Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles
Identifieur interne : 000163 ( Ncbi/Merge ); précédent : 000162; suivant : 000164Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles
Auteurs : Jonathan E. Kohn [États-Unis] ; Pavel V. Afonine [États-Unis] ; Jory Z. Ruscio [États-Unis] ; Paul D. Adams [États-Unis] ; Teresa Head-Gordon [États-Unis]Source :
- PLoS Computational Biology [ 1553-734X ] ; 2010.
Abstract
It is widely recognized that representing a protein as a single static conformation is inadequate to describe the dynamics essential to the performance of its biological function. We contrast the amino acid displacements below and above the protein dynamical transition temperature, TD∼215K, of hen egg white lysozyme using X-ray crystallography ensembles that are analyzed by molecular dynamics simulations as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above TD, and they remain virtually identical to structural motions measured at 300K. Our results highlight the ability to observe functional structural variations across an ensemble of X-ray crystallographic data, and that residue fluctuations measured in MD simulations at room temperature are in quantitative agreement with the experimental observable.
Url:
DOI: 10.1371/journal.pcbi.1000911
PubMed: 20865158
PubMed Central: 2928775
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Kohn</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, University of California, Berkeley, Berkeley, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Afonine, Pavel V" sort="Afonine, Pavel V" uniqKey="Afonine P" first="Pavel V." last="Afonine">Pavel V. Afonine</name><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Ruscio, Jory Z" sort="Ruscio, Jory Z" uniqKey="Ruscio J" first="Jory Z." last="Ruscio">Jory Z. Ruscio</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, University of California, Berkeley, Berkeley, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Adams, Paul D" sort="Adams, Paul D" uniqKey="Adams P" first="Paul D." last="Adams">Paul D. Adams</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, University of California, Berkeley, Berkeley, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Head Gordon, Teresa" sort="Head Gordon, Teresa" uniqKey="Head Gordon T" first="Teresa" last="Head-Gordon">Teresa Head-Gordon</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, University of California, Berkeley, Berkeley, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California</wicri:regionArea><placeName><region type="state">Californie</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="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>It is widely recognized that representing a protein as a single static conformation is inadequate to describe the dynamics essential to the performance of its biological function. We contrast the amino acid displacements below and above the protein dynamical transition temperature, T<sub>D</sub>∼215K, of hen egg white lysozyme using X-ray crystallography ensembles that are analyzed by molecular dynamics simulations as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above T<sub>D</sub>, and they remain virtually identical to structural motions measured at 300K. Our results highlight the ability to observe functional structural variations across an ensemble of X-ray crystallographic data, and that residue fluctuations measured in MD simulations at room temperature are in quantitative agreement with the experimental observable.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Rasmussen, Bf" uniqKey="Rasmussen B">BF Rasmussen</name></author><author><name sortKey="Stock, Am" uniqKey="Stock A">AM Stock</name></author><author><name sortKey="Ringe, D" uniqKey="Ringe D">D Ringe</name></author><author><name sortKey="Petsko, Ga" uniqKey="Petsko G">GA Petsko</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bizzarri, Ar" uniqKey="Bizzarri A">AR Bizzarri</name></author><author><name sortKey="Cannistraro, S" uniqKey="Cannistraro S">S Cannistraro</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Karplus, M" uniqKey="Karplus M">M 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS Comput Biol</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">ploscomp</journal-id><journal-title-group><journal-title>PLoS Computational Biology</journal-title></journal-title-group><issn pub-type="ppub">1553-734X</issn><issn pub-type="epub">1553-7358</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">20865158</article-id><article-id pub-id-type="pmc">2928775</article-id><article-id pub-id-type="publisher-id">10-PLCB-RA-2054R2</article-id><article-id pub-id-type="doi">10.1371/journal.pcbi.1000911</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline"><subject>Biophysics/Experimental Biophysical Methods</subject><subject>Biophysics/Theory and Simulation</subject></subj-group></article-categories><title-group><article-title>Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles</article-title><alt-title alt-title-type="running-head">Protein Dynamics from X-Ray Crystallography</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Kohn</surname><given-names>Jonathan E.