Keytruda - Revision history

Michal Harel at 08:01, 21 January 2019

2019-01-21T08:01:32Z

← Older revision		Revision as of 08:01, 21 January 2019
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	== Structure and Function ==		== Structure and Function ==

	Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding occurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is <scene name='74/745945/Glycosylation/1'>glycosylated at Asp297</scene> at both CH<sub>2</sub> domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at <scene name='74/745945/Pro228/1'>amino acid 228</scene>, which prevents Fab-arm exchange and stabilizes the molecule <ref name="log">DOI:10.1080/17425255.2016.1216976</ref>.		'''Pembrolizumab''', trade name '''Keytruda''', is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding occurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is <scene name='74/745945/Glycosylation/1'>glycosylated at Asp297</scene> at both CH<sub>2</sub> domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at <scene name='74/745945/Pro228/1'>amino acid 228</scene>, which prevents Fab-arm exchange and stabilizes the molecule <ref name="log">DOI:10.1080/17425255.2016.1216976</ref>.

	== Mechanism ==		== Mechanism ==

Michal Harel at 08:00, 21 January 2019

2019-01-21T08:00:55Z

← Older revision		Revision as of 08:00, 21 January 2019
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	==Pembrolizumab antibody against programmed cell death-1 receptor==		==Pembrolizumab antibody against programmed cell death-1 receptor==
	<StructureSection load='5dk3' size='350' side='right' caption='Full-Length Crystal Structure of Pembrolizumab (PDB code [[5dk3]])'>		<StructureSection load='5dk3' size='350' side='right' caption='Full-Length Crystal Structure of glycosylated Pembrolizumab complex with sulfate (PDB code [[5dk3]])'>
	== Structure and Function ==		== Structure and Function ==

Emily Bradshaw.: Melanie Kusakavtich was also a major contributor to this project.

2018-01-15T21:44:44Z

Melanie Kusakavtich was also a major contributor to this project.

← Older revision		Revision as of 21:44, 15 January 2018
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	== References ==		== References ==
	<references/>		<references/>
			Melanie Kusakavitch also contributed equally to this project, but the computer program is not showing her name due to malfunction.

Emily Bradshaw. at 03:08, 6 December 2016

2016-12-06T03:08:20Z

← Older revision		Revision as of 03:08, 6 December 2016
Line 3:		Line 3:
	== Structure and Function ==		== Structure and Function ==

	Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding ~~orccurs~~, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is <scene name='74/745945/Glycosylation/1'>glycosylated at Asp297</scene> at both CH<sub>2</sub> domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at <scene name='74/745945/Pro228/1'>amino acid 228</scene>, which prevents Fab-arm exchange and stabilizes the molecule <ref name="log">DOI:10.1080/17425255.2016.1216976</ref>.		Pembrolizumab, trade name Keytruda, is an immunoglobulin G4 (IgG4)-kappa humanized monoclonal antibody against the programmed cell death-1 (PD-1) receptor. It contains an Fv fragment (PemFv) that is the variable region of the molecule where binding occurs, as well as a Fab fragment (PemFab) that constitutes the entire molecule. Pembrolizumab is a very compact molecule with an asymmetrical Y-shape. The short compact hinge region inflicts constraints on the molecule that creates the abnormal crystallizable heavy chain/tail region (Fc domain) compared to other immunoglobulin G (IgG) proteins. The heavy chain is <scene name='74/745945/Glycosylation/1'>glycosylated at Asp297</scene> at both CH<sub>2</sub> domains on each chain and one of them is distinctively rotated 120° compared to other similar structures, making the glycan chain more solvent accessible. IgG4s have a unique function where they form dynamic bispecific antibodies by exchanging half-molecules (one heavy chain/light chain pair) among themselves, called Fab-arm exchange. This makes the molecule particularly unstable and unpredictable as a treatment, but is conquered by introducing the serine-to-proline mutation at <scene name='74/745945/Pro228/1'>amino acid 228</scene>, which prevents Fab-arm exchange and stabilizes the molecule <ref name="log">DOI:10.1080/17425255.2016.1216976</ref>.

