DDXX(XX)D and DDXXD respectively. FARM and SARM are found on opposite sides on the active site cavity facing one another<ref>DOI: 10.1021/acs.biochem.0c00432</ref>.

When FPPS interacts with bisphosphonates, the bisphosphonates bind in the homoallylic binding sites and are coordinated by three divalent cations (Ca2+ or Mg2+). The identity of the bisphosphonate influences which divalent cations bind, as well as whether IPP binds. In the <scene name='48/485622/Lmfpps_rbs/6'>structure</scene> of LmFPPS with 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium, three Ca 2+ ions and IPP are present.
FPS <scene name='48/485622/Cv/12'>active site</scene> contains <scene name='48/485622/Cv/13'>Mg+2 ions coordination sites</scene> and binds <scene name='48/485622/Cv/11'>bisphosphonate inhibitors</scene>; see also <scene name='48/485622/Cv/14'>phosphates coordination sites</scene>, (PDB code [[2opm]])<ref>PMID:19309137</ref>, water molecules are shown as red spheres.

== Relevance ==

FPS bisphosphonate inhibitors (like zoledronic acid) are used as drugs for treatment of bone resorption diseases<ref>PMID:24369118</ref>. FPS inhibitor [[Alendronate]] or Fosamax is used in treatment of osteoporosis<ref>PMID:9116385</ref>. Bisphosphonates have been explored as antiparasitic drugs with FPPS because current treatments are expensive, have low efficacy, and have dangerous side effects. FPPS is important in the lengthening of hydrophobic chains and determination of their specificity.

<html5media height="640" width="640">https://vimeo.com/540292892>

.

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. In light green there are nine amino acids sandwiched in between alpha helices of HLA that are part of p53R175H.

==Published 3D structures of FPPS==
[[Farnesyl diphosphate synthase 3D structures]]

</StructureSection>

== References ==
<references/>

[[Category:Topic Page]]

Farnesyl diphosphate synthase

2021-04-22T18:30:31Z

Hannah Campbell:

== Introduction ==
<StructureSection load='2opm' size='350' side='right' scene='48/485622/Cv/15' caption='Human farnesyl diphosphate synthase complex with lipophylic bisphosphonate inhibitor and Mg+2 ions (green) (PDB code [[2opm]]) '>
__TOC__
'''Farnesyl pyrophosphate synthase''' (FPPS) is a chain elongation enzyme that catalyzes carbon-carbon formation in two consecutive condensation reactions that convert one equivalent of dimethylallyl diphosphate (DMAPP) and two equivalents of isopentyl diphosphates (IPP) into one equivalent of Farnesyl pyrophosphate (FPP). <ref>PMID:11152452</ref>In the first step, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second step, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). It is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FFPS has been studied in conjunction with different parasites. Bisphosphonates have been shown to inhibit FPPS and are currently being used for osteoporosis and the treatment of various bone diseases. Inhibition of FPPS in parasites such Trypanosoma cruzi (Tc), Trypanosoma brucei (Tb), Toxoplasma gondii and Leishmania major (Lm) displays antiparasitic activity which is being evaluated as putative therapeutics. <ref> PMID: 24598749</ref> <ref> PMID: 30926449</ref> <ref> PMID: 16835450</ref> <ref> PMID: 12089677</ref> <ref> PMID: 31296439 </ref> <ref>DOI: 10.1016/j.ijantimicag.2003.07.020</ref> <ref>DOI: 10.1074/jbc.M103950200</ref> <ref> DOI: 10.1128/AAC.46.3.929-931.2002</ref> <ref> DOI:10.1021/jm040132t</ref> <ref>DOI: 10.1021/jm0002578</ref> <ref>DOI:10.1021/jm0102809 </ref> <ref> DOI: 10.1128/AAC.01873-15</ref>

== Function ==
In the first condensation reaction, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second condensation reaction, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). FPP is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FPPS has been studied in conjunction with different parasites. TcFPPS refers to FPPS in the Typanosoma cruzi parasite while LmFPPS refers to FPPS in the Leishmania major parasite. Bisphosphonates have been shown to inhibit FPPS and are currently being used as antiparasitic drugs as well as a treatment for various bone diseases.

[[Image:FPPSynthesisDiagram.png|700x750px]]

== Structure ==

FPPS exists as a homodimer, with each monomer having an active site. The monomers have the characteristic FPPS fold of a ten-helix bundle and four other helices that run perpendicular to the bundle. There are two substrate sites, one is allylic and the other is homoallylic. GPP and DMAPP bind to the allylic site, while IPP binds to the homoallylic site. These two sites are connected to the top of the bundle and exist as part of a cavity<ref>PMID:24598749</ref>. Another characteristic feature of all FPPS enzymes are two highly conserved aspartate rich motifs. These motifs are called <scene name='48/485622/Lmfpps_rbs/5'>First Aspartate Rich Motif (FARM) and Second Aspartate Rich Motif (SARM)</scene>, and have sequences of DDXX(XX)D and DDXXD respectively. FARM and SARM are found on opposite sides on the active site cavity facing one another<ref>DOI: 10.1021/acs.biochem.0c00432</ref>.

When FPPS interacts with bisphosphonates, the bisphosphonates bind in the homoallylic binding sites and are coordinated by three divalent cations (Ca2+ or Mg2+). The identity of the bisphosphonate influences which divalent cations bind, as well as whether IPP binds. In the <scene name='48/485622/Lmfpps_rbs/6'>structure</scene> of LmFPPS with 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium, three Ca 2+ ions and IPP are present.
FPS <scene name='48/485622/Cv/12'>active site</scene> contains <scene name='48/485622/Cv/13'>Mg+2 ions coordination sites</scene> and binds <scene name='48/485622/Cv/11'>bisphosphonate inhibitors</scene>; see also <scene name='48/485622/Cv/14'>phosphates coordination sites</scene>, (PDB code [[2opm]])<ref>PMID:19309137</ref>, water molecules are shown as red spheres.

== Relevance ==

FPS bisphosphonate inhibitors (like zoledronic acid) are used as drugs for treatment of bone resorption diseases<ref>PMID:24369118</ref>. FPS inhibitor [[Alendronate]] or Fosamax is used in treatment of osteoporosis<ref>PMID:9116385</ref>. Bisphosphonates have been explored as antiparasitic drugs with FPPS because current treatments are expensive, have low efficacy, and have dangerous side effects. FPPS is important in the lengthening of hydrophobic chains and determination of their specificity.

<html5media height="640" width="640">https://vimeo.com/540292892>

. The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. In light green there are nine amino acids sandwiched in between alpha helices of HLA that are part of p53R175H.

