Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations
Identifieur interne : 000141 ( Main/Exploration ); précédent : 000140; suivant : 000142Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations
Auteurs : Federica Chiappori [Italie] ; Ivan Merelli [Italie] ; Giorgio Colombo [Italie] ; Luciano Milanesi [Italie] ; Giulia Morra [Italie]Source :
- PLoS Computational Biology [ 1553-734X ] ; 2012.
Abstract
Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD) modulate substrate recognition at the Substrate Binding Domain (SBD). Herein, a comparative analysis of an allosteric (Hsp70-DnaK) and a non-allosteric structural homolog (Hsp110-Sse1) of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.
Url:
DOI: 10.1371/journal.pcbi.1002844
PubMed: 23300424
PubMed Central: 3531320
Affiliations:
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Consiglio Nazionale delle Ricerche (ICRM-CNR), Milano, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Chimica del Riconoscimento Molecolare - Consiglio Nazionale delle Ricerche (ICRM-CNR), Milano</wicri:regionArea><wicri:noRegion>Milano</wicri:noRegion></affiliation></author><author><name sortKey="Milanesi, Luciano" sort="Milanesi, Luciano" uniqKey="Milanesi L" first="Luciano" last="Milanesi">Luciano Milanesi</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Istituto di Tecnologie Biomediche – Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate (Mi), Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Tecnologie Biomediche – Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate (Mi)</wicri:regionArea><wicri:noRegion>Segrate (Mi)</wicri:noRegion></affiliation></author><author><name sortKey="Morra, Giulia" sort="Morra, Giulia" uniqKey="Morra G" first="Giulia" last="Morra">Giulia Morra</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Istituto di Chimica del Riconoscimento Molecolare - Consiglio Nazionale delle Ricerche (ICRM-CNR), Milano, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Chimica del Riconoscimento Molecolare - Consiglio Nazionale delle Ricerche (ICRM-CNR), Milano</wicri:regionArea><wicri:noRegion>Milano</wicri:noRegion></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="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD) modulate substrate recognition at the Substrate Binding Domain (SBD). Herein, a comparative analysis of an allosteric (Hsp70-DnaK) and a non-allosteric structural homolog (Hsp110-Sse1) of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Young, Jc" uniqKey="Young J">JC Young</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mayer, Mp" uniqKey="Mayer M">MP Mayer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Luders, J" uniqKey="Luders J">J Lüders</name></author><author><name sortKey="Demand, J" uniqKey="Demand J">J Demand</name></author><author><name sortKey="Hohfeld, J" uniqKey="Hohfeld J">J Höhfeld</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mayer, Mp" uniqKey="Mayer M">MP Mayer</name></author><author><name 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Fraaije</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Essman, U" uniqKey="Essman U">U Essman</name></author><author><name sortKey="Perera, L" uniqKey="Perera L">L Perera</name></author><author><name sortKey="Berkowitz, Ml" uniqKey="Berkowitz M">ML Berkowitz</name></author><author><name sortKey="Darden, T" uniqKey="Darden T">T Darden</name></author><author><name sortKey="Lee, H" uniqKey="Lee H">H Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daura, X" uniqKey="Daura X">X Daura</name></author><author><name sortKey="Gademann, K" uniqKey="Gademann K">K Gademann</name></author><author><name sortKey="Jaun, B" uniqKey="Jaun B">B Jaun</name></author><author><name sortKey="Seebach, D" uniqKey="Seebach D">D Seebach</name></author><author><name sortKey="Van Gunsteren, Vf" uniqKey="Van Gunsteren V">VF van Gunsteren</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pontiggia, F" uniqKey="Pontiggia F">F Pontiggia</name></author><author><name sortKey="Colombo, G" uniqKey="Colombo G">G Colombo</name></author><author><name sortKey="Micheletti, C" uniqKey="Micheletti C">C Micheletti</name></author><author><name sortKey="Orland, H" uniqKey="Orland H">H Orland</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Amadei, A" uniqKey="Amadei A">A Amadei</name></author><author><name sortKey="Linssen, Ab" uniqKey="Linssen A">AB Linssen</name></author><author><name sortKey="Berendsen, Hj" uniqKey="Berendsen H">HJ Berendsen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pontiggia, F" uniqKey="Pontiggia F">F Pontiggia</name></author><author><name sortKey="Zen, A" uniqKey="Zen A">A Zen</name></author><author><name sortKey="Micheletti, C" uniqKey="Micheletti C">C Micheletti</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Italie</li></country></list><tree><country name="Italie"><noRegion><name sortKey="Chiappori, Federica" sort="Chiappori, Federica" uniqKey="Chiappori F" first="Federica" last="Chiappori">Federica Chiappori</name></noRegion><name sortKey="Colombo, Giorgio" sort="Colombo, Giorgio" uniqKey="Colombo G" first="Giorgio" last="Colombo">Giorgio Colombo</name><name sortKey="Merelli, Ivan" sort="Merelli, Ivan" uniqKey="Merelli I" first="Ivan" last="Merelli">Ivan Merelli</name><name sortKey="Milanesi, Luciano" sort="Milanesi, Luciano" uniqKey="Milanesi L" first="Luciano" last="Milanesi">Luciano Milanesi</name><name sortKey="Morra, Giulia" sort="Morra, Giulia" uniqKey="Morra G" first="Giulia" last="Morra">Giulia Morra</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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