	== Mechanism ==		== Mechanism ==

Lauren Riley at 02:53, 6 December 2016

2016-12-06T02:53:49Z

← Older revision		Revision as of 02:53, 6 December 2016
Line 6:		Line 6:

	== Mechanism ==		== Mechanism ==
	~~[http://www.nature.com/articles/srep35297/figures/2 A schematic diagram of polar interactions]~~
	===Pembrolizumab/PD-1 Interaction===		===Pembrolizumab/PD-1 Interaction===
	In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 <ref name="horita">DOI:10.1038/srep35297</ref>.		In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced [http://www.nature.com/articles/srep35297/figures/2 interaction between Pembrolizumab and PD-1] gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 <ref name="horita">DOI:10.1038/srep35297</ref>.
	===PemFv/PD-1 Interaction===		===PemFv/PD-1 Interaction===
	The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1<sub>ECD</sub> contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1<sub>ECD</sub> residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. <scene name='74/745945/Chain_b_amino_acids/1'>Thr30, Tyr33, Ser54, Tyr101, Arg102</scene> on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface <ref name="horita" />.		The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1<sub>ECD</sub> contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1<sub>ECD</sub> residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. <scene name='74/745945/Chain_b_amino_acids/1'>Thr30, Tyr33, Ser54, Tyr101, Arg102</scene> on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface <ref name="horita" />.

Lauren Riley at 02:43, 6 December 2016

2016-12-06T02:43:33Z

← Older revision		Revision as of 02:43, 6 December 2016
Line 6:		Line 6:

	== Mechanism ==		== Mechanism ==
			[http://www.nature.com/articles/srep35297/figures/2 A schematic diagram of polar interactions]
	===Pembrolizumab/PD-1 Interaction===		===Pembrolizumab/PD-1 Interaction===
	In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 <ref name="horita">DOI:10.1038/srep35297</ref>.		In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 <ref name="horita">DOI:10.1038/srep35297</ref>.

Emily Bradshaw. at 02:19, 6 December 2016

2016-12-06T02:19:37Z

← Older revision		Revision as of 02:19, 6 December 2016
Line 9:		Line 9:
	In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 <ref name="horita">DOI:10.1038/srep35297</ref>.		In order for Pembrolizumab to block PD-1, Pembrolizumab forms a large, flat paratope (antigen-binding site) that can sustain PD-1’s large epitope (where antibody attaches on antigen). The induced interaction between Pembrolizumab and PD-1 gives rise to a surface conformational change on PD-1. The new structure of PD-1 becomes a very shallow, “crescent”-like shape, in contrast to the flat conformation when bound to PD-L1 <ref name="horita">DOI:10.1038/srep35297</ref>.
	===PemFv/PD-1 Interaction===		===PemFv/PD-1 Interaction===
	The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1<sub>ECD</sub> contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1<sub>ECD</sub> residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. <scene name='74/745945/Chain_b_amino_acids/1'>Thr30, Tyr33, Ser54, ~~Tys101~~, Arg102</scene> on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface <ref name="horita" />.		The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1<sub>ECD</sub> contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1<sub>ECD</sub> residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. <scene name='74/745945/Chain_b_amino_acids/1'>Thr30, Tyr33, Ser54, Tyr101, Arg102</scene> on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface <ref name="horita" />.
	===PD-L1/PD-1 Interaction===		===PD-L1/PD-1 Interaction===
	The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1<sub>ECD</sub> residues that are involved in forming the complex with the N-terminus of PD-L1<sub>ECD</sub> (PD-L1<sub>ECD-N</sub>). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1<sub>ECD</sub>/PD-L1<sub>ECD-N</sub> interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1<sub>ECD</sub> is in complex with PD-L1<sub>ECD-N</sub>. The PD-1<sub>ECD</sub> residues involved in this include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1<sub>ECD-N</sub> form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1<sub>ECD</sub> <ref name="horita" />.		The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1<sub>ECD</sub> residues that are involved in forming the complex with the N-terminus of PD-L1<sub>ECD</sub> (PD-L1<sub>ECD-N</sub>). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1<sub>ECD</sub>/PD-L1<sub>ECD-N</sub> interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1<sub>ECD</sub> is in complex with PD-L1<sub>ECD-N</sub>. The PD-1<sub>ECD</sub> residues involved in this include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1<sub>ECD-N</sub> form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1<sub>ECD</sub> <ref name="horita" />.

