1k5r: Difference between revisions
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[[Image: | ==YAP65 WW domain S24-Amino-Ethylsulfanyl-Acetic Acid mutant== | ||
<StructureSection load='1k5r' size='340' side='right' caption='[[1k5r]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1k5r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K5R FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ESD:(2-AMINO-ETHYLSULFANYL)-ACETIC+ACID'>ESD</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr> | |||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jmq|1jmq]], [[1eom|1eom]], [[1eg3|1eg3]], [[1eg4|1eg4]], [[1i5h|1i5h]]</td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k5r RCSB], [http://www.ebi.ac.uk/pdbsum/1k5r PDBsum]</span></td></tr> | |||
<table> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/1k5r_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Chemical synthesis allows the incorporation of nonnatural amino acids into proteins that may provide previously untried probes of their folding pathway and thermodynamic stability. We have used a flexible thioether linker as a loop mimetic in the human yes kinase-associated protein (YAP 65) WW domain, a three-stranded, 44-residue, beta-sheet protein. This linkage avoids problems of incorporating sequences that constrain loops to the extent that they significantly change the nature of the denatured state with concomitant effects on the folding kinetics. An NMR solution structure shows that the thioether linker had little effect on the global fold of the domain, although the loop is apparently more dynamic. The thioether variants are destabilized by up to 1.4 kcal/mol (1 cal = 4.18 J). Preliminary Phi-value analysis showed that the first loop is highly structured in the folding transition state, and the second loop is essentially unstructured. These data are consistent with results from simulated unfolding and detailed protein-engineering studies of structurally homologous WW domains. Previously, Phi-value analysis was limited to studying side-chain interactions. The linkers used here extend the protein engineering method directly to secondary-structure interactions. | |||
Using flexible loop mimetics to extend phi-value analysis to secondary structure interactions.,Ferguson N, Pires JR, Toepert F, Johnson CM, Pan YP, Volkmer-Engert R, Schneider-Mergener J, Daggett V, Oschkinat H, Fersht A Proc Natl Acad Sci U S A. 2001 Nov 6;98(23):13008-13. Epub 2001 Oct 30. PMID:11687614<ref>PMID:11687614</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
< | |||
[[Category: Daggett, V.]] | [[Category: Daggett, V.]] | ||
[[Category: Ferguson, N.]] | [[Category: Ferguson, N.]] | ||
Revision as of 14:19, 28 September 2014
YAP65 WW domain S24-Amino-Ethylsulfanyl-Acetic Acid mutantYAP65 WW domain S24-Amino-Ethylsulfanyl-Acetic Acid mutant
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedChemical synthesis allows the incorporation of nonnatural amino acids into proteins that may provide previously untried probes of their folding pathway and thermodynamic stability. We have used a flexible thioether linker as a loop mimetic in the human yes kinase-associated protein (YAP 65) WW domain, a three-stranded, 44-residue, beta-sheet protein. This linkage avoids problems of incorporating sequences that constrain loops to the extent that they significantly change the nature of the denatured state with concomitant effects on the folding kinetics. An NMR solution structure shows that the thioether linker had little effect on the global fold of the domain, although the loop is apparently more dynamic. The thioether variants are destabilized by up to 1.4 kcal/mol (1 cal = 4.18 J). Preliminary Phi-value analysis showed that the first loop is highly structured in the folding transition state, and the second loop is essentially unstructured. These data are consistent with results from simulated unfolding and detailed protein-engineering studies of structurally homologous WW domains. Previously, Phi-value analysis was limited to studying side-chain interactions. The linkers used here extend the protein engineering method directly to secondary-structure interactions. Using flexible loop mimetics to extend phi-value analysis to secondary structure interactions.,Ferguson N, Pires JR, Toepert F, Johnson CM, Pan YP, Volkmer-Engert R, Schneider-Mergener J, Daggett V, Oschkinat H, Fersht A Proc Natl Acad Sci U S A. 2001 Nov 6;98(23):13008-13. Epub 2001 Oct 30. PMID:11687614[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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