Thermodynamics of folding and association of lattice-model proteins.
Identifieur interne : 002332 ( PubMed/Corpus ); précédent : 002331; suivant : 002333Thermodynamics of folding and association of lattice-model proteins.
Auteurs : Troy Cellmer ; Dusan Bratko ; John M. Prausnitz ; Harvey BlanchSource :
- The Journal of chemical physics [ 0021-9606 ] ; 2005.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Proteins.
- chemical , ultrastructure : Proteins.
- Binding Sites, Computer Simulation, Kinetics, Models, Chemical, Models, Molecular, Phase Transition, Protein Binding, Protein Conformation, Protein Folding, Thermodynamics.
Abstract
Closely related to the "protein folding problem" is the issue of protein misfolding and aggregation. Protein aggregation has been associated with the pathologies of nearly 20 human diseases and presents serious difficulties during the manufacture of pharmaceutical proteins. Computational studies of multiprotein systems have recently emerged as a powerful complement to experimental efforts aimed at understanding the mechanisms of protein aggregation. We describe the thermodynamics of systems containing two lattice-model 64-mers. A parallel tempering algorithm abates problems associated with glassy systems and the weighted histogram analysis method improves statistical quality. The presence of a second chain has a substantial effect on single-chain conformational preferences. The melting temperature is substantially reduced, and the increase in the population of unfolded states is correlated with an increase in interactions between chains. The transition from two native chains to a non-native aggregate is entropically favorable. Non-native aggregates receive approximately 25% of their stabilizing energy from intraprotein contacts not found in the lowest-energy structure. Contact maps show that for non-native dimers, nearly 50% of the most probable interprotein contacts involve pairs of residues that form native contacts, suggesting that a domain-swapping mechanism is involved in self-association.
DOI: 10.1063/1.1888545
PubMed: 15910070
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Prausnitz</name></author><author><name sortKey="Blanch, Harvey" sort="Blanch, Harvey" uniqKey="Blanch H" first="Harvey" last="Blanch">Harvey Blanch</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="RBID">pubmed:15910070</idno><idno type="pmid">15910070</idno><idno type="doi">10.1063/1.1888545</idno><idno type="wicri:Area/PubMed/Corpus">002332</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002332</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Thermodynamics of folding and association of lattice-model proteins.</title><author><name sortKey="Cellmer, Troy" sort="Cellmer, Troy" uniqKey="Cellmer T" first="Troy" last="Cellmer">Troy Cellmer</name><affiliation><nlm:affiliation>Department of Chemical Engineering, University of California, Berkeley, 94720, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Bratko, Dusan" sort="Bratko, Dusan" uniqKey="Bratko D" first="Dusan" last="Bratko">Dusan Bratko</name></author><author><name sortKey="Prausnitz, John M" sort="Prausnitz, John M" uniqKey="Prausnitz J" first="John M" last="Prausnitz">John M. Prausnitz</name></author><author><name sortKey="Blanch, Harvey" sort="Blanch, Harvey" uniqKey="Blanch H" first="Harvey" last="Blanch">Harvey Blanch</name></author></analytic><series><title level="j">The Journal of chemical physics</title><idno type="ISSN">0021-9606</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Computer Simulation</term><term>Kinetics</term><term>Models, Chemical</term><term>Models, Molecular</term><term>Phase Transition</term><term>Protein Binding</term><term>Protein Conformation</term><term>Protein Folding</term><term>Proteins (chemistry)</term><term>Proteins (ultrastructure)</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="ultrastructure" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Computer Simulation</term><term>Kinetics</term><term>Models, Chemical</term><term>Models, Molecular</term><term>Phase Transition</term><term>Protein Binding</term><term>Protein Conformation</term><term>Protein Folding</term><term>Thermodynamics</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Closely related to the "protein folding problem" is the issue of protein misfolding and aggregation. Protein aggregation has been associated with the pathologies of nearly 20 human diseases and presents serious difficulties during the manufacture of pharmaceutical proteins. Computational studies of multiprotein systems have recently emerged as a powerful complement to experimental efforts aimed at understanding the mechanisms of protein aggregation. We describe the thermodynamics of systems containing two lattice-model 64-mers. A parallel tempering algorithm abates problems associated with glassy systems and the weighted histogram analysis method improves statistical