Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase
Identifieur interne : 001C00 ( Ncbi/Merge ); précédent : 001B99; suivant : 001C01Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase
Auteurs : Olivier Delalande ; Sophie Sacquin-Mora ; Marc BaadenSource :
- Biophysical Journal [ 0006-3495 ] ; 2011.
Abstract
We investigate the conformational dynamics and mechanical properties of guanylate kinase (GK) using a multiscale approach combining high-resolution atomistic molecular dynamics and low-resolution Brownian dynamics simulations. The GK enzyme is subject to large conformational changes, leading from an open to a closed form, which are further influenced by the presence of nucleotides. As suggested by recent work on simple coarse-grained models of
Url:
DOI: 10.1016/j.bpj.2011.07.048
PubMed: 21943425
PubMed Central: 3177050
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase</title><author><name sortKey="Delalande, Olivier" sort="Delalande, Olivier" uniqKey="Delalande O" first="Olivier" last="Delalande">Olivier Delalande</name></author><author><name sortKey="Sacquin Mora, Sophie" sort="Sacquin Mora, Sophie" uniqKey="Sacquin Mora S" first="Sophie" last="Sacquin-Mora">Sophie Sacquin-Mora</name></author><author><name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21943425</idno><idno type="pmc">3177050</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177050</idno><idno type="RBID">PMC:3177050</idno><idno type="doi">10.1016/j.bpj.2011.07.048</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">001306</idno><idno type="wicri:Area/Pmc/Curation">001306</idno><idno type="wicri:Area/Pmc/Checkpoint">001B57</idno><idno type="wicri:Area/Ncbi/Merge">001C00</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase</title><author><name sortKey="Delalande, Olivier" sort="Delalande, Olivier" uniqKey="Delalande O" first="Olivier" last="Delalande">Olivier Delalande</name></author><author><name sortKey="Sacquin Mora, Sophie" sort="Sacquin Mora, Sophie" uniqKey="Sacquin Mora S" first="Sophie" last="Sacquin-Mora">Sophie Sacquin-Mora</name></author><author><name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name></author></analytic><series><title level="j">Biophysical Journal</title><idno type="ISSN">0006-3495</idno><idno type="eISSN">1542-0086</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>We investigate the conformational dynamics and mechanical properties of guanylate kinase (GK) using a multiscale approach combining high-resolution atomistic molecular dynamics and low-resolution Brownian dynamics simulations. The GK enzyme is subject to large conformational changes, leading from an open to a closed form, which are further influenced by the presence of nucleotides. As suggested by recent work on simple coarse-grained models of <italic>apo</italic>-GK, we primarily focus on GK's closure mechanism with the aim to establish a detailed picture of the hierarchy and chronology of structural events essential for the enzymatic reaction. We have investigated open-versus-closed, <italic>apo</italic>-versus-<italic>holo</italic>, and substrate-versus-product-loaded forms of the GK enzyme. Bound ligands significantly modulate the mechanical and dynamical properties of GK and rigidity profiles of open and closed states hint at functionally important differences. Our data emphasizes the role of magnesium, highlights a water channel permitting active site hydration, and reveals a structural lock that stabilizes the closed form of the enzyme.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Biophys J</journal-id><journal-title-group><journal-title>Biophysical Journal</journal-title></journal-title-group><issn pub-type="ppub">0006-3495</issn><issn pub-type="epub">1542-0086</issn><publisher><publisher-name>The Biophysical Society</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21943425</article-id><article-id pub-id-type="pmc">3177050</article-id><article-id pub-id-type="publisher-id">BPJ3075</article-id><article-id pub-id-type="doi">10.1016/j.bpj.2011.07.048</article-id><article-categories><subj-group subj-group-type="heading"><subject>Protein</subject></subj-group></article-categories><title-group><article-title>Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Delalande</surname><given-names>Olivier</given-names></name></contrib><contrib contrib-type="author"><name><surname>Sacquin-Mora</surname><given-names>Sophie</given-names></name></contrib><contrib contrib-type="author"><name><surname>Baaden</surname><given-names>Marc</given-names></name><email>baaden@smplinux.de</email><xref rid="cor1" ref-type="corresp">∗</xref></contrib></contrib-group><aff>Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique, Centre National de la Recherche Scientifique, UPR9080, Université Paris Diderot, Sorbonne Paris Cité, Paris, France</aff><author-notes><corresp id="cor1"><label>∗</label>Corresponding author <email>baaden@smplinux.de</email></corresp></author-notes><pub-date pub-type="ppub"><day>21</day><month>9</month><year>2011</year></pub-date><volume>101</volume><issue>6</issue><fpage>1440</fpage><lpage>1449</lpage><history><date date-type="received"><day>10</day><month>3</month><year>2011</year></date><date date-type="accepted"><day>28</day><month>7</month><year>2011</year></date></history><permissions><copyright-statement>© 2011 by the Biophysical Society.</copyright-statement><copyright-year>2011</copyright-year><copyright-holder>Biophysical Society</copyright-holder></permissions><abstract><p>We investigate the conformational dynamics and mechanical properties of guanylate kinase (GK) using a multiscale approach combining high-resolution atomistic molecular dynamics and low-resolution Brownian dynamics simulations. The GK enzyme is subject to large conformational changes, leading from an open to a closed form, which are further influenced by the presence of nucleotides. As suggested by recent work on simple coarse-grained models of <italic>apo</italic>-GK, we primarily focus on GK's closure mechanism with the aim to establish a detailed picture of the hierarchy and chronology of structural events essential for the enzymatic reaction. We have investigated open-versus-closed, <italic>apo</italic>-versus-<italic>holo</italic>, and substrate-versus-product-loaded forms of the GK enzyme. Bound ligands significantly modulate the mechanical and dynamical properties of GK and rigidity profiles of open and closed states hint at functionally important differences. Our data emphasizes the role of magnesium, highlights a water channel permitting active site hydration, and reveals a structural lock that stabilizes the closed form of the enzyme.</p></abstract></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name><name sortKey="Delalande, Olivier" sort="Delalande, Olivier" uniqKey="Delalande O" first="Olivier" last="Delalande">Olivier Delalande</name><name sortKey="Sacquin Mora, Sophie" sort="Sacquin Mora, Sophie" uniqKey="Sacquin Mora S" first="Sophie" last="Sacquin-Mora">Sophie Sacquin-Mora</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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