Emily Bradshaw. at 02:18, 6 December 2016

2016-12-06T02:18:50Z

← Older revision		Revision as of 02:18, 6 December 2016
Line 11:		Line 11:
	The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1<sub>ECD</sub> contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1<sub>ECD</sub> residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. <scene name='74/745945/Chain_b_amino_acids/1'>Thr30, Tyr33, Ser54, Tys101, Arg102</scene> on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface <ref name="horita" />.		The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1<sub>ECD</sub> contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1<sub>ECD</sub> residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. <scene name='74/745945/Chain_b_amino_acids/1'>Thr30, Tyr33, Ser54, Tys101, Arg102</scene> on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface <ref name="horita" />.
	===PD-L1/PD-1 Interaction===		===PD-L1/PD-1 Interaction===
	The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1<sub>ECD</sub> residues that are involved in forming the complex with the N-terminus of PD-L1<sub>ECD</sub> (PD-L1<sub>ECD-N</sub>). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1<sub>ECD</sub>/PD-L1<sub>ECD-N</sub> interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1<sub>ECD</sub> is in complex with PD-L1<sub>ECD-N</sub>. The PD-1<sub>ECD</sub> residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1<sub>ECD-N</sub> form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1<sub>ECD</sub> <ref name="horita" />.		The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1<sub>ECD</sub> residues that are involved in forming the complex with the N-terminus of PD-L1<sub>ECD</sub> (PD-L1<sub>ECD-N</sub>). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1<sub>ECD</sub>/PD-L1<sub>ECD-N</sub> interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1<sub>ECD</sub> is in complex with PD-L1<sub>ECD-N</sub>. The PD-1<sub>ECD</sub> residues involved in this include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1<sub>ECD-N</sub> form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1<sub>ECD</sub> <ref name="horita" />.
	== Disease in Humans ==		== Disease in Humans ==

Emily Bradshaw. at 02:14, 6 December 2016

2016-12-06T02:14:34Z

← Older revision		Revision as of 02:14, 6 December 2016
Line 11:		Line 11:
	The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1<sub>ECD</sub> contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1<sub>ECD</sub> residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. <scene name='74/745945/Chain_b_amino_acids/1'>Thr30, Tyr33, Ser54, Tys101, Arg102</scene> on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface <ref name="horita" />.		The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1<sub>ECD</sub> contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1<sub>ECD</sub> residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. <scene name='74/745945/Chain_b_amino_acids/1'>Thr30, Tyr33, Ser54, Tys101, Arg102</scene> on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface <ref name="horita" />.
	===PD-L1/PD-1 Interaction===		===PD-L1/PD-1 Interaction===
	The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1<sub>ECD</sub> residues that are involved in forming the complex with the N-terminus of PD-L1<sub>ECD</sub> (PD-L1<sub>ECD-N</sub>). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1<sub>ECD</sub>/PD-1<sub>ECD-N</sub> interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1<sub>ECD</sub> is in complex with PD-L1<sub>ECD-N</sub>. The PD-1<sub>ECD</sub> residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1<sub>ECD-N</sub> form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1<sub>ECD</sub> <ref name="horita" />.		The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1<sub>ECD</sub> residues that are involved in forming the complex with the N-terminus of PD-L1<sub>ECD</sub> (PD-L1<sub>ECD-N</sub>). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1<sub>ECD</sub>/PD-L1<sub>ECD-N</sub> interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1<sub>ECD</sub> is in complex with PD-L1<sub>ECD-N</sub>. The PD-1<sub>ECD</sub> residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1<sub>ECD-N</sub> form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1<sub>ECD</sub> <ref name="horita" />.
	== Disease in Humans ==		== Disease in Humans ==

