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==STAPHYLOCOCCAL PROTEIN A, B-DOMAIN, Y15W MUTANT, NMR, 25 STRUCTURES== | |||
<StructureSection load='1ss1' size='340' side='right'caption='[[1ss1]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1ss1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SS1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SS1 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ss1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ss1 OCA], [https://pdbe.org/1ss1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ss1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ss1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ss1 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
''' | [https://www.uniprot.org/uniprot/SPA_STAAU SPA_STAAU] | ||
== 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/ss/1ss1_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/main_output.php?pdb_ID=1ss1 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We have assessed the published predictions of the pathway of folding of the B domain of protein A, the pathway most studied by computer simulation. We analyzed the transition state for folding of the three-helix bundle protein, by using experimental Phi values on some 70 suitable mutants. Surprisingly, the third helix, which has the most stable alpha-helical structure as a peptide fragment, is poorly formed in the transition state, especially at its C terminus. The protein folds around a nearly fully formed central helix, which is stabilized by extensive hydrophobic side chain interactions. The turn connecting the poorly structured first helix to the central helix is unstructured, but the turn connecting the central helix to the third is in the process of being formed as the N-terminal region of the third helix begins to coalesce. The transition state is inconsistent with a classical framework mechanism and is closer to nucleation-condensation. None of the published atomistic simulations are fully consistent with the experimental picture although many capture important features. There is a continuing need for combining simulation with experiment to describe folding pathways, and of continued testing to improve predictive methods. | We have assessed the published predictions of the pathway of folding of the B domain of protein A, the pathway most studied by computer simulation. We analyzed the transition state for folding of the three-helix bundle protein, by using experimental Phi values on some 70 suitable mutants. Surprisingly, the third helix, which has the most stable alpha-helical structure as a peptide fragment, is poorly formed in the transition state, especially at its C terminus. The protein folds around a nearly fully formed central helix, which is stabilized by extensive hydrophobic side chain interactions. The turn connecting the poorly structured first helix to the central helix is unstructured, but the turn connecting the central helix to the third is in the process of being formed as the N-terminal region of the third helix begins to coalesce. The transition state is inconsistent with a classical framework mechanism and is closer to nucleation-condensation. None of the published atomistic simulations are fully consistent with the experimental picture although many capture important features. There is a continuing need for combining simulation with experiment to describe folding pathways, and of continued testing to improve predictive methods. | ||
Testing protein-folding simulations by experiment: B domain of protein A.,Sato S, Religa TL, Daggett V, Fersht AR Proc Natl Acad Sci U S A. 2004 May 4;101(18):6952-6. Epub 2004 Apr 6. PMID:15069202<ref>PMID:15069202</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 1ss1" style="background-color:#fffaf0;"></div> | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Staphylococcus aureus]] | [[Category: Staphylococcus aureus]] | ||
[[Category: Daggett | [[Category: Daggett V]] | ||
[[Category: Fersht | [[Category: Fersht AR]] | ||
[[Category: Religa | [[Category: Religa TL]] | ||
[[Category: Sato | [[Category: Sato S]] | ||
Latest revision as of 12:09, 22 May 2024
STAPHYLOCOCCAL PROTEIN A, B-DOMAIN, Y15W MUTANT, NMR, 25 STRUCTURESSTAPHYLOCOCCAL PROTEIN A, B-DOMAIN, Y15W MUTANT, NMR, 25 STRUCTURES
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedWe have assessed the published predictions of the pathway of folding of the B domain of protein A, the pathway most studied by computer simulation. We analyzed the transition state for folding of the three-helix bundle protein, by using experimental Phi values on some 70 suitable mutants. Surprisingly, the third helix, which has the most stable alpha-helical structure as a peptide fragment, is poorly formed in the transition state, especially at its C terminus. The protein folds around a nearly fully formed central helix, which is stabilized by extensive hydrophobic side chain interactions. The turn connecting the poorly structured first helix to the central helix is unstructured, but the turn connecting the central helix to the third is in the process of being formed as the N-terminal region of the third helix begins to coalesce. The transition state is inconsistent with a classical framework mechanism and is closer to nucleation-condensation. None of the published atomistic simulations are fully consistent with the experimental picture although many capture important features. There is a continuing need for combining simulation with experiment to describe folding pathways, and of continued testing to improve predictive methods. Testing protein-folding simulations by experiment: B domain of protein A.,Sato S, Religa TL, Daggett V, Fersht AR Proc Natl Acad Sci U S A. 2004 May 4;101(18):6952-6. Epub 2004 Apr 6. PMID:15069202[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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