==Published 3D structures of FPPS==
[[Farnesyl diphosphate synthase 3D structures]]

</StructureSection>

== References ==
<references/>

[[Category:Topic Page]]

Farnesyl diphosphate synthase

2021-04-22T18:28:51Z

Hannah Campbell:

== Introduction ==
<StructureSection load='2opm' size='350' side='right' scene='48/485622/Cv/15' caption='Human farnesyl diphosphate synthase complex with lipophylic bisphosphonate inhibitor and Mg+2 ions (green) (PDB code [[2opm]]) '>
__TOC__
'''Farnesyl pyrophosphate synthase''' (FPPS) is a chain elongation enzyme that catalyzes carbon-carbon formation in two consecutive condensation reactions that convert one equivalent of dimethylallyl diphosphate (DMAPP) and two equivalents of isopentyl diphosphates (IPP) into one equivalent of Farnesyl pyrophosphate (FPP). <ref>PMID:11152452</ref>In the first step, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second step, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). It is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FFPS has been studied in conjunction with different parasites. Bisphosphonates have been shown to inhibit FPPS and are currently being used for osteoporosis and the treatment of various bone diseases. Inhibition of FPPS in parasites such Trypanosoma cruzi (Tc), Trypanosoma brucei (Tb), Toxoplasma gondii and Leishmania major (Lm) displays antiparasitic activity which is being evaluated as putative therapeutics. <ref> PMID: 24598749</ref> <ref> PMID: 30926449</ref> <ref> PMID: 16835450</ref> <ref> PMID: 12089677</ref> <ref> PMID: 31296439 </ref> <ref>DOI: 10.1016/j.ijantimicag.2003.07.020</ref> <ref>DOI: 10.1074/jbc.M103950200</ref> <ref> DOI: 10.1128/AAC.46.3.929-931.2002</ref> <ref> DOI:10.1021/jm040132t</ref> <ref>DOI: 10.1021/jm0002578</ref> <ref>DOI:10.1021/jm0102809 </ref> <ref> DOI: 10.1128/AAC.01873-15</ref>

== Function ==
In the first condensation reaction, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second condensation reaction, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). FPP is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FPPS has been studied in conjunction with different parasites. TcFPPS refers to FPPS in the Typanosoma cruzi parasite while LmFPPS refers to FPPS in the Leishmania major parasite. Bisphosphonates have been shown to inhibit FPPS and are currently being used as antiparasitic drugs as well as a treatment for various bone diseases.

[[Image:FPPSynthesisDiagram.png|700x750px]]

== Structure ==

FPPS exists as a homodimer, with each monomer having an active site. The monomers have the characteristic FPPS fold of a ten-helix bundle and four other helices that run perpendicular to the bundle. There are two substrate sites, one is allylic and the other is homoallylic. GPP and DMAPP bind to the allylic site, while IPP binds to the homoallylic site. These two sites are connected to the top of the bundle and exist as part of a cavity<ref>PMID:24598749</ref>. Another characteristic feature of all FPPS enzymes are two highly conserved aspartate rich motifs. These motifs are called <scene name='48/485622/Lmfpps_rbs/5'>First Aspartate Rich Motif (FARM) and Second Aspartate Rich Motif (SARM)</scene>, and have sequences of DDXX(XX)D and DDXXD respectively. FARM and SARM are found on opposite sides on the active site cavity facing one another<ref>DOI: 10.1021/acs.biochem.0c00432</ref>.

When FPPS interacts with bisphosphonates, the bisphosphonates bind in the homoallylic binding sites and are coordinated by three divalent cations (Ca2+ or Mg2+). The identity of the bisphosphonate influences which divalent cations bind, as well as whether IPP binds. In the <scene name='48/485622/Lmfpps_rbs/6'>structure</scene> of LmFPPS with 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium, three Ca 2+ ions and IPP are present.
FPS <scene name='48/485622/Cv/12'>active site</scene> contains <scene name='48/485622/Cv/13'>Mg+2 ions coordination sites</scene> and binds <scene name='48/485622/Cv/11'>bisphosphonate inhibitors</scene>; see also <scene name='48/485622/Cv/14'>phosphates coordination sites</scene>, (PDB code [[2opm]])<ref>PMID:19309137</ref>, water molecules are shown as red spheres.

== Relevance ==

FPS bisphosphonate inhibitors (like zoledronic acid) are used as drugs for treatment of bone resorption diseases<ref>PMID:24369118</ref>. FPS inhibitor [[Alendronate]] or Fosamax is used in treatment of osteoporosis<ref>PMID:9116385</ref>. Bisphosphonates have been explored as antiparasitic drugs with FPPS because current treatments are expensive, have low efficacy, and have dangerous side effects. FPPS is important in the lengthening of hydrophobic chains and determination of their specificity.

<html5 height=640 width=640><https://vimeo.com/540292892>

. The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. In light green there are nine amino acids sandwiched in between alpha helices of HLA that are part of p53R175H.

==Published 3D structures of FPPS==
[[Farnesyl diphosphate synthase 3D structures]]

</StructureSection>

== References ==
<references/>

[[Category:Topic Page]]

User:Hannah Campbell

2021-04-08T11:37:59Z

Hannah Campbell:

* Full Real Name:Hannah Campbell

* Position:Student

* Institution (NO ABBREVIATIONS):Notre Dame of Maryland University

* City, State/Province, Country:Baltimore, MD, USA

* Field of Expertise or Study:Chemistry
My pages
*[[FPPS]]
*[[NudT16]]
*[[WWP2]]
*[[Major Histocompatibility Complex Class I]]

Phosphoinositide 3-Kinases

2021-03-25T20:34:06Z

Hannah Campbell:

{{BAMBED
|DATE=November 15, 2010
|OLDID=1144475
|BAMBEDDOI=10.1002/bmb.20540
}}
<StructureSection load='3hhm' size='350' side='right' scene='' caption='PI3K (grey) complex with NISH2 P85α and wortmannin (PDB code [[3hhm]]) '>

[[Image: PI3KOpener.PNG|250px|left|thumb| PI3K p110α Subunit, [[3hhm]]]]
{{Clear}}
__TOC__
== Function ==
[[Phosphoinositide 3-Kinases]] or '''phosphatidylinositol 3-kinase''' (PI3K) are a family of ubiquitously distributed lipid kinases, that play a critical role in the regulation of numerous cellular processes including cellular growth and morphology, programmed cell death, cell motility and adhesion, mitogenesis and glucose uptake. <ref name="Driscoll"> PMID: 12151228</ref> PI3K generates important second messengers by catalyzing the transfer of the γ-phosphate group of ATP to the D3 position of phosphoinositides. <ref name="Wymann"> PMID: 9838078</ref> The PI3K preferred substrate is Phosphatidylinositol-4,5-bisphosphate (PIP2), which is converted into phosphatidylinositol-3,4,5-triphosphate (PIP3) upon phosphorylation at the cell membrane. The importance of PI3K is evident in knockout mice studies in which those mice with disruptions of critical PI3K components have significant deficiencies in immune and inflammatory response <ref name="Fubar"> PMID:10972292</ref> sometimes resulting in embryonic death.<ref>PMID:10196176</ref> Aberrations in PIP3 levels, either through activation of PI3ks or through inactivation of lipid phosphatase [[PTEN]], occur frequently in numerous forms of cancer, making PI3K an exciting new target to treat [[Cancer|cancer]] among other human diseases.<ref name="Miled"> PMID: 17626883</ref> For additional details see 
* [[PI3K Activation, Inhibition, & Medical Implications]] 
* [[Human PI3K p110alpha/p85alpha]] 
* [[The Structure of PI3K]] 
* [[Diabetes & Hypoglycemia]].

==The Classes of PI3Ks==
[[Image:PI3KTransduction.PNG|250px|left|thumb| Signal Transduction Pathway. PI3K Highlighted in Red. Click to Expand]]
{{Clear}}
PI3Ks can be grouped into three distinct classes, Class I-III. Class I PI3Ks, the most well understood and thoroughly explored PI3K class, are composed of a 110kDa <scene name='Phosphoinositide_3-Kinases/Model_cat/2'>catalytic subunit</scene> and a 50-100 kDa <scene name='Phosphoinositide_3-Kinases/Model_ada/1'>adaptor subunit</scene>. Activation of Class I PI3Ks is controlled by extracellular signaling via receptors with intrinsic tyrosine kinase activity, G protein-linked receptors, or receptors coupled to [[SRC]] like protein tyrosine kinases. <ref>PMID:1851250</ref> Class II PI3Ks are relatively poorly understood but are 170-210 kDa and have in vitro substrate specificity toward PtdIns 4-P. Class III PI3Ks depend on Vps15p protein Ser/Thr kinases, which recruits the phosphatidylinositol kinase to late Golgi Compartments. <ref name="Wymann"/>
===Class I Subclasses===
PI3Ks are activated by extracellular agonists via the translocation of PI3Ks to the plasma membrane for easy access to lipid substrates. Depending on the adaptor proteins involved in the process, Class I PI3Ks are segregated into two subgroups. Those that associate with p85 will be directed to phosphorylated tyrosine motifs (Class IA), '''Phosphatidylinositol-4, 5-bisphosphate 3-kinase''' (PI3Kγ) catalyzes the conversion of 1-phosphatidyl-1D-myo-inositol-4, 5-bisphosphate and ATP to 1-phosphatidyl-1D-myo-inositol-4, 5-trisphosphate. PI3Kγ interacts with trimeric G proteins and the p101 protein (Class IB) <ref name="Wymann"/>
==Structure of PI3K==
For Full Article, See: [[The Structure of PI3K]] 

