Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles
Identifieur interne : 000902 ( Main/Merge ); précédent : 000901; suivant : 000903Evidence 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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Daniel</name></author><author><name sortKey="Dunn, Rv" uniqKey="Dunn R">RV Dunn</name></author><author><name sortKey="Finney, Jl" uniqKey="Finney J">JL Finney</name></author><author><name sortKey="Smith, Jc" uniqKey="Smith J">JC Smith</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Phillips, Gn" uniqKey="Phillips G">GN Phillips</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kondrashov, Da" uniqKey="Kondrashov D">DA Kondrashov</name></author><author><name sortKey="Van Wynsberghe, Aw" uniqKey="Van Wynsberghe A">AW Van Wynsberghe</name></author><author><name sortKey="Bannen, Rm" uniqKey="Bannen R">RM Bannen</name></author><author><name sortKey="Cui, Q" uniqKey="Cui Q">Q Cui</name></author><author><name sortKey="Phillips, Gn" uniqKey="Phillips G">GN Phillips</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meinhold, L" uniqKey="Meinhold L">L Meinhold</name></author><author><name 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