quality. The presence of a second chain has a substantial effect on single-chain conformational preferences. The melting temperature is substantially reduced, and the increase in the population of unfolded states is correlated with an increase in interactions between chains. The transition from two native chains to a non-native aggregate is entropically favorable. Non-native aggregates receive approximately 25% of their stabilizing energy from intraprotein contacts not found in the lowest-energy structure. Contact maps show that for non-native dimers, nearly 50% of the most probable interprotein contacts involve pairs of residues that form native contacts, suggesting that a domain-swapping mechanism is involved in self-association.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15910070</PMID><DateCompleted><Year>2007</Year><Month>01</Month><Day>30</Day></DateCompleted><DateRevised><Year>2005</Year><Month>05</Month><Day>24</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0021-9606</ISSN><JournalIssue CitedMedium="Print"><Volume>122</Volume><Issue>17</Issue><PubDate><Year>2005</Year><Month>May</Month><Day>01</Day></PubDate></JournalIssue><Title>The Journal of chemical physics</Title><ISOAbbreviation>J Chem Phys</ISOAbbreviation></Journal><ArticleTitle>Thermodynamics of folding and association of lattice-model proteins.</ArticleTitle><Pagination><MedlinePgn>174908</MedlinePgn></Pagination><Abstract><AbstractText>Closely related to the "protein folding problem" is the issue of protein misfolding and aggregation. Protein aggregation has been associated with the pathologies of nearly 20 human diseases and presents serious difficulties during the manufacture of pharmaceutical proteins. Computational studies of multiprotein systems have recently emerged as a powerful complement to experimental efforts aimed at understanding the mechanisms of protein aggregation. We describe the thermodynamics of systems containing two lattice-model 64-mers. A parallel tempering algorithm abates problems associated with glassy systems and the weighted histogram analysis method improves statistical quality. The presence of a second chain has a substantial effect on single-chain conformational preferences. The melting temperature is substantially reduced, and the increase in the population of unfolded states is correlated with an increase in interactions between chains. The transition from two native chains to a non-native aggregate is entropically favorable. Non-native aggregates receive approximately 25% of their stabilizing energy from intraprotein contacts not found in the lowest-energy structure. Contact maps show that for non-native dimers, nearly 50% of the most probable interprotein contacts involve pairs of residues that form native contacts, suggesting that a domain-swapping mechanism is involved in self-association.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cellmer</LastName><ForeName>Troy</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Chemical Engineering, University of California, Berkeley, 94720, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bratko</LastName><ForeName>Dusan</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Prausnitz</LastName><ForeName>John M</ForeName><Initials>JM</Initials></Author><Author ValidYN="Y"><LastName>Blanch</LastName><ForeName>Harvey</ForeName><Initials>H</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Chem Phys</MedlineTA><NlmUniqueID>0375360</NlmUniqueID><ISSNLinking>0021-9606</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011506">Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007700" MajorTopicYN="N">Kinetics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008956" MajorTopicYN="Y">Models, Chemical</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="Y">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D044367" MajorTopicYN="N">Phase Transition</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011485" MajorTopicYN="N">Protein Binding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011487" MajorTopicYN="N">Protein Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017510" MajorTopicYN="Y">Protein Folding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011506" MajorTopicYN="N">Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000648" MajorTopicYN="Y">ultrastructure</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013816" MajorTopicYN="N">Thermodynamics</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2005</Year><Month>5</Month><Day>25</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2007</Year><Month>1</Month><Day>31</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2005</Year><Month>5</Month><Day>25</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">15910070</ArticleId><ArticleId IdType="doi">10.1063/1.1888545</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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