Class I PI3Ks, which are tightly regulated by tyrosine kinases, are composed of an 85kDa regulatory/adapter subunit (p85) and a 110kDa catalytic subunit (p110). <ref name="Flip"> PMID: 10525402</ref>
 

The video below depicts the ATP binding pocket of PI3K.
<html5media height="360" width="360">https://vimeo.com/528973238</html5media>

==PI3K Activation, Inhibition, and Medical Implications==
For Full Article, See: [[PI3K Activation, Inhibition, & Medical Implications]] 

A number of inhibitors for PI3K have been developed to understand how PI3K is activated and functions. These analysis have massive medical implications for the treatment of [[Cancer]] and [[Diabetes]]. Inhibitors of Type I PI3K p110γ and Type I PI3K p110δ are tested as therapeutic drugs against inflammatory etiologists <ref>PMID:19876783</ref>.
 

== 3D Structures of PI3K==
[[Phosphoinositide 3-kinase 3D structures]]

</StructureSection>

==Additional Resources==
* See: [[Cancer]] For Additional Proteins involved in the disease. 
* See: [[Oncogenes]] for Additional examples of oncogenes and tumor suppressor genes.
 

==References==
<references />

[[Category:Topic Page]]
[[Category:Featured in BAMBED]]

__NOEDITSECTION__

Phosphoinositide 3-Kinases

2021-03-25T20:24:54Z

Hannah Campbell:

{{BAMBED
|DATE=November 15, 2010
|OLDID=1144475
|BAMBEDDOI=10.1002/bmb.20540
}}
<StructureSection load='3hhm' size='350' side='right' scene='' caption='PI3K (grey) complex with NISH2 P85α and wortmannin (PDB code [[3hhm]]) '>

[[Image: PI3KOpener.PNG|250px|left|thumb| PI3K p110α Subunit, [[3hhm]]]]
{{Clear}}
__TOC__
== Function ==
[[Phosphoinositide 3-Kinases]] or '''phosphatidylinositol 3-kinase''' (PI3K) are a family of ubiquitously distributed lipid kinases, that play a critical role in the regulation of numerous cellular processes including cellular growth and morphology, programmed cell death, cell motility and adhesion, mitogenesis and glucose uptake. <ref name="Driscoll"> PMID: 12151228</ref> PI3K generates important second messengers by catalyzing the transfer of the γ-phosphate group of ATP to the D3 position of phosphoinositides. <ref name="Wymann"> PMID: 9838078</ref> The PI3K preferred substrate is Phosphatidylinositol-4,5-bisphosphate (PIP2), which is converted into phosphatidylinositol-3,4,5-triphosphate (PIP3) upon phosphorylation at the cell membrane. The importance of PI3K is evident in knockout mice studies in which those mice with disruptions of critical PI3K components have significant deficiencies in immune and inflammatory response <ref name="Fubar"> PMID:10972292</ref> sometimes resulting in embryonic death.<ref>PMID:10196176</ref> Aberrations in PIP3 levels, either through activation of PI3ks or through inactivation of lipid phosphatase [[PTEN]], occur frequently in numerous forms of cancer, making PI3K an exciting new target to treat [[Cancer|cancer]] among other human diseases.<ref name="Miled"> PMID: 17626883</ref> For additional details see 
* [[PI3K Activation, Inhibition, & Medical Implications]] 
* [[Human PI3K p110alpha/p85alpha]] 
* [[The Structure of PI3K]] 
* [[Diabetes & Hypoglycemia]].

==The Classes of PI3Ks==
[[Image:PI3KTransduction.PNG|250px|left|thumb| Signal Transduction Pathway. PI3K Highlighted in Red. Click to Expand]]
{{Clear}}
PI3Ks can be grouped into three distinct classes, Class I-III. Class I PI3Ks, the most well understood and thoroughly explored PI3K class, are composed of a 110kDa <scene name='Phosphoinositide_3-Kinases/Model_cat/2'>catalytic subunit</scene> and a 50-100 kDa <scene name='Phosphoinositide_3-Kinases/Model_ada/1'>adaptor subunit</scene>. Activation of Class I PI3Ks is controlled by extracellular signaling via receptors with intrinsic tyrosine kinase activity, G protein-linked receptors, or receptors coupled to [[SRC]] like protein tyrosine kinases. <ref>PMID:1851250</ref> Class II PI3Ks are relatively poorly understood but are 170-210 kDa and have in vitro substrate specificity toward PtdIns 4-P. Class III PI3Ks depend on Vps15p protein Ser/Thr kinases, which recruits the phosphatidylinositol kinase to late Golgi Compartments. <ref name="Wymann"/>
===Class I Subclasses===
PI3Ks are activated by extracellular agonists via the translocation of PI3Ks to the plasma membrane for easy access to lipid substrates. Depending on the adaptor proteins involved in the process, Class I PI3Ks are segregated into two subgroups. Those that associate with p85 will be directed to phosphorylated tyrosine motifs (Class IA), '''Phosphatidylinositol-4, 5-bisphosphate 3-kinase''' (PI3Kγ) catalyzes the conversion of 1-phosphatidyl-1D-myo-inositol-4, 5-bisphosphate and ATP to 1-phosphatidyl-1D-myo-inositol-4, 5-trisphosphate. PI3Kγ interacts with trimeric G proteins and the p101 protein (Class IB) <ref name="Wymann"/>
==Structure of PI3K==
For Full Article, See: [[The Structure of PI3K]] 

Class I PI3Ks, which are tightly regulated by tyrosine kinases, are composed of an 85kDa regulatory/adapter subunit (p85) and a 110kDa catalytic subunit (p110). <ref name="Flip"> PMID: 10525402</ref>
 

The video below depicts the ATP binding pocket of PI3K.
https://vimeo.com/528973238

==PI3K Activation, Inhibition, and Medical Implications==
For Full Article, See: [[PI3K Activation, Inhibition, & Medical Implications]] 

A number of inhibitors for PI3K have been developed to understand how PI3K is activated and functions. These analysis have massive medical implications for the treatment of [[Cancer]] and [[Diabetes]]. Inhibitors of Type I PI3K p110γ and Type I PI3K p110δ are tested as therapeutic drugs against inflammatory etiologists <ref>PMID:19876783</ref>.
 

== 3D Structures of PI3K==
[[Phosphoinositide 3-kinase 3D structures]]

</StructureSection>

==Additional Resources==
* See: [[Cancer]] For Additional Proteins involved in the disease. 
* See: [[Oncogenes]] for Additional examples of oncogenes and tumor suppressor genes.
 

