3D-Lattice Monte Carlo simulations of model proteins. Size effects on folding thermodynamics and kinetics.
Identifieur interne : 002432 ( PubMed/Curation ); précédent : 002431; suivant : 0024333D-Lattice Monte Carlo simulations of model proteins. Size effects on folding thermodynamics and kinetics.
Auteurs : K. Leonhard [États-Unis] ; J M Prausnitz ; C J RadkeSource :
- Biophysical chemistry [ 0301-4622 ] ; 2003.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Proteins.
- chemical , metabolism : Proteins.
- Amino Acid Sequence, Kinetics, Molecular Sequence Data, Monte Carlo Method, Protein Folding, Temperature, Thermodynamics.
Abstract
Recently, we devised an energy scale to vary systematically amino-acid residue-solvent interactions for Monte Carlo simulations of lattice-model proteins in water. For 27-mer proteins, the folding behavior varies appreciably with the choice of interaction parameters. We now perform similar simulations with 64-mers to study the size dependence of the optimal energy parameter set for representing realistic behavior typical of many real proteins (i.e. fast folding and high cooperativity for single chains). We find that 64-mers are considerably more stable and more cooperative compared to 27-mers. The optimal interfacial-interaction-energy parameter set, however, is relatively size independent.
DOI: 10.1016/s0301-4622(03)00185-6
PubMed: 14516915
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Leonhard</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemical Engineering, University of California, Berkeley, CA 94720-1462, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical Engineering, University of California, Berkeley, CA 94720-1462</wicri:regionArea></affiliation></author><author><name sortKey="Prausnitz, J M" sort="Prausnitz, J M" uniqKey="Prausnitz J" first="J M" last="Prausnitz">J M Prausnitz</name></author><author><name sortKey="Radke, C J" sort="Radke, C J" uniqKey="Radke C" first="C J" last="Radke">C J Radke</name></author></analytic><series><title level="j">Biophysical chemistry</title><idno type="ISSN">0301-4622</idno><imprint><date when="2003" type="published">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Kinetics</term><term>Molecular Sequence Data</term><term>Monte Carlo Method</term><term>Protein Folding</term><term>Proteins (chemistry)</term><term>Proteins (metabolism)</term><term>Temperature</term><term>Thermodynamics</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cinétique</term><term>Données de séquences moléculaires</term><term>Méthode de Monte-Carlo</term><term>Pliage des protéines</term><term>Protéines ()</term><term>Protéines (métabolisme)</term><term>Séquence d'acides aminés</term><term>Température</term><term>Thermodynamique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Kinetics</term><term>Molecular Sequence Data</term><term>Monte Carlo Method</term><term>Protein Folding</term><term>Temperature</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cinétique</term><term>Données de séquences moléculaires</term><term>Méthode de Monte-Carlo</term><term>Pliage des protéines</term><term>Protéines</term><term>Séquence d'acides aminés</term><term>Température</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Recently, we devised an energy scale to vary systematically amino-acid residue-solvent interactions for Monte Carlo simulations of lattice-model proteins in water. For 27-mer proteins, the folding behavior varies appreciably with the choice of interaction parameters. We now perform similar simulations with 64-mers to study the size dependence of the optimal energy parameter set for representing realistic behavior typical of many real proteins (i.e. fast folding and high cooperativity for single chains). We find that 64-mers are considerably more stable and more cooperative compared to 27-mers. The optimal interfacial-interaction-energy parameter set, however, is relatively size independent.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">14516915</PMID><DateCompleted><Year>2004</Year><Month>08</Month><Day>18</Day></DateCompleted><DateRevised><Year>2019</Year><Month>09</Month><Day>01</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0301-4622</ISSN><JournalIssue CitedMedium="Print"><Volume>106</Volume><Issue>1</Issue><PubDate><Year>2003</Year><Month>Oct</Month><Day>01</Day></PubDate></JournalIssue><Title>Biophysical chemistry</Title><ISOAbbreviation>Biophys. Chem.</ISOAbbreviation></Journal><ArticleTitle>3D-Lattice Monte Carlo simulations of model proteins. 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