2014-01-05T20:50:08Z

Dimitri Feltrin:

{{Sandbox_Reserved_ESBS}}

== '''FKBP12-rapamycin binding domain of mTOR''' ==
''' FRB domain''' ('''[http://www.rcsb.org/pdb/explore/explore.do?structureId=2npu 2NPU]) of '''mTOR''' is responsible for the binding of the inhibitory cyclic macrolide [http://en.wikipedia.org/wiki/Sirolimus Rapamycin]

== '''Introduction''' ==

{{clear}}

<Structure load='2npu' size='250' frame='true' align='left' caption='Cartoon model of the FRB domain of mTOR: {{Template:ColorKey_N2CRainbow}}' scene='56/568023/2npu_cartoon_rainbow/4' />
As a member of '''the phosphatidylinositol kinase-related kinases''' ([http://en.wikipedia.org/wiki/Phosphatidylinositol_3-kinase-related_kinase PIKK]) the mammalian targert of rapamycin ([http://en.wikipedia.org/wiki/Mammalian_target_of_rapamycin mTOR])
is a multi domain protein which is involved in the regulation of cell growth and is an important target of survival
signals in cancer cells.

The sequence of the 2549 residues is '''highly conserved''' across eukaryotes (40-60% precent sequence identity).
The protein consists of several functional domains: At the N-terminus there are twelve [http://en.wikipedia.org/wiki/HEAT_repeat_domain HEAT] repeats followed by a
central [http://en.wikipedia.org/wiki/Focal_adhesion_targeting_region FAT] domain (residues 1513-1910), a '''FRB domain''' (residues 2015-2114) a [http://en.wikipedia.org/?title=Serine/threonine-specific_protein_kinase serine-threonine kinase] domain
(residues 2181-2484) and a C-terminal FATC domain (residues 2515-2549).

[[Image:The domain structure of mTOR.jpg|center|upright=3| thumb |Fig.1 Structure of mTOR http://dev.biologists.org/content/138/16/3343.full ]]

The FKBP12-rapamycin binding (FRB) domain mediates ligand-dependent regulation of the kinase domain by binding different molecules.
FRB binds the inhibitory cyclic macroloide '''rapamycin''' in complex with the small '''peptidyl-prolyl cis-trans isomerase [http://en.wikipedia.org/wiki/FKBP FKBP12]''' leading to a decreased activity of the kinase domain. Due to its inhibitory effect rapamycin has been a widely used tool for studying mTOR. FRB is also capable of binding '''the activator [http://en.wikipedia.org/wiki/Phosphatidic_acid phosphatidic acid]''' and small molecules, for example amino acids like '''[http://en.wikipedia.org/wiki/Leucine leucine]'''. <ref> Russell, R. C., Fang, C., & Guan, K. L. (2011). An emerging role for TOR signaling in mammalian tissue and stem cell physiology. Development, 138(16), 3343-3356. doi: http://dev.biologists.org/content/138/16/3343.full </ref>

{{clear}}

== '''Structure of FRB''' ==

[[Image:FRB Phosphatidic Acid.png|upright=1.25|right|thumb| Fig.2 A representative view of phosphatidic acid docked into its binding site on the FRB domain.]]

The FRB domain is made up of an <scene name='56/568023/N-terminal_domain_of_frb/2'>N-terminal</scene> disordered domain and a four α-helices bundle joined by short loops (<scene name='56/568023/Helix_1/1'>α1</scene>, <scene name='56/568023/Helix_2/1'>α2</scene>, <scene name='56/568023/Helix_3/1'>α3</scene>, <scene name='56/568023/Helix_4/1'>α4</scene>). <ref> PMID: 17684489 </ref>
Helix 3 contains a <scene name='56/568023/Helix_3_bend_residues/1'>bend</scene> of approximately 45° and its N-terminal half is largely disordered.