==References==
<references />

[[Category:Topic Page]]
[[Category:Featured in BAMBED]]

__NOEDITSECTION__

Phosphoinositide 3-Kinases

2021-03-25T20:15:27Z

Hannah Campbell:

{{BAMBED
|DATE=November 15, 2010
|OLDID=1144475
|BAMBEDDOI=10.1002/bmb.20540
}}
<StructureSection load='3hhm' size='350' side='right' scene='' caption='PI3K (grey) complex with NISH2 P85α and wortmannin (PDB code [[3hhm]]) '>

[[Image: PI3KOpener.PNG|250px|left|thumb| PI3K p110α Subunit, [[3hhm]]]]
{{Clear}}
__TOC__
== Function ==
[[Phosphoinositide 3-Kinases]] or '''phosphatidylinositol 3-kinase''' (PI3K) are a family of ubiquitously distributed lipid kinases, that play a critical role in the regulation of numerous cellular processes including cellular growth and morphology, programmed cell death, cell motility and adhesion, mitogenesis and glucose uptake. <ref name="Driscoll"> PMID: 12151228</ref> PI3K generates important second messengers by catalyzing the transfer of the γ-phosphate group of ATP to the D3 position of phosphoinositides. <ref name="Wymann"> PMID: 9838078</ref> The PI3K preferred substrate is Phosphatidylinositol-4,5-bisphosphate (PIP2), which is converted into phosphatidylinositol-3,4,5-triphosphate (PIP3) upon phosphorylation at the cell membrane. The importance of PI3K is evident in knockout mice studies in which those mice with disruptions of critical PI3K components have significant deficiencies in immune and inflammatory response <ref name="Fubar"> PMID:10972292</ref> sometimes resulting in embryonic death.<ref>PMID:10196176</ref> Aberrations in PIP3 levels, either through activation of PI3ks or through inactivation of lipid phosphatase [[PTEN]], occur frequently in numerous forms of cancer, making PI3K an exciting new target to treat [[Cancer|cancer]] among other human diseases.<ref name="Miled"> PMID: 17626883</ref> For additional details see 
* [[PI3K Activation, Inhibition, & Medical Implications]] 
* [[Human PI3K p110alpha/p85alpha]] 
* [[The Structure of PI3K]] 
* [[Diabetes & Hypoglycemia]].

==The Classes of PI3Ks==
[[Image:PI3KTransduction.PNG|250px|left|thumb| Signal Transduction Pathway. PI3K Highlighted in Red. Click to Expand]]
{{Clear}}
PI3Ks can be grouped into three distinct classes, Class I-III. Class I PI3Ks, the most well understood and thoroughly explored PI3K class, are composed of a 110kDa <scene name='Phosphoinositide_3-Kinases/Model_cat/2'>catalytic subunit</scene> and a 50-100 kDa <scene name='Phosphoinositide_3-Kinases/Model_ada/1'>adaptor subunit</scene>. Activation of Class I PI3Ks is controlled by extracellular signaling via receptors with intrinsic tyrosine kinase activity, G protein-linked receptors, or receptors coupled to [[SRC]] like protein tyrosine kinases. <ref>PMID:1851250</ref> Class II PI3Ks are relatively poorly understood but are 170-210 kDa and have in vitro substrate specificity toward PtdIns 4-P. Class III PI3Ks depend on Vps15p protein Ser/Thr kinases, which recruits the phosphatidylinositol kinase to late Golgi Compartments. <ref name="Wymann"/>
===Class I Subclasses===
PI3Ks are activated by extracellular agonists via the translocation of PI3Ks to the plasma membrane for easy access to lipid substrates. Depending on the adaptor proteins involved in the process, Class I PI3Ks are segregated into two subgroups. Those that associate with p85 will be directed to phosphorylated tyrosine motifs (Class IA), '''Phosphatidylinositol-4, 5-bisphosphate 3-kinase''' (PI3Kγ) catalyzes the conversion of 1-phosphatidyl-1D-myo-inositol-4, 5-bisphosphate and ATP to 1-phosphatidyl-1D-myo-inositol-4, 5-trisphosphate. PI3Kγ interacts with trimeric G proteins and the p101 protein (Class IB) <ref name="Wymann"/>
==Structure of PI3K==
For Full Article, See: [[The Structure of PI3K]] 

Class I PI3Ks, which are tightly regulated by tyrosine kinases, are composed of an 85kDa regulatory/adapter subunit (p85) and a 110kDa catalytic subunit (p110). <ref name="Flip"> PMID: 10525402</ref>
 

The video below depicts the ATP binding pocket of PI3K.

==PI3K Activation, Inhibition, and Medical Implications==
For Full Article, See: [[PI3K Activation, Inhibition, & Medical Implications]] 

A number of inhibitors for PI3K have been developed to understand how PI3K is activated and functions. These analysis have massive medical implications for the treatment of [[Cancer]] and [[Diabetes]]. Inhibitors of Type I PI3K p110γ and Type I PI3K p110δ are tested as therapeutic drugs against inflammatory etiologists <ref>PMID:19876783</ref>.
 

== 3D Structures of PI3K==
[[Phosphoinositide 3-kinase 3D structures]]

</StructureSection>

==Additional Resources==
* See: [[Cancer]] For Additional Proteins involved in the disease. 
* See: [[Oncogenes]] for Additional examples of oncogenes and tumor suppressor genes.
 

==References==
<references />

[[Category:Topic Page]]
[[Category:Featured in BAMBED]]

__NOEDITSECTION__

WWP2

2021-03-25T18:43:20Z

Hannah Campbell:

<StructureSection load='5TJ7' size='350' side='right' caption="WWP2 Ubiquitin Ligase Chimeric Structure (PDB entry [[5TJ7]]). The 2,3-linker (red) connects the WW2 domain (yellow) to the WW3 domain. The hinge (magenta) connects the C-terminal lobe (green) and N-terminal lobe (silver) of the HECT domain." scene="84/848928/Overallcolored/14">
__TOC__
==Introduction==
'''WWP2''' (WW domain-containing protein 2) is a type of [[ubiquitin protein ligase]]. Ubiquitination can serve as a signal for degradation, lead to translocation within the cell, and result in altered activity and altered protein-protein interactions. The ubiquitination pathway comprises of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-ligating (E3) enzymes. WWP2 is a member of the HECT ('''H'''omologous to the '''E'''6-AP '''C'''arboxyl '''T'''erminus) E3 Ligase class of enzymes. HECT E3 Ligases accept a [[ubiquitin]] molecule from E2 enzymes and transfer the ubiquitin to a Lysine residue in the target signaling molecule or transcription factor <ref>PMID:15021885</ref>.

The thioester bond formation between an active site Cystine on HECT E3 Ligases and the ubiquitin ligand differentiates the HECT family of enzymes from the more abundant RING ('''R'''eally '''I'''nteresting '''N'''ew '''G'''ene) family of ubiquitin ligases which mediate ubiquitin transfer through non-covalent interactions. Within HECT E3 Ligases, WWP2 falls into the NEDD 4 family (named after the instance in which the first member was discovered: a study of developmentally down-regulated proteins in neuronal embryonic mouse cells) which generally target proteins with a PPxY motif. NEDD4 E3 Ligases consist of an amino-terminal C2 domain, between two and four WW domains, and a carboxy-terminal HECT domain. Two conformational states (a ground state inverse T shape and catalytically active L shape) have been observed.

==Structure==
[[Image:WWP2 Scheme from paper fig 1A top.png|300px|right|thumb| WWP2 Scheme without C2 Domain]]
[[Image:WWP2 Scheme from paper D3.png|300px|right|thumb| WWP2 Scheme WW2-2,3-linker-HECT]]
Full-length WWP2 consists of an amino-terminal C2 domain, four WW domains (labeled WW1-WW4), and a carboxy-terminal HECT domain. WW domains are one of the smallest studied protein modules, consisting of less than 40 amino acids, fold into three-stranded beta-sheets. They are characterized by two highly conserved <scene name='84/848928/Trpsinww2/2'>Trp residues</scene> positioned 20-22 amino acids apart and a high affinity for proline-rich motifs. Linkers of varying length and secondary structure connect the C2 domain to WW1, WW1 to WW2, WW2 to WW3, WW3 to WW4, and WW4 to the HECT domain. A chimeric <scene name='84/848928/Overallcolored/12'>structure</scene> of WWP2 consisting of the <scene name='84/848928/Ww2_domain/8'>WW2 domain</scene>, the WW2-WW3 linker (<scene name='84/848928/Linkeronly/1'>2,3-linker</scene>), and the HECT domain is shown on the right.