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Afonine</surname><given-names>Pavel V.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ruscio</surname><given-names>Jory Z.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Adams</surname><given-names>Paul D.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Head-Gordon</surname><given-names>Teresa</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Levitt</surname><given-names>Michael</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">Stanford University, United States of America</aff><author-notes><corresp id="cor1">* E-mail: <email>TLHead-Gordon@lbl.gov</email></corresp><fn fn-type="con"><p>Conceived and designed the experiments: THG. Performed the experiments: JEK PVA JZR. Analyzed the data: JEK PDA THG. Wrote the paper: THG.</p></fn></author-notes><pub-date pub-type="collection"><month>8</month><year>2010</year></pub-date><pmc-comment> Fake ppub added to accomodate plos workflow change from 03/2008 and 03/2009 </pmc-comment>
<pub-date pub-type="ppub"><month>8</month><year>2010</year></pub-date><pub-date pub-type="epub"><day>26</day><month>8</month><year>2010</year></pub-date><volume>6</volume><issue>8</issue><elocation-id>e1000911</elocation-id><history><date date-type="received"><day>11</day><month>4</month><year>2010</year></date><date date-type="accepted"><day>28</day><month>7</month><year>2010</year></date></history><permissions><copyright-statement>Kohn et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</copyright-statement></permissions><abstract><p>It is widely recognized that representing a protein as a single static conformation is inadequate to describe the dynamics essential to the performance of its biological function. We contrast the amino acid displacements below and above the protein dynamical transition temperature, T<sub>D</sub>∼215K, of hen egg white lysozyme using X-ray crystallography ensembles that are analyzed by molecular dynamics simulations as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above T<sub>D</sub>, and they remain virtually identical to structural motions measured at 300K. Our results highlight the ability to observe functional structural variations across an ensemble of X-ray crystallographic data, and that residue fluctuations measured in MD simulations at room temperature are in quantitative agreement with the experimental observable.</p></abstract><abstract abstract-type="summary"><title>Author Summary</title><p>There is a well-recognized gap between the dynamical motions of proteins required to execute function and the experimental techniques capable of capturing that motion at the atomic level. We show that much experimental detail of dynamical motion is already present in X-ray crystallographic data, which arises from being solved by different research groups using different methodologies under different crystallization conditions, which then capture an ensemble of structures whose variations can be quantified on a residue-by-residue level using local density correlations. We contrast the amino acid displacements below and above the protein dynamical transition temperature, T<sub>D</sub>∼215K, of hen egg white lysozyme by comparing the X-ray ensemble to MD ensembles as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above T<sub>D</sub> and they remain virtually identical to structural motions measured at 300K. It provides a novel analysis of large X-ray ensemble data that is useful for the broader structural biology community.</p></abstract><counts><page-count count="5"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Kohn, Jonathan E" sort="Kohn, Jonathan E" uniqKey="Kohn J" first="Jonathan E." last="Kohn">Jonathan E. Kohn</name></region><name sortKey="Adams, Paul D" sort="Adams, Paul D" uniqKey="Adams P" first="Paul D." last="Adams">Paul D. Adams</name><name sortKey="Adams, Paul D" sort="Adams, Paul D" uniqKey="Adams P" first="Paul D." last="Adams">Paul D. Adams</name><name sortKey="Afonine, Pavel V" sort="Afonine, Pavel V" uniqKey="Afonine P" first="Pavel V." last="Afonine">Pavel V. Afonine</name><name sortKey="Head Gordon, Teresa" sort="Head Gordon, Teresa" uniqKey="Head Gordon T" first="Teresa" last="Head-Gordon">Teresa Head-Gordon</name><name sortKey="Head Gordon, Teresa" sort="Head Gordon, Teresa" uniqKey="Head Gordon T" first="Teresa" last="Head-Gordon">Teresa Head-Gordon</name><name sortKey="Ruscio, Jory Z" sort="Ruscio, Jory Z" uniqKey="Ruscio J" first="Jory Z." last="Ruscio">Jory Z. Ruscio</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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