Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model
Identifieur interne : 001943 ( Ncbi/Curation ); précédent : 001942; suivant : 001944Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model
Auteurs : Avisek Das [États-Unis] ; Mert Gur [États-Unis] ; Mary Hongying Cheng [États-Unis] ; Sunhwan Jo [États-Unis] ; Ivet Bahar [États-Unis] ; Benoît Roux [États-Unis]Source :
- PLoS Computational Biology [ 1553-734X ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Adenylate Kinase, Amino Acid Transport System X-AG, Carrier Proteins, Leucine, Sarcoplasmic Reticulum Calcium-Transporting ATPases.
- enzymology : Sarcoplasmic Reticulum.
- Models, Molecular, Protein Conformation.
Abstract
Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called
Url:
DOI: 10.1371/journal.pcbi.1003521
PubMed: 24699246
PubMed Central: 3974643
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PMC:3974643Le document en format XML
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Model</title><author><name sortKey="Das, Avisek" sort="Das, Avisek" uniqKey="Das A" first="Avisek" last="Das">Avisek Das</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Gur, Mert" sort="Gur, Mert" uniqKey="Gur M" first="Mert" last="Gur">Mert Gur</name><affiliation wicri:level="4"><nlm:aff id="aff2"><addr-line>Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Cheng, Mary Hongying" sort="Cheng, Mary Hongying" uniqKey="Cheng M" first="Mary Hongying" last="Cheng">Mary Hongying Cheng</name><affiliation wicri:level="4"><nlm:aff id="aff2"><addr-line>Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Jo, Sunhwan" sort="Jo, Sunhwan" uniqKey="Jo S" first="Sunhwan" last="Jo">Sunhwan Jo</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Bahar, Ivet" sort="Bahar, Ivet" uniqKey="Bahar I" first="Ivet" last="Bahar">Ivet Bahar</name><affiliation wicri:level="4"><nlm:aff id="aff2"><addr-line>Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Roux, Benoit" sort="Roux, Benoit" uniqKey="Roux B" first="Benoît" last="Roux">Benoît Roux</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author></analytic><series><title level="j">PLoS Computational Biology</title><idno type="ISSN">1553-734X</idno><idno type="eISSN">1553-7358</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adenylate Kinase (chemistry)</term><term>Amino Acid Transport System X-AG (chemistry)</term><term>Carrier Proteins (chemistry)</term><term>Leucine (chemistry)</term><term>Models, Molecular</term><term>Protein Conformation</term><term>Sarcoplasmic Reticulum (enzymology)</term><term>Sarcoplasmic Reticulum Calcium-Transporting ATPases (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Adenylate kinase ()</term><term>Conformation des protéines</term><term>Leucine ()</term><term>Modèles moléculaires</term><term>Protéines de transport ()</term><term>Réticulum sarcoplasmique (enzymologie)</term><term>Sarcoplasmic Reticulum Calcium-Transporting ATPases ()</term><term>Système X-AG de transport d'acides aminés ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Adenylate Kinase</term><term>Amino Acid Transport System X-AG</term><term>Carrier Proteins</term><term>Leucine</term><term>Sarcoplasmic Reticulum Calcium-Transporting ATPases</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Réticulum sarcoplasmique</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Sarcoplasmic Reticulum</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Models, Molecular</term><term>Protein Conformation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Adenylate kinase</term><term>Conformation des protéines</term><term>Leucine</term><term>Modèles moléculaires</term><term>Protéines de transport</term><term>Sarcoplasmic Reticulum Calcium-Transporting ATPases</term><term>Système X-AG de transport d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called <italic>ANMPathway</italic>, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that <italic>ANMPathway</italic> yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver <italic>ANMPathway</italic> results.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Henzler Wildman, Ka" uniqKey="Henzler Wildman K">KA Henzler-Wildman</name></author><author><name sortKey="Thai, V" uniqKey="Thai V">V Thai</name></author><author><name sortKey="Lei, M" uniqKey="Lei M">M Lei</name></author><author><name sortKey="Ott, M" uniqKey="Ott M">M Ott</name></author><author><name sortKey="Wolf Watz, M" uniqKey="Wolf Watz M">M Wolf-Watz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lei, M" uniqKey="Lei M">M Lei</name></author><author><name sortKey="Velos, J" uniqKey="Velos J">J Velos</name></author><author><name sortKey="Gardino, A" uniqKey="Gardino A">A Gardino</name></author><author><name sortKey="Kivenson, A" uniqKey="Kivenson A">A Kivenson</name></author><author><name sortKey="Karplus, M" uniqKey="Karplus M">M 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