The HECT domain is divided into two lobes (labeled N and C). The N-lobe serves as a binding site for the E2-ubiquitin complex and includes an exosite for non-covalent ubiquitin binding relevant to autoinhibition while the C-lobe contains an active site with a catalytic Cys residue to which the substrate ubiquitin molecule can covalently attach. The <scene name='84/848928/Hinge_zoomed/7'>hinge</scene> (magenta) connects the N and C lobes of the HECT domain and allows for flexible movement of the lobes as ubiquitin is transferred from the E2-ubiquitin complex docked on the N-lobe to the ubiquitin binding site in the C-lobe. A transthiolation reaction in this active site results in a thioester bond between the ubiquitin and a Cys residue. The HECT domain is in an inverse T shape when inactive (autoinhibited) and takes on an L shape when active. WW2 interaction with HECT is mediated by the six C terminal residues.
<html5media height="360" width="360">https://vimeo.com/528973813</html5media>
The video above shows the protein WWP2, with emphasis on the hinge loop shown in magenta.

The alpha-helical 2,3-linker is subject to tyrosine phosphorylation at either end of the linker at residues <scene name='84/848928/Tyr392tyr369/2'>Tyr369 and Tyr392</scene>. Chen et. al. have shown that the phosphorylation of Tyr369 allows for allosteric activation by ubiquitination at the exosite in the N-lobe, while phosphorylation of Tyr392 residue leads to a destabilization of the T conformation of the HECT domain.

== Function ==
Studies suggest that the C2 domain, with calcium ion and phospholipid binding properties, is required for membrane binding while the WW domains play a critical role in substrate specificity. Genetic deletions of WW domains and linkers have shown increased autoubiquitination activity. The WW domains and linkers play a role in altering protein conformation, with the 2,3-linker playing the greatest role.

This linker plays an autoinhibitory role. The ground state conformation of the protein has the 2,3-linker close to the N-lobe, while WW1 and WW2 domains block the N lobe’s ubiquitin-binding site. Upon phosphorylation the 2,3-linker changes conformation, moving further from the N lobe, allowing the protein to bind ubiquitin in the E2 and N lobe binding sites. This binding will further open the protein up to bind possible substrates, like PTEN.
Interactions between the hinge and the 2,3-linker appear to restrict flexibility of the C-lobe which is necessary for ubiquitin transferase activity. This interaction further locks the protein into the T position. A current model of WWP2 activation by Chen et. al. proposes the following: (1) autoinhibited WWP2 gets phosphorylated at the 2,3-linker, (2) loosening of the 2,3-linker interactions with the hinge and ubiquitin binding exosite allow ubiquitin to bind in the C-lobe, (3) the target substrate protein binds with specifity towards the WW domains, (4) the substrate protein gets ubiquitinated, and (5) the 2,3-linker gets dephosphorylated, allowing WWP2 to return to the autoinhibited ground state conformation. <ref>PMID:28475870</ref>

== Relevance ==
Mutations in the NEDD4 family of proteins have been associated with several cancers and immune disorders. Many of these mutations occur in the 2,3-linker/HECT autoinhibited domains and the modified activity of the E3 Ligases as a result of these mutations can lead to an increase in the growth of tumor cells. WWP2 may play a role in the regulation of oncogenic signaling pathways through interactions with its substrate [[PTEN]], a tumor suppressor in the [[PI3K]] pathway. The downregulation of voltage-gated sodium channels by WWP2 and other members of the NEDD4 family is an active area of research. Other known targets of WWP2 include SMADs, OCT4, EGR2, and TIRF. <ref>PMID:25216927</ref>
</StructureSection>

== References ==
<references/>

WWP2

2021-03-25T18:42:51Z

Hannah Campbell:

<StructureSection load='5TJ7' size='350' side='right' caption="WWP2 Ubiquitin Ligase Chimeric Structure (PDB entry [[5TJ7]]). The 2,3-linker (red) connects the WW2 domain (yellow) to the WW3 domain. The hinge (magenta) connects the C-terminal lobe (green) and N-terminal lobe (silver) of the HECT domain." scene="84/848928/Overallcolored/14">
__TOC__
==Introduction==
'''WWP2''' (WW domain-containing protein 2) is a type of [[ubiquitin protein ligase]]. Ubiquitination can serve as a signal for degradation, lead to translocation within the cell, and result in altered activity and altered protein-protein interactions. The ubiquitination pathway comprises of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-ligating (E3) enzymes. WWP2 is a member of the HECT ('''H'''omologous to the '''E'''6-AP '''C'''arboxyl '''T'''erminus) E3 Ligase class of enzymes. HECT E3 Ligases accept a [[ubiquitin]] molecule from E2 enzymes and transfer the ubiquitin to a Lysine residue in the target signaling molecule or transcription factor <ref>PMID:15021885</ref>.

The thioester bond formation between an active site Cystine on HECT E3 Ligases and the ubiquitin ligand differentiates the HECT family of enzymes from the more abundant RING ('''R'''eally '''I'''nteresting '''N'''ew '''G'''ene) family of ubiquitin ligases which mediate ubiquitin transfer through non-covalent interactions. Within HECT E3 Ligases, WWP2 falls into the NEDD 4 family (named after the instance in which the first member was discovered: a study of developmentally down-regulated proteins in neuronal embryonic mouse cells) which generally target proteins with a PPxY motif. NEDD4 E3 Ligases consist of an amino-terminal C2 domain, between two and four WW domains, and a carboxy-terminal HECT domain. Two conformational states (a ground state inverse T shape and catalytically active L shape) have been observed.

==Structure==
[[Image:WWP2 Scheme from paper fig 1A top.png|300px|right|thumb| WWP2 Scheme without C2 Domain]]
[[Image:WWP2 Scheme from paper D3.png|300px|right|thumb| WWP2 Scheme WW2-2,3-linker-HECT]]
Full-length WWP2 consists of an amino-terminal C2 domain, four WW domains (labeled WW1-WW4), and a carboxy-terminal HECT domain. WW domains are one of the smallest studied protein modules, consisting of less than 40 amino acids, fold into three-stranded beta-sheets. They are characterized by two highly conserved <scene name='84/848928/Trpsinww2/2'>Trp residues</scene> positioned 20-22 amino acids apart and a high affinity for proline-rich motifs. Linkers of varying length and secondary structure connect the C2 domain to WW1, WW1 to WW2, WW2 to WW3, WW3 to WW4, and WW4 to the HECT domain. A chimeric <scene name='84/848928/Overallcolored/12'>structure</scene> of WWP2 consisting of the <scene name='84/848928/Ww2_domain/8'>WW2 domain</scene>, the WW2-WW3 linker (<scene name='84/848928/Linkeronly/1'>2,3-linker</scene>), and the HECT domain is shown on the right.

The HECT domain is divided into two lobes (labeled N and C). The N-lobe serves as a binding site for the E2-ubiquitin complex and includes an exosite for non-covalent ubiquitin binding relevant to autoinhibition while the C-lobe contains an active site with a catalytic Cys residue to which the substrate ubiquitin molecule can covalently attach. The <scene name='84/848928/Hinge_zoomed/7'>hinge</scene> (magenta) connects the N and C lobes of the HECT domain and allows for flexible movement of the lobes as ubiquitin is transferred from the E2-ubiquitin complex docked on the N-lobe to the ubiquitin binding site in the C-lobe. A transthiolation reaction in this active site results in a thioester bond between the ubiquitin and a Cys residue. The HECT domain is in an inverse T shape when inactive (autoinhibited) and takes on an L shape when active. WW2 interaction with HECT is mediated by the six C terminal residues.
<html5media height="360" width="360">https://vimeo.com/528973813</html5media>

The video above shows the protein WWP2, with emphasis on the hinge loop shown in magenta.

