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1kat

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(New page: 200px<br /> <applet load="1kat" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kat" /> '''Solution Structure of a Phage-Derived Pepti...)
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[[Image:1kat.gif|left|200px]]<br />
 
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<applet load="1kat" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kat" />
 
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'''Solution Structure of a Phage-Derived Peptide Antagonist in Complex with Vascular Endothelial Growth Factor'''<br />
 
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==Overview==
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==Solution Structure of a Phage-Derived Peptide Antagonist in Complex with Vascular Endothelial Growth Factor==
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Vascular endothelial growth factor (VEGF) is a potent endothelial, cell-specific mediator of angiogenesis and vasculogenesis. VEGF is, involved pathologically in cancer, proliferative retinopathy and, rheumatoid arthritis, and as such represents an important therapeutic, target. Three classes of disulfide-constrained peptides that antagonize, binding of the VEGF dimer to its receptors, KDR and Flt-1, were identified, previously using phage display methods. NMR studies of a representative, peptide from the most potent class of these peptide antagonists, v107, (GGNECDAIRMWEWECFERL), were undertaken to characterize its interactions, with VEGF. v107 has no defined structure free in solution, but binding to, VEGF induces folding of the peptide. The solution structure of the VEGF, receptor-binding domain-v107 complex was determined using 3940 (1970 per, VEGF monomer) internuclear distance and 476 (238 per VEGF monomer), dihedral angle restraints derived from NMR data obtained using samples, containing either (13)C/(15)N-labeled protein plus excess unlabeled, peptide or (13)C/(15)N-labeled peptide plus excess unlabeled protein., Residual dipolar coupling restraints supplemented the structure, determination of the complex and were found to increase significantly both, the global precision of VEGF in the complex and the agreement with, available crystal structures of VEGF. The calculated ensemble of, structures is of high precision and is in excellent agreement with the, experimental restraints. v107 has a turn-helix conformation with, hydrophobic residues partitioned to one face of the peptide and polar or, charged residues at the other face. Contacts between two v107 peptides and, the VEGF dimer are mediated by primarily hydrophobic side-chain, interactions. The v107-binding site on VEGF overlaps partially with the, binding site of KDR and is similar to that for domain 2 of Flt-1. The, structure of the VEGF-v107 complex provides new insight into how binding, to VEGF can be achieved that may be useful for the design of small, molecule antagonists.
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<StructureSection load='1kat' size='340' side='right'caption='[[1kat]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1kat]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KAT FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kat OCA], [https://pdbe.org/1kat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kat RCSB], [https://www.ebi.ac.uk/pdbsum/1kat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kat ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/VEGFA_HUMAN VEGFA_HUMAN] Defects in VEGFA are a cause of susceptibility to microvascular complications of diabetes type 1 (MVCD1) [MIM:[https://omim.org/entry/603933 603933]. These are pathological conditions that develop in numerous tissues and organs as a consequence of diabetes mellitus. They include diabetic retinopathy, diabetic nephropathy leading to end-stage renal disease, and diabetic neuropathy. Diabetic retinopathy remains the major cause of new-onset blindness among diabetic adults. It is characterized by vascular permeability and increased tissue ischemia and angiogenesis.
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== Function ==
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[https://www.uniprot.org/uniprot/VEGFA_HUMAN VEGFA_HUMAN] Growth factor active in angiogenesis, vasculogenesis and endothelial cell growth. Induces endothelial cell proliferation, promotes cell migration, inhibits apoptosis and induces permeabilization of blood vessels. Binds to the FLT1/VEGFR1 and KDR/VEGFR2 receptors, heparan sulfate and heparin. NRP1/Neuropilin-1 binds isoforms VEGF-165 and VEGF-145. Isoform VEGF165B binds to KDR but does not activate downstream signaling pathways, does not activate angiogenesis and inhibits tumor growth.<ref>PMID:11427521</ref> <ref>PMID:15520188</ref> <ref>PMID:16489009</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ka/1kat_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kat ConSurf].
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<div style="clear:both"></div>
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==Disease==
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==See Also==
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Known disease associated with this structure: Diabetic retinopathy, NIDDM-related, susceptibility to OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=192240 192240]]
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*[[VEGF 3D Structures|VEGF 3D Structures]]
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== References ==
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==About this Structure==
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<references/>
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1KAT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KAT OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Solution structure of a phage-derived peptide antagonist in complex with vascular endothelial growth factor., Pan B, Li B, Russell SJ, Tom JY, Cochran AG, Fairbrother WJ, J Mol Biol. 2002 Feb 22;316(3):769-87. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11866530 11866530]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Cochran, A.G.]]
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[[Category: Cochran AG]]
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[[Category: Fairbrother, W.J.]]
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[[Category: Fairbrother WJ]]
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[[Category: Li, B.]]
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[[Category: Li B]]
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[[Category: Pan, B.]]
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[[Category: Pan B]]
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[[Category: Russell, S.J.]]
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[[Category: Russell SJ]]
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[[Category: Tom, J.Y.K.]]
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[[Category: Tom JYK]]
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[[Category: cystine knot]]
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[[Category: homodimer]]
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[[Category: protein-peptide complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 17:49:17 2007''
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Current revision

Solution Structure of a Phage-Derived Peptide Antagonist in Complex with Vascular Endothelial Growth Factor

PDB ID 1kat

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