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== '''FKBP12-rapamycin binding domain of mTOR''' == | == '''FKBP12-rapamycin binding domain of mTOR''' == | ||
''' FRB domain''' ( | ''' 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''' == | == '''Introduction''' == | ||
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<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' /> | <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]) | As a member of '''the phosphatidylinositol 3-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 a multi domain protein which is involved in the regulation of cell growth and an important target of survival | ||
signals in cancer cells. | signals in cancer cells. | ||
The sequence of the 2549 residues is '''highly conserved''' across eukaryotes (40-60% | The sequence of the 2549 residues is '''highly conserved''' across eukaryotes (40-60% sequence identity). | ||
The protein consists of several functional | The protein consists of several functional domains:<br />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 | 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). | (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 ]] | [[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 ]] | ||
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== '''Structure of FRB''' == | == '''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 surface structure reveals two main interaction sites, a shallow <scene name='56/568023/Hydrophobic_pocket/ | <Structure load='2npu' size='275' frame='true' align='left' caption='Surface structure of FRB' scene='56/568023/Surface/1' /> | ||
which is responsible for | |||
The FRB domain is made up of a disordered N-terminal domain and a four <scene name='56/568023/Four_helix_bundle/4'>helices bundle</scene> joined by short loops (α-helix1: W2023-G2040, α-helix2: V2044-R2060, α-helix3: L2065-L2090, α-helix4: V2094-S2112). <ref> PMID: 17684489 </ref> | |||
Helix 3 contains a <scene name='56/568023/Helix_3_bend_residues/3'>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/2'>hydrophobic patch</scene> made up of helix 1 and helix 4 | |||
which is responsible for binding rapamycin and a <scene name='56/568023/Deep_cleft_helix_2_and_3/10'>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 | charged and hydrophobic residues and is expected to function as a binding site for small molecules to regulate | ||
mTOR activity. | mTOR activity. | ||
The binding sites for '''phosphatidic acid''' and '''rapamycin''' show significant <scene name='56/568023/ | The binding sites for '''phosphatidic acid''' and '''rapamycin''' show significant <scene name='56/568023/Aminoacids_binding_site/3'>overlapping</scene> (L2031, F2039, Y2105, H2106, R2109) suggesting that rapamycin inhibits kinase activity of mTOR by blocking access of the activator phosphatidic acid.<br /> | ||
Active residues are exposed to water and interact with the ligand. Passive residues are also in contact with water and are situated proximate to the active ones.<ref> Roterman-Konieczna, Irena. Identification of ligand binding site and protein-protein interaction area. Vol. 8. Springer, 2013. </ref> <br /> | |||
There are <scene name='56/568023/Aminoacids_binding_site2/1'>five amino acids</scene> 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. 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.<br /> | |||
<scene name='56/568023/Passive_residues_binding/2'>Three amino acids</scene> at the FRB domain contribute passively to the binding of the activator (L2031, S2035, W2101). | |||
{{clear}} | |||
[[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.]] | |||
Other molecules like the novel class inhibitor '''HTS-1''' (4-[6-{[(1S,2R)-2-(benzyloxy)cyclopentyl] | Other molecules like the novel class inhibitor '''HTS-1''' (4-[6-{[(1S,2R)-2-(benzyloxy)cyclopentyl]acetyl}-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. | 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/ | There are <scene name='56/568023/Hts-1_binding_residues/2'>ten</scene> residues at the FRB domain that are predominantly involved in HTS-1 binding | ||
binding. <ref> | (active residues: E2032, S2035, Y2038, F2039, T2098, W2101, Y2105, F2108, passive residues: H2028, L2031). <br /> | ||
At least <scene name='56/568023/Ovelap_pa_and_hts-1/4'>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> | |||
{{clear}} | {{clear}} | ||
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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]).<br /> | 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]).<br /> | ||
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 | While mTORC1 is bound and inhibited by rapamycin-FKBP12 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. <br /> | ||
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><br /> | 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><br /> | ||
The FRB domain is responsible for the ligand-mediated regulation of mTOR activity. Though the inhibitor rapamycin has been successfully | The FRB domain is responsible for the ligand-mediated regulation of mTOR activity. Though the inhibitor rapamycin has been successfully applied as an immunosuppressant it cannot be used to treat cancer since rapamycin has no effect on mTORC2. <br /> | ||
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> | 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''' == | ||