The alpha-helical 2,3-linker is subject to tyrosine phosphorylation at either end of the linker at residues <scene name='84/848928/Tyr392tyr369/2'>Tyr369 and Tyr392</scene>. Chen et. al. have shown that the phosphorylation of Tyr369 allows for allosteric activation by ubiquitination at the exosite in the N-lobe, while phosphorylation of Tyr392 residue leads to a destabilization of the T conformation of the HECT domain.

== Function ==
Studies suggest that the C2 domain, with calcium ion and phospholipid binding properties, is required for membrane binding while the WW domains play a critical role in substrate specificity. Genetic deletions of WW domains and linkers have shown increased autoubiquitination activity. The WW domains and linkers play a role in altering protein conformation, with the 2,3-linker playing the greatest role.

This linker plays an autoinhibitory role. The ground state conformation of the protein has the 2,3-linker close to the N-lobe, while WW1 and WW2 domains block the N lobe’s ubiquitin-binding site. Upon phosphorylation the 2,3-linker changes conformation, moving further from the N lobe, allowing the protein to bind ubiquitin in the E2 and N lobe binding sites. This binding will further open the protein up to bind possible substrates, like PTEN.
Interactions between the hinge and the 2,3-linker appear to restrict flexibility of the C-lobe which is necessary for ubiquitin transferase activity. This interaction further locks the protein into the T position. A current model of WWP2 activation by Chen et. al. proposes the following: (1) autoinhibited WWP2 gets phosphorylated at the 2,3-linker, (2) loosening of the 2,3-linker interactions with the hinge and ubiquitin binding exosite allow ubiquitin to bind in the C-lobe, (3) the target substrate protein binds with specifity towards the WW domains, (4) the substrate protein gets ubiquitinated, and (5) the 2,3-linker gets dephosphorylated, allowing WWP2 to return to the autoinhibited ground state conformation. <ref>PMID:28475870</ref>

== Relevance ==
Mutations in the NEDD4 family of proteins have been associated with several cancers and immune disorders. Many of these mutations occur in the 2,3-linker/HECT autoinhibited domains and the modified activity of the E3 Ligases as a result of these mutations can lead to an increase in the growth of tumor cells. WWP2 may play a role in the regulation of oncogenic signaling pathways through interactions with its substrate [[PTEN]], a tumor suppressor in the [[PI3K]] pathway. The downregulation of voltage-gated sodium channels by WWP2 and other members of the NEDD4 family is an active area of research. Other known targets of WWP2 include SMADs, OCT4, EGR2, and TIRF. <ref>PMID:25216927</ref>
</StructureSection>

== References ==
<references/>

WWP2

2021-03-25T18:36:27Z

Hannah Campbell:

<StructureSection load='5TJ7' size='350' side='right' caption="WWP2 Ubiquitin Ligase Chimeric Structure (PDB entry [[5TJ7]]). The 2,3-linker (red) connects the WW2 domain (yellow) to the WW3 domain. The hinge (magenta) connects the C-terminal lobe (green) and N-terminal lobe (silver) of the HECT domain." scene="84/848928/Overallcolored/14">
__TOC__
==Introduction==
'''WWP2''' (WW domain-containing protein 2) is a type of [[ubiquitin protein ligase]]. Ubiquitination can serve as a signal for degradation, lead to translocation within the cell, and result in altered activity and altered protein-protein interactions. The ubiquitination pathway comprises of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-ligating (E3) enzymes. WWP2 is a member of the HECT ('''H'''omologous to the '''E'''6-AP '''C'''arboxyl '''T'''erminus) E3 Ligase class of enzymes. HECT E3 Ligases accept a [[ubiquitin]] molecule from E2 enzymes and transfer the ubiquitin to a Lysine residue in the target signaling molecule or transcription factor <ref>PMID:15021885</ref>.

The thioester bond formation between an active site Cystine on HECT E3 Ligases and the ubiquitin ligand differentiates the HECT family of enzymes from the more abundant RING ('''R'''eally '''I'''nteresting '''N'''ew '''G'''ene) family of ubiquitin ligases which mediate ubiquitin transfer through non-covalent interactions. Within HECT E3 Ligases, WWP2 falls into the NEDD 4 family (named after the instance in which the first member was discovered: a study of developmentally down-regulated proteins in neuronal embryonic mouse cells) which generally target proteins with a PPxY motif. NEDD4 E3 Ligases consist of an amino-terminal C2 domain, between two and four WW domains, and a carboxy-terminal HECT domain. Two conformational states (a ground state inverse T shape and catalytically active L shape) have been observed.

==Structure==
[[Image:WWP2 Scheme from paper fig 1A top.png|300px|right|thumb| WWP2 Scheme without C2 Domain]]
[[Image:WWP2 Scheme from paper D3.png|300px|right|thumb| WWP2 Scheme WW2-2,3-linker-HECT]]
Full-length WWP2 consists of an amino-terminal C2 domain, four WW domains (labeled WW1-WW4), and a carboxy-terminal HECT domain. WW domains are one of the smallest studied protein modules, consisting of less than 40 amino acids, fold into three-stranded beta-sheets. They are characterized by two highly conserved <scene name='84/848928/Trpsinww2/2'>Trp residues</scene> positioned 20-22 amino acids apart and a high affinity for proline-rich motifs. Linkers of varying length and secondary structure connect the C2 domain to WW1, WW1 to WW2, WW2 to WW3, WW3 to WW4, and WW4 to the HECT domain. A chimeric <scene name='84/848928/Overallcolored/12'>structure</scene> of WWP2 consisting of the <scene name='84/848928/Ww2_domain/8'>WW2 domain</scene>, the WW2-WW3 linker (<scene name='84/848928/Linkeronly/1'>2,3-linker</scene>), and the HECT domain is shown on the right.

The HECT domain is divided into two lobes (labeled N and C). The N-lobe serves as a binding site for the E2-ubiquitin complex and includes an exosite for non-covalent ubiquitin binding relevant to autoinhibition while the C-lobe contains an active site with a catalytic Cys residue to which the substrate ubiquitin molecule can covalently attach. The <scene name='84/848928/Hinge_zoomed/7'>hinge</scene> (magenta) connects the N and C lobes of the HECT domain and allows for flexible movement of the lobes as ubiquitin is transferred from the E2-ubiquitin complex docked on the N-lobe to the ubiquitin binding site in the C-lobe. A transthiolation reaction in this active site results in a thioester bond between the ubiquitin and a Cys residue. The HECT domain is in an inverse T shape when inactive (autoinhibited) and takes on an L shape when active. WW2 interaction with HECT is mediated by the six C terminal residues.
<html5media height="360" width="360">https://vimeo.com/528973813</html5media>

The alpha-helical 2,3-linker is subject to tyrosine phosphorylation at either end of the linker at residues <scene name='84/848928/Tyr392tyr369/2'>Tyr369 and Tyr392</scene>. Chen et. al. have shown that the phosphorylation of Tyr369 allows for allosteric activation by ubiquitination at the exosite in the N-lobe, while phosphorylation of Tyr392 residue leads to a destabilization of the T conformation of the HECT domain.

== Function ==
Studies suggest that the C2 domain, with calcium ion and phospholipid binding properties, is required for membrane binding while the WW domains play a critical role in substrate specificity. Genetic deletions of WW domains and linkers have shown increased autoubiquitination activity. The WW domains and linkers play a role in altering protein conformation, with the 2,3-linker playing the greatest role.

