Protein folding dynamics via quantification of kinematic energy landscape.
Identifieur interne : 002274 ( PubMed/Corpus ); précédent : 002273; suivant : 002275Protein folding dynamics via quantification of kinematic energy landscape.
Auteurs : Sëma Kachalo ; Hsiao-Mei Lu ; Jie LiangSource :
- Physical review letters [ 0031-9007 ] ; 2006.
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Abstract
We study folding dynamics of proteinlike sequences on a square lattice using a physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of occupancy of all 802 075 conformations of 16 mers over 7 orders of time span. We find that (i) folding rates of these proteinlike sequences of the same length can differ by 4 orders of magnitude, (ii) folding rates of sequences of the same conformation can differ by a factor of 190, and (iii) parameters of the native structures, designability, and thermodynamic properties are weak predictors of the folding rates; rather, a basin analysis of the kinematic energy landscape defined by the moves can provide an excellent account of the observed folding rates.
DOI: 10.1103/PhysRevLett.96.058106
PubMed: 16487000
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By analytically solving the master equation, we follow the time-dependent probabilities of occupancy of all 802 075 conformations of 16 mers over 7 orders of time span. We find that (i) folding rates of these proteinlike sequences of the same length can differ by 4 orders of magnitude, (ii) folding rates of sequences of the same conformation can differ by a factor of 190, and (iii) parameters of the native structures, designability, and thermodynamic properties are weak predictors of the folding rates; rather, a basin analysis of the kinematic energy landscape defined by the moves can provide an excellent account of the observed folding rates.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16487000</PMID><DateCompleted><Year>2006</Year><Month>05</Month><Day>02</Day></DateCompleted><DateRevised><Year>2013</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0031-9007</ISSN><JournalIssue CitedMedium="Print"><Volume>96</Volume><Issue>5</Issue><PubDate><Year>2006</Year><Month>Feb</Month><Day>10</Day></PubDate></JournalIssue><Title>Physical review letters</Title><ISOAbbreviation>Phys. Rev. Lett.</ISOAbbreviation></Journal><ArticleTitle>Protein folding dynamics via quantification of kinematic energy landscape.</ArticleTitle><Pagination><MedlinePgn>058106</MedlinePgn></Pagination><Abstract><AbstractText>We study folding dynamics of proteinlike sequences on a square lattice using a physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of occupancy of all 802 075 conformations of 16 mers over 7 orders of time span. We find that (i) folding rates of these proteinlike sequences of the same length can differ by 4 orders of magnitude, (ii) folding rates of sequences of the same conformation can differ by a factor of 190, and (iii) parameters of the native structures, designability, and thermodynamic properties are weak predictors of the folding rates; rather, a basin analysis of the kinematic energy landscape defined by the moves can provide an excellent account of the observed folding rates.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kachalo</LastName><ForeName>Sëma</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Bioengineering, MC-063, University of Illinois at Chicago, Chicago, Illinois 60305, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Hsiao-Mei</ForeName><Initials>HM</Initials></Author><Author ValidYN="Y"><LastName>Liang</LastName><ForeName>Jie</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>GM68958</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>02</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Phys Rev Lett</MedlineTA><NlmUniqueID>0401141</NlmUniqueID><ISSNLinking>0031-9007</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001696" MajorTopicYN="N">Biomechanical Phenomena</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008956" MajorTopicYN="Y">Models, Chemical</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017510" MajorTopicYN="Y">Protein Folding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013816" MajorTopicYN="N">Thermodynamics</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2005</Year><Month>08</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>2</Month><Day>21</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>5</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>2</Month><Day>21</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16487000</ArticleId><ArticleId IdType="doi">10.1103/PhysRevLett.96.058106</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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