The surface structure reveals two main interaction sites, a shallow <scene name='56/568023/Hydrophobic_pocket/1'>hydrophobic patch</scene> made up of helix 1 and helix 4
which is responsible for the binding of rapamycin and a <scene name='56/568023/Deep_cleft_helix_2_and_3/1'>deep cleft</scene> between helix 2 and helix 3. This cleft contains
charged and hydrophobic residues and is expected to function as a binding site for small molecules to regulate
mTOR activity.

The binding sites for '''phosphatidic acid''' and '''rapamycin''' show significant <scene name='56/568023/Overlapping_residues/3'>overlapping</scene> (E2031, F2039, Y2105, H2106, R2109) suggesting that rapamycin inhibits kinase activity of mTOR by blocking access of the activator phosphatidic acid. There are five amino acids whose side chains are exposed to the solvent and who play an active role in phosphatidic acid binding (E2031, F2039, Y2105, H2106, R2109). Those are the residues that also take part in rapamycin binding. Three amino acids at the FRB domain contribute passively to the binding of the activator (L2031, S2035, W2101). The positive charged arginine residue '''R2109''' plays a key role in the binding of phosphatidic acid as it binds to the negetively charged phosphate group.

Other molecules like the novel class inhibitor '''HTS-1''' (4-[6-{[(1S,2R)-2-(benzyloxy)cyclopentyl]acety}-4-(2-thienyl)pyridin-2-yl]-4-oxobutanoic acid)
are also capable of inhibiting the kinase activity of mTOR by partially occupying the binding site for phosphatidic acid.
There are <scene name='56/568023/Hts-1_binding_residues/1'>ten</scene> residues at the FRB domain that are predominantly involved in HTS-1 binding (actively: E2032, S2035, Y2038, F2039, T2098, W2101, Y2105, F2108, passively: H2028, L2031). At least <scene name='56/568023/Ovelap_pa_and_hts-1/1'>six</scene> of those residues also take part in phosphatidic acid
binding (L2031, W2101, E2032, F2039, Y2105, S2035). <ref> DOI: 10.1007/s12154-008-0003-5
</ref>

[[Image:FRB HTS-1 Rapamycin.png|left|upright=2| thumb| Fig.3 A representative view of the mTOR inhibitor HTS-1 docked into its binding site on the FRB domain on the left. On the right, the location and conformation of rapamycin bound to the FRB domain in the ternary complex formed with FKBP12 is illustrated, with the domain shown in the same orientation as on the left.]]

{{clear}}

== '''Biological Significance''' ==

MTOR has been found to form two distinct complexes called '''mTOR complex 1''' ([http://en.wikipedia.org/wiki/MTORC1 mTORC1]) and '''mTOR complex 2''' ([http://en.wikipedia.org/wiki/MTORC2 mTORC2]). 
While mTORC1 is bound and inhibited by rapamycin mTORC2 is not affected by rapamycin presence. <ref> PMID: 20005306 </ref> Depending on the formed complex mTOR activity can provoke different cellular responses. MTORC1 for example leads to activation of translation and inhibition of autophagy. 

MTORC2 on the other hand regulates the assembly of cytoskeleton and activates the '''Protein Kinase B''' ([http://en.wikipedia.org/wiki/Protein_Kinase_B Akt]) which plays a central role in the phosphoinositide 3-kinase [http://en.wikipedia.org/wiki/PI3K/AKT/mTOR_pathway pathway] , which leads to cell survival and [http://en.wikipedia.org/wiki/S_phase S-phase] entry and is revealed to be overactive in many human cancers. <ref> PMID: 12040186 </ref> 

The FRB domain is responsible for the ligand-mediated regulation of mTOR activity. Though the inhibitor rapamycin has been successfully used as an immunosuppressant it cannot be used to treat cancer since rapamycin has no effect on mTORC2. 
Therefore scientists are interessted in discovering new binding sites for inhibitors like HTS-1 that inhibit mTORC2 and can help to fight cancer. <ref> PMID: 20384580 </ref>

== '''References''' ==
<references/>

== '''Contributors''' ==
Arthur Charbonné, Dimitri Feltrin

Sandbox Reserved 825

2014-01-05T20:39:03Z

Dimitri Feltrin:

{{Sandbox_Reserved_ESBS}}

== '''FKBP12-rapamycin binding domain of mTOR''' ==
''' FRB domain''' ('''[http://www.rcsb.org/pdb/explore/explore.do?structureId=2npu 2NPU]) of '''mTOR''' is responsible for the binding of the inhibitory cyclic macrolide [http://en.wikipedia.org/wiki/Sirolimus Rapamycin]

== '''Introduction''' ==

{{clear}}

<Structure load='2npu' size='250' frame='true' align='left' caption='Cartoon model of the FRB domain of mTOR: {{Template:ColorKey_N2CRainbow}}' scene='56/568023/2npu_cartoon_rainbow/4' />
As a member of '''the phosphatidylinositol kinase-related kinases''' ([http://en.wikipedia.org/wiki/Phosphatidylinositol_3-kinase-related_kinase PIKK]) the mammalian targert of rapamycin ([http://en.wikipedia.org/wiki/Mammalian_target_of_rapamycin mTOR])
is a multi domain protein which is involved in the regulation of cell growth and is an important target of survival
signals in cancer cells. (Veverka et al.)

The sequence of the 2549 residues is '''highly conserved''' across eukaryotes (40-60% precent sequence identity).
The protein consists of several functional domain. At the N-terminus there are 12 [http://en.wikipedia.org/wiki/HEAT_repeat_domain HEAT] repeats followed by a
central [http://en.wikipedia.org/wiki/Focal_adhesion_targeting_region FAT] domain (residues 1513-1910), a '''FRB domain''' (residues 2015-2114) a [http://en.wikipedia.org/?title=Serine/threonine-specific_protein_kinase serine-threonine kinase] domain
(residues 2181-2484) and a C-terminal FATC domain (residues 2515-2549).

[[Image:The domain structure of mTOR.jpg|center|upright=3| thumb |Fig.1 Structure of mTOR http://dev.biologists.org/content/138/16/3343.full ]]

The FKBP12-rapamycin binding (FRB) domain mediates ligand-dependent regulation of the kinase domain by binding different molecules.
FRB binds the inhibitory cyclic macroloide '''rapamycin''' in complex with the small '''peptidyl-prolyl cis-trans isomerase [http://en.wikipedia.org/wiki/FKBP FKBP12]''' leading to a decreased activity of the kinase domain. Due to its inhibitory effect rapamycin has been a widely used tool for studying mTOR. FRB is also capable of binding '''the activator [http://en.wikipedia.org/wiki/Phosphatidic_acid phosphatidic acid]''' and small molecules, for example amino acids like '''[http://en.wikipedia.org/wiki/Leucine leucine]'''. <ref> Russell, R. C., Fang, C., & Guan, K. L. (2011). An emerging role for TOR signaling in mammalian tissue and stem cell physiology. Development, 138(16), 3343-3356. doi: http://dev.biologists.org/content/138/16/3343.full </ref>

{{clear}}

== '''Structure of FRB''' ==

[[Image:FRB Phosphatidic Acid.png|upright=1.25|right|thumb| Fig.2 A representative view of phosphatidic acid docked into its binding site on the FRB domain.]]

The FRB domain is made up of an <scene name='56/568023/N-terminal_domain_of_frb/2'>N-terminal</scene> disordered domain and a four α-helices bundle joined by short loops (<scene name='56/568023/Helix_1/1'>α1</scene>, <scene name='56/568023/Helix_2/1'>α2</scene>, <scene name='56/568023/Helix_3/1'>α3</scene>, <scene name='56/568023/Helix_4/1'>α4</scene>). <ref> PMID: 17684489 </ref>
Helix 3 contains a <scene name='56/568023/Helix_3_bend_residues/1'>bend</scene> of approximately 45° and its N-terminal half is largely disordered.