This linker plays an autoinhibitory role. The ground state conformation of the protein has the 2,3-linker close to the N-lobe, while WW1 and WW2 domains block the N lobe’s ubiquitin-binding site. Upon phosphorylation the 2,3-linker changes conformation, moving further from the N lobe, allowing the protein to bind ubiquitin in the E2 and N lobe binding sites. This binding will further open the protein up to bind possible substrates, like PTEN.
Interactions between the hinge and the 2,3-linker appear to restrict flexibility of the C-lobe which is necessary for ubiquitin transferase activity. This interaction further locks the protein into the T position. A current model of WWP2 activation by Chen et. al. proposes the following: (1) autoinhibited WWP2 gets phosphorylated at the 2,3-linker, (2) loosening of the 2,3-linker interactions with the hinge and ubiquitin binding exosite allow ubiquitin to bind in the C-lobe, (3) the target substrate protein binds with specifity towards the WW domains, (4) the substrate protein gets ubiquitinated, and (5) the 2,3-linker gets dephosphorylated, allowing WWP2 to return to the autoinhibited ground state conformation. <ref>PMID:28475870</ref>

== Relevance ==
Mutations in the NEDD4 family of proteins have been associated with several cancers and immune disorders. Many of these mutations occur in the 2,3-linker/HECT autoinhibited domains and the modified activity of the E3 Ligases as a result of these mutations can lead to an increase in the growth of tumor cells. WWP2 may play a role in the regulation of oncogenic signaling pathways through interactions with its substrate [[PTEN]], a tumor suppressor in the [[PI3K]] pathway. The downregulation of voltage-gated sodium channels by WWP2 and other members of the NEDD4 family is an active area of research. Other known targets of WWP2 include SMADs, OCT4, EGR2, and TIRF. <ref>PMID:25216927</ref>
</StructureSection>

== References ==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T22:42:57Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC I (HLA A2:01) by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers discovered that neoantigen p53R175H is displayed by HLA:A2 on the cell surface at very low density. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are easier to graft into different therapuetic formats and are an off the shelf ready to use therapy. Specifically, researchers developed a bispecific antibody constructed from H2 and an antiCD3 antibody, (H2- scDb) that can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC I can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T22:42:38Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC I (HLA A2:01) by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers discovered that neoantigen p53R175H is displayed by HLA:A2 on the cell surface at very low density. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are easier to graft into different therapuetic formats and are an off the shelf ready to use therapy. Specifically, researchers developed a bispecific antibody constructed from H2 and an antiCD3 antibody, (H2- scDb) that can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC Ican be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T22:41:47Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHCI (HLA A2:01) by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers discovered that neoantigen p53R175H is displayed by HLA:A2 on the cell surface at very low density. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are easier to graft into different therapuetic formats and are an off the shelf ready to use therapy. Specifically, researchers developed a bispecific antibody constructed from H2 and an antiCD3 antibody, (H2- scDb) that can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T22:41:11Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHCI (HLA A2:01) by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers discovered that neoantigen p53R175H is displayed by HLA:A2 on the cell surface at very low density. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are easier to graft into different therapuetic formats and are an off the shelf ready to use therapy. Specifically, researchers developed a bispecific antibody constructed from H2 and an antiCD3 antibody, (H2- scDb) can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T22:39:34Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHCI (HLA A2:01) by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers discovered that neoantigen p53R175H is displayed by HLA:A2 on the cell surface at very low density. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are easier to graft into different therapuetic formats and are an off the shelf ready to use therapy. Specifically, researchers developed a bispecific antibody constructed from H2 and an antiCD3 (H2- scDb) can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T22:38:00Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHCI (HLA A2:01) by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers discovered that neoantigen p53R175H is displayed by HLA:A2 on the cell surface at very low density. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are easier to graft into different therapuetic formats and are an off the shelf ready to use therapy. As a final result, researchers developed a bispecific antibody constructed from H2 (H2- scDb) can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T22:36:31Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHCI (HLA A2:01) by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers discovered that neoantigen p53R175H is displayed by HLA:A2 on the cell surface at very low density. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are easier to graft into different therapuetic formats and are an off the shelf ready to use therapy. '' for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts.'' As a final result, researchers developed a bispecific antibody constructed from H2 (H2- scDb) can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T22:33:14Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHCI (HLA A2:01) by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers discovered that neoantigen p53R175H is displayed by HLA:A2 on the cell surface at very low density. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts. As a final result, researchers developed a bispecific antibody constructed from H2 (H2- scDb) can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T22:22:22Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetic Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts. As a final result, researchers developed a bispecific antibody constructed from H2 (H2- scDb) can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T21:40:13Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts. As a final result, researchers developed a bispecific antibody constructed from H2 (H2- scDb) can activate T cells even when the pHLA complex is expressed at very low, endogenous levels. This promising research shows that MHC can be a key player in the fight against cancers caused by p53 mutations. <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T20:52:01Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

This video shows the same structure from above, but zooming in shows the interaction of the pHLA with complementarity-determining regions. Hydrogen bonds are shown as dashed lines.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T19:42:34Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>
This video shows the same structure from above, but zooming in shows the interaction of the pHLA with CDRs.

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T19:39:48Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts <ref>DOI: 10.1126/science.abc8697</ref>. See below for interactive figures from this research.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold. Sandwiched in between alpha helices of HLA are nine amino acids that are part of p53R175H shown light green.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T19:33:25Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts <ref>DOI: 10.1126/science.abc8697</ref>.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA (p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan). The Fab fragment is bound to the C terminus of the pHLA complex, where HLA-A*02:01 is colored gray and the β2 microglobulin is colored in gold.

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T19:28:40Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts <ref>DOI: 10.1126/science.abc8697</ref>.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA ( p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan).

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T19:27:44Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts <ref>DOI: 10.1126/science.abc8697</ref>.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA ( p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB [[6W51]]). The Fab fragment is colored according to its heavy chains (dark blue) and light chains (cyan).

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T19:25:25Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts <ref>DOI: 10.1126/science.abc8697</ref>.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

The video above depicts the 3D structure of the pHLA ( p53R175H/HLA-A*02:01) that is bound to an H2-Fab fragment (PDB 6W51)

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T18:26:32Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called ''Targeting a neoantigen derived from a common TP53 mutation'' describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts <ref>DOI: 10.1126/science.abc8697</ref>.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T18:24:45Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called Targeting a neoantigen derived from a common TP53 mutation describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts <ref>DOI: 10.1126/science.abc8697</ref>.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T18:22:53Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called Targeting a neoantigen derived from a common TP53 mutation describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts <ref>DOI: 10.1126/science.abc8697<ref/>.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T18:15:23Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called Targeting a neoantigen derived from a common TP53 mutation describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

==References==
<references/>

Major Histocompatibility Complex Class I

2021-03-18T18:04:22Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called Targeting a neoantigen derived from a common TP53 mutation describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

Major Histocompatibility Complex Class I

2021-03-18T18:00:21Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called Targeting a neoantigen derived from a common TP53 mutation describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts.