Gina Rossi. at 02:07, 6 December 2016

2016-12-06T02:07:42Z

← Older revision		Revision as of 02:07, 6 December 2016
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	The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1<sub>ECD</sub> contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1<sub>ECD</sub> residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. <scene name='74/745945/Chain_b_amino_acids/1'>Thr30, Tyr33, Ser54, Tys101, Arg102</scene> on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface <ref name="horita" />.		The Fv fragment of Pembrolizumab can form a complex with the extracellular domain (ECD) of PD-1. Both PemFv and PD-1<sub>ECD</sub> contain interchain disulfide bonds. PemFv interacts predominantly in the major groove of PD-1, which is formed on one surface by the CC’FG antiparallel β−sheet and the BC, C’D, and FG loops. There are 15 direct hydrogen bonds between the residues, 15 water-mediated hydrogen bonds, 2 salt bridges, and many hydrophobic interactions. There are a total of 26 PD-1<sub>ECD</sub> residues involved in the interaction with PemFv, with residues in loop C’D (Pro84 to Gly90) and strand C’ (Gln75 to Lys 78) playing a major role. These key components of PD-1 mainly form interactions through salt bridges and hydrogen bonds with complementary determining regions, the variable domains, of Pembrolizumab. <scene name='74/745945/Chain_b_amino_acids/1'>Thr30, Tyr33, Ser54, Tys101, Arg102</scene> on Chain B of Pembrolizumab form bonds with Asp77, Gln75, Lys78, Thr76, Tyr68, and Asn66 of PD-1. It is believed that the sugar chains of PD-1 have no physical contact with Pembrolizumab due to the N-linked glycosylated residues (Asn49, Asn58, Asn74, and Asn116) being located away from the interface <ref name="horita" />.
	===PD-L1/PD-1 Interaction===		===PD-L1/PD-1 Interaction===
	The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1<sub>ECD</sub> residues that are involved in forming the complex with the N-terminus of PD-L1<sub>ECD</sub> (PD-1<sub>ECD-N</sub>). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1<sub>ECD</sub>/PD-1<sub>ECD-N</sub> interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1<sub>ECD</sub> is in complex with PD-L1<sub>ECD-N</sub>. The PD-1<sub>ECD</sub> residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1<sub>ECD-N</sub> form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1<sub>ECD</sub> <ref name="horita" />.		The complex formed when protein-derived ligand, PD-L1, interacts with the inhibitory receptor, PD-1, suppresses immune responses against autoantigens and helps in peripheral immune tolerance. However, when tumors over express PD-L1, the interaction with PD-1 inhibits T-lymphocyte proliferation, release of cytokines, and cytotoxicity, exhausting tumor-specific T-cells. There are a total of 12 PD-1<sub>ECD</sub> residues that are involved in forming the complex with the N-terminus of PD-L1<sub>ECD</sub> (PD-L1<sub>ECD-N</sub>). Nine hydrogen bonds, 3 water-mediated hydrogen bonds, 2 salt bridges, and numerous hydrophobic interactions make up the PD-1<sub>ECD</sub>/PD-1<sub>ECD-N</sub> interaction. The CC’FG sheet within both proteins is the main interaction point. A hydrophobic surface patch is formed when the PD-1<sub>ECD</sub> is in complex with PD-L1<sub>ECD-N</sub>. The PD-1<sub>ECD</sub> residues involved include Val64, Tyr68, Ile126, Leu128, Ala132 and Ile134. Numerous [http://www.nature.com/articles/srep35297/figures/1 Hydrophilic amino acids] that encircle PD-L1<sub>ECD-N</sub> form salt bridges and hydrogen bonds with Asn66, Tyr68, Gln75, Thr76, Asp77, Lys78, Ala132 and Glu136 of PD-1<sub>ECD</sub> <ref name="horita" />.
	== Disease in Humans ==		== Disease in Humans ==