The surface structure reveals two main interaction sites, a shallow <scene name='56/568023/Hydrophobic_pocket/1'>hydrophobic patch</scene> made up by helix 1 and helix 4
which is responsible for the binding of rapamycin and a <scene name='56/568023/Deep_cleft_helix_2_and_3/1'>deep cleft</scene> between helix 2 and helix 3. This cleft contains
charged and hydrophobic residues and is expected to function as a binding site for small molecules to regulate
mTOR activity.

The binding sites for '''phosphatidic acid''' and '''rapamycin''' show significant <scene name='56/568023/Overlapping_residues/3'>overlapping</scene> suggesting that rapamycin inhibits kinase activity of mTOR by blocking access of the activator phosphatidic acid. There are five amino acids whose side chains are exposed to the solvent and who play an active role in phosphatidic acid binding (E2031, F2039, Y2105, H2106, R2109). Those are the residues that also take part in rapamycin binding. Three amino acids at the FRB domain contribute passively to the binding of the activator (L2031, S2035, W2101). The positive charged arginine residue '''R2109''' plays a key role in the binding of phosphatidic acid as it binds to the negetively charged phosphate group.

Other molecules like the novel class inhibitor '''HTS-1''' (4-[6-{[(1S,2R)-2-(benzyloxy)cyclopentyl]acety}-4-(2-thienyl)pyridin-2-yl]-4-oxobutanoic acid)
are also capable of inhibiting the kinase activity of mTOR by partially occupying the binding site for phosphatidic acid.
There are <scene name='56/568023/Hts-1_binding_residues/1'>ten</scene> residues at the FRB domain that are predominantly involved in HTS-1 binding (actively: E2032, S2035, Y2038, F2039, T2098, W2101, Y2105, F2108, passively: H2028, L2031). At least <scene name='56/568023/Ovelap_pa_and_hts-1/1'>six</scene> of those residues also take part in phosphatidic acid
binding (L2031, W2101, E2032, F2039, Y2105, S2035). <ref> DOI: 10.1007/s12154-008-0003-5
</ref>

[[Image:FRB HTS-1 Rapamycin.png|left|upright=2| thumb| Fig.3 A representative view of the mTOR inhibitor HTS-1 docked into its binding site on the FRB domain on the left. On the right, the location and conformation of rapamycin bound to the FRB domain in the ternary complex formed with FKBP12 is illustrated, with the domain shown in the same orientation as on the left.]]

{{clear}}

== '''Biological Significance''' ==

MTOR has been found to form two distinct complexes called '''mTOR complex 1''' ([http://en.wikipedia.org/wiki/MTORC1 mTORC1]) and '''mTOR complex 2''' ([http://en.wikipedia.org/wiki/MTORC2 mTORC2]). 
While mTORC1 is bound and inhibited by rapamycin mTORC2 is not affected by rapamycin presence. <ref> PMID: 20005306 </ref> Depending on the formed complex mTOR activity can provoke different cellular responses like activation of translation, inhibition of autophagy (mTORC1). 

MTORC2 on the other hand regulates the assembly of cytoskeleton and activates the '''Protein Kinase B''' ([http://en.wikipedia.org/wiki/Protein_Kinase_B Akt]) which plays a central role in the phosphoinositide 3-kinase [http://en.wikipedia.org/wiki/PI3K/AKT/mTOR_pathway pathway] , which leads to cell survival and [http://en.wikipedia.org/wiki/S_phase S-phase] entry and is revealed to be overactive in many human cancers. <ref> PMID: 12040186 </ref> 

The FRB domain is responsible for the ligand-mediated regulation of mTOR activity. Though the inhibitor rapamycin has been successfully used as an immunosuppressant it cannot be used to treat cancer since rapamycin has no effect on mTORC2. 
Therefore scientists are interessted in discovering new binding sites for inhibitors like HTS-1 that inhibit mTORC2 and can help to fight cancer. <ref> PMID: 20384580 </ref>

== '''References''' ==
<references/>

== '''Contributors''' ==
Arthur Charbonné, Dimitri Feltrin