<html5media height="640" width="640"|right|thumb|>https://vimeo.com/525610220</html5media>

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

Major Histocompatibility Complex Class I

2021-03-18T17:59:34Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called Targeting a neoantigen derived from a common TP53 mutation describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts.

|right|thumb|<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

Major Histocompatibility Complex Class I

2021-03-18T17:57:44Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called Targeting a neoantigen derived from a common TP53 mutation describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most [[P53]] is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

Major Histocompatibility Complex Class I

2021-03-18T17:51:18Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called Targeting a neoantigen derived from a common TP53 mutation describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most P53 is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to Histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex researchers created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

Major Histocompatibility Complex Class I

2021-03-18T17:49:49Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==
A recent study called Targeting a neoantigen derived from a common TP53 mutation describes the means by which T Cell Receptor mimic (TCRm) antibodies were created a new class of immunotherapy. TP53, tumor protein 53, is a tumor suppressor gene, and is the most commonly mutated protein in cancers. Most P53 is located inside the cell, the largest concentration is in the nucleus, which makes it difficult to find a treatment for TP53. Scientists have been struggling to design a drug to target this inactivated tumor suppressor gene. However, a small percentage is degraded by proteasomes and is present on the cell surface by MHC, Human Leukocyte Antigen (HLA). The most frequent mutation in the TP53 gene is a substitution from Arginine to histidine at codon 175 (R175H). Most mutations within this gene occur as single-nucleotide variants at positions nearest to the DNA-binding domain. Using an HLA TP53 complex they created a neoantigen that presents on the cell surface. These peptide-HLA (pHLA) complexes are naturally ligands for T-cell receptors (TCRs). The advantage of using TCRm’s for immunotherapies is that they are of higher affinity for pHLA and are more easily converted to different therapeutics when compared to their TCR counterparts.

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].

Major Histocompatibility Complex Class I

2021-03-18T15:02:06Z

Hannah Campbell:

''Major Histocompatibility Complex'' (MHC) genes, and the proteins they specify, play centrally important roles in adaptive immune responses. Each MHC protein molecule contains a groove that is loaded with a peptide fragment derived from an intracellular protein. The MHC proteins carry these peptides to the outer surface of the cell, where thymus-derived ("T") lymphocytes examine them. When the peptides are deemed to be foreign by the T lymphocytes, appropriate immune defenses are activated. T lymphocytes are centrally important in all adaptive immune responses, including antibody production and the elimination of intracellular parasites, and their responses depend entirely on the presentation of peptides by MHC. Class I MHC proteins, in particular, reveal the presence of otherwise hidden intracellular parasites (such as viruses and some bacteria) by displaying peptide fragments of parasite proteins on the cell surface. For more detail, please see [http://en.wikipedia.org/wiki/Major_histocompatibility_complex Wikipedia: Major Histocompatibility Complex].

The 3D structure of MHC proteins was one of the [[Highest_impact_structures | highest impact crystallographic strucures of all time]]. In order to appreciate why, some historical background is helpful.

==Major Histocompatibility Complex (MHC) Class I: Historical Background==
''Major Histocompatibility Complex'' (MHC) refers to a complex of closely linked genes first identified in the early to mid-20th century as being the major factors in the rejection of living tissue allografts (grafts between members of the same species). It was these studies that gave MHC its name. Many other genes contribute to tissue allograft rejection to minor degrees, and these were called ''minor histocompatibility genes''. MHC genes code for MHC proteins that are the major antigens responsible for tissue allograft rejection. George D. Snell received one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for his contributions to the identification and characterization of these genes. Of course many other researchers made crucial contributions and they are credited in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/snell-lecture.pdf Snell's Nobel Lecture]. Jean Dausset received a third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for demonstrating the existence of MHC genes and proteins in humans, the latter being called ''Human Leukocyte Antigens'' ('''HLA'''). In mice, the most-used experimental model for studying MHC, the histocompatibility genetic loci were numbered H-1, H-2, H-3, and so forth. '''H-2''' is the major histocompatibility locus, while all the others are minor. Both HLA and H-2 turned out to be large complexes of closely-linked genes.

Independently, in the early 1960's, Baruj Benacerraf and coworkers demonstrated the existence of ''immune response genes'' (Ir genes) that controlled the ability of an individual guinea pig's immune system to respond to simple synthetic amino acid polymers. Benacerraf was awarded one third of the [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/ 1980 Nobel Prize in Physiology or Medicine] for discovering immune response genes. In the late 1960's, McDevitt and others found that the Ir genes were linked to MHC (for details, see [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture]).

In 1975, Zinkernagel and Doherty made the surprising discovery that the ability of virus-specific T lymphocytes to recognize virus infection, in virus-infected cells, depended upon the MHC genotype of the infected cells. The MHC had to match that present when the T lymphocytes were first activated by the virus. This "restriction" of antigen recognition by T cells was confirmed in many other systems. In 1996, Zinkernagel and Doherty were awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/1996/ Nobel Prize in Physiology or Medicine] for this discovery. By that time, the mechanism of the "restriction" they had observed was clear -- thanks to the 3D structure of MHC Class I.

==3D Structure and Its Significance==
By the mid-1980's, there was abundant evidence that the ability of T lymphocytes to recognize antigen is "restricted" by MHC. However, what this "restriction" meant in terms of molecular mechanism was far from clear. Speculation about possible mechanisms raged for over a decade following Zinkernagel and Doherty's 1975 insight. But no experimental evidence available at the time was able to explain the "restriction". As an illustration, Figure 7 in [http://nobelprize.org/nobel_prizes/medicine/laureates/1980/benacerraf-lecture.html Benacerraf's Nobel Lecture] shows his thinking in 1980. The figure shows an "Ia molecule" hypothetically "specifically interacting" with an "antigen fragment". Note that although the genetic linkage between Ia (the molecule coded for by immune response genes) and MHC was well established, it was not yet clear that Ia was MHC. Benacerraf's thinking was correct, as far as it went, but the details were not yet available.

[[Image:1hla_edm_fig6b.jpg|right|thumb|340 px|Electron density of HLA-A2 peptide-binding groove showing density of mixed peptides. Figure 6b from [[1hla#Reference | Bjorkman et al., Nature 329:506]], used with permission of Dr. Pamela Bjorkman.]]
In 1987, Bjorkman and coworkers (in the laboratory of Don Wiley at Harvard) published the first empirical structure of MHC, a crystallographic structure of the human MHC Class I protein HLA-A2 ([[1hla]]). Although the resolution was low (3.5 Å), there was sufficient information to explain the decade-long mystery of how MHC restricts the recognition of foreign antigens by T lymphocytes. It is difficult to exaggerate the impact that this structure, and those that followed, had on the field of immunology.

Wiley's team struggled for many years to obtain sufficient MHC protein and high quality crystals. During this struggle, their funding ran out but they persevered, using funds from other projects (personal communication to [[User:Eric Martz |Eric Martz]] from Wiley, ca. 1989). The MHC protein was obtained from cultures of human cells (the JY B lymphocyte cell line) by a well-established but arduous process that earlier had been used for obtaining the amino acid sequences of HLA proteins by Strominger and coworkers. Papain was used to cleave the soluble extracellular domains of the HLA MHC proteins from their transmembrane domains, and the HLA-A2 domains were purified, separating them from HLA-B7 among many other proteins present on these cells.

Because the protein was obtained from living cells, its '''peptide-accomodating groove (blue in figure at right)''' contained a '''mixture of unknown peptides (salmon-colored in figure at right)'''. These appeared in the crystal structure of [[1hla]] as an electron density that could not be explained by the known sequence of HLA-A2, lying within a groove the alpha chain of that molecule, in their Fig. 6b (at right). This phenomenally enlightening preview of ghostly peptides being presented to T cells by MHC gave goosebumps to cellular immunologists of the time.

==MHC Structure Tutorial==
A tutorial about the structure of MHC is available at [http://molviz.org MolviZ.Org]. It includes side by side comparisons of two different viral epitopes in MHC class I (with synchronized mouse rotation), of epitopes in MHC I vs. II, and a chapter on MHC class II structure.

==Recognition of MHC by T Cell Receptor Mimetric Antibodies==

<html5media height="640" width="640">https://vimeo.com/525610220</html5media>

<html5media height="640" width="640">https://vimeo.com/525601759</html5media>

==MHC Structures==

A list of MHC structures is at [[Major histocompatibility complex]].