Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding.
Identifieur interne : 000141 ( PubMed/Checkpoint ); précédent : 000140; suivant : 000142Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding.
Auteurs : Hongchun Li [République populaire de Chine] ; Pemra Doruker [États-Unis] ; Guang Hu [République populaire de Chine] ; Ivet Bahar [États-Unis]Source :
- Biophysical journal [ 1542-0086 ] ; 2020.
Abstract
Toroidal proteins serve as molecular machines and play crucial roles in biological processes such as DNA replication and RNA transcription. Despite progress in the structural characterization of several toroidal proteins, we still lack a mechanistic understanding of the significance of their architecture, oligomerization states, and intermolecular interactions in defining their biological function. In this work, we analyze the collective dynamics of toroidal proteins with different oligomerization states, namely, dimeric and trimeric DNA sliding clamps, nucleocapsid proteins (4-, 5-, and 6-mers) and Trp RNA-binding attenuation proteins (11- and 12-mers). We observe common global modes, among which cooperative rolling stands out as a mechanism enabling DNA processivity, and clamshell motions as those underlying the opening/closure of the sliding clamps. Alterations in global dynamics due to complexation with DNA or the clamp loader are shown to assist in enhancing motions to enable robust function. The analysis provides new insights into the differentiation and enhancement of functional motions upon intersubunit and intermolecular interactions.
DOI: 10.1016/j.bpj.2020.01.046
PubMed: 32130874
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Electronic address: huguang@suda.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou</wicri:regionArea><wicri:noRegion>Suzhou</wicri:noRegion></affiliation></author><author><name sortKey="Bahar, Ivet" sort="Bahar, Ivet" uniqKey="Bahar I" first="Ivet" last="Bahar">Ivet Bahar</name><affiliation wicri:level="2"><nlm:affiliation>Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania. Electronic address: bahar@pitt.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Pennsylvanie</region></placeName><wicri:cityArea>Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh</wicri:cityArea></affiliation></author></analytic><series><title level="j">Biophysical journal</title><idno type="eISSN">1542-0086</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Toroidal proteins serve as molecular machines and play crucial roles in biological processes such as DNA replication and RNA transcription. Despite progress in the structural characterization of several toroidal proteins, we still lack a mechanistic understanding of the significance of their architecture, oligomerization states, and intermolecular interactions in defining their biological function. In this work, we analyze the collective dynamics of toroidal proteins with different oligomerization states, namely, dimeric and trimeric DNA sliding clamps, nucleocapsid proteins (4-, 5-, and 6-mers) and Trp RNA-binding attenuation proteins (11- and 12-mers). We observe common global modes, among which cooperative rolling stands out as a mechanism enabling DNA processivity, and clamshell motions as those underlying the opening/closure of the sliding clamps. Alterations in global dynamics due to complexation with DNA or the clamp loader are shown to assist in enhancing motions to enable robust function. The analysis provides new insights into the differentiation and enhancement of functional motions upon intersubunit and intermolecular interactions.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">32130874</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>11</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1542-0086</ISSN><JournalIssue CitedMedium="Internet"><Volume>118</Volume><Issue>7</Issue><PubDate><Year>2020</Year><Month>Apr</Month><Day>07</Day></PubDate></JournalIssue><Title>Biophysical journal</Title><ISOAbbreviation>Biophys. J.</ISOAbbreviation></Journal><ArticleTitle>Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding.</ArticleTitle><Pagination><MedlinePgn>1782-1794</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0006-3495(20)30130-2</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.bpj.2020.01.046</ELocationID><Abstract><AbstractText>Toroidal proteins serve as molecular machines and play crucial roles in biological processes such as DNA replication and RNA transcription. Despite progress in the structural characterization of several toroidal proteins, we still lack a mechanistic understanding of the significance of their architecture, oligomerization states, and intermolecular interactions in defining their biological function. In this work, we analyze the collective dynamics of toroidal proteins with different oligomerization states, namely, dimeric and trimeric DNA sliding clamps, nucleocapsid proteins (4-, 5-, and 6-mers) and Trp RNA-binding attenuation proteins (11- and 12-mers). We observe common global modes, among which cooperative rolling stands out as a mechanism enabling DNA processivity, and clamshell motions as those underlying the opening/closure of the sliding clamps. Alterations in global dynamics due to complexation with DNA or the clamp loader are shown to assist in enhancing motions to enable robust function. The analysis provides new insights into the differentiation and enhancement of functional motions upon intersubunit and intermolecular interactions.</AbstractText><CopyrightInformation>Copyright © 2020. Published by Elsevier Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Hongchun</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Research Center for Computer-Aided Drug Discovery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Doruker</LastName><ForeName>Pemra</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Guang</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China. 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Hongchun" uniqKey="Li H" first="Hongchun" last="Li">Hongchun Li</name></region><name sortKey="Hu, Guang" sort="Hu, Guang" uniqKey="Hu G" first="Guang" last="Hu">Guang Hu</name></country><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Doruker, Pemra" sort="Doruker, Pemra" uniqKey="Doruker P" first="Pemra" last="Doruker">Pemra Doruker</name></region><name sortKey="Bahar, Ivet" sort="Bahar, Ivet" uniqKey="Bahar I" first="Ivet" last="Bahar">Ivet Bahar</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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