Folding helical proteins in explicit solvent using dihedral-biased tempering
Identifieur interne : 000400 ( Pmc/Corpus ); précédent : 000399; suivant : 000401Folding helical proteins in explicit solvent using dihedral-biased tempering
Auteurs : Cheng Zhang ; Jianpeng MaSource :
- Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 2012.
Abstract
Using a single-trajectory-based tempering method with a high-temperature dihedral bias, we repeatedly folded four helical proteins [
Url:
DOI: 10.1073/pnas.1112143109
PubMed: 22573819
PubMed Central: 3361456
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Folding helical proteins in explicit solvent using dihedral-biased tempering</title><author><name sortKey="Zhang, Cheng" sort="Zhang, Cheng" uniqKey="Zhang C" first="Cheng" last="Zhang">Cheng Zhang</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Applied Physics Program and Department of Bioengineering, Rice University, Houston, TX 77005</nlm:aff></affiliation></author><author><name sortKey="Ma, Jianpeng" sort="Ma, Jianpeng" uniqKey="Ma J" first="Jianpeng" last="Ma">Jianpeng Ma</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Applied Physics Program and Department of Bioengineering, Rice University, Houston, TX 77005</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22573819</idno><idno type="pmc">3361456</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361456</idno><idno type="RBID">PMC:3361456</idno><idno type="doi">10.1073/pnas.1112143109</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000400</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Folding helical proteins in explicit solvent using dihedral-biased tempering</title><author><name sortKey="Zhang, Cheng" sort="Zhang, Cheng" uniqKey="Zhang C" first="Cheng" last="Zhang">Cheng Zhang</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Applied Physics Program and Department of Bioengineering, Rice University, Houston, TX 77005</nlm:aff></affiliation></author><author><name sortKey="Ma, Jianpeng" sort="Ma, Jianpeng" uniqKey="Ma J" first="Jianpeng" last="Ma">Jianpeng Ma</name><affiliation><nlm:aff wicri:cut="; and" id="aff1">Applied Physics Program and Department of Bioengineering, Rice University, Houston, TX 77005</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030</nlm:aff></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><idno type="eISSN">1091-6490</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>Using a single-trajectory-based tempering method with a high-temperature dihedral bias, we repeatedly folded four helical proteins [<italic>α</italic><sub>3</sub>D (PDB ID: 2A3D, 73 residues), <italic>α</italic><sub>3</sub>W (1LQ7, 67 residues), Fap1-NR<sub><italic>α</italic></sub> (2KUB, 81 residues) and S-836 (2JUA, 102 residues)] and some of the mutants in explicit solvent within several microseconds. The lowest root-mean-square deviations of backbone atoms from the experimentally determined structures were 1.9, 1.4, 1.0, and 2.1 Å, respectively. Cluster analyses of folding trajectories showed the native conformation usually occupied the most populated cluster. The simulation protocol can be applied to large-scale simulations of other helical proteins on commonly accessible computing platforms.</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">Proc Natl Acad Sci U S A</journal-id><journal-id journal-id-type="iso-abbrev">Proc. Natl. Acad. Sci. U.S.A</journal-id><journal-id journal-id-type="hwp">pnas</journal-id><journal-id journal-id-type="pmc">pnas</journal-id><journal-id journal-id-type="publisher-id">PNAS</journal-id><journal-title-group><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title></journal-title-group><issn pub-type="ppub">0027-8424</issn><issn pub-type="epub">1091-6490</issn><publisher><publisher-name>National Academy of Sciences</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22573819</article-id><article-id pub-id-type="pmc">3361456</article-id><article-id pub-id-type="publisher-id">201112143</article-id><article-id pub-id-type="doi">10.1073/pnas.1112143109</article-id><article-categories><subj-group subj-group-type="heading"><subject>Biological Sciences</subject><subj-group><subject>Biophysics and Computational Biology</subject></subj-group></subj-group></article-categories><title-group><article-title>Folding helical proteins in explicit solvent using dihedral-biased tempering</article-title><alt-title alt-title-type="short">Folding helical proteins in explicit solvent</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Cheng</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ma</surname><given-names>Jianpeng</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><aff id="aff1"><label>a</label>Applied Physics Program and Department of Bioengineering, Rice University, Houston, TX 77005; and</aff><aff id="aff2"><label>b</label>Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030</aff></contrib-group><author-notes><corresp id="cor1"><sup>1</sup>To whom correspondence should be addressed. E-mail: <email>jpma@bcm.tmc.edu</email>.</corresp><fn fn-type="edited-by"><p>Edited by Alan R Fersht, Medical Research Council Laboratory of Molecular Biology, Cambridge University, Cambridge, United Kingdom, and approved March 30, 2012 (received for review July 25, 2011)</p></fn><fn fn-type="participating-researchers"><p>Author contributions: C.Z. and J.M. designed research; C.Z. and J.M. performed research; C.Z. and J.M. analyzed data; and C.Z. and J.M. wrote the paper.</p></fn></author-notes><pub-date pub-type="ppub"><day>22</day><month>5</month><year>2012</year></pub-date><pub-date pub-type="epub"><day>9</day><month>5</month><year>2012</year></pub-date><volume>109</volume><issue>21</issue><fpage>8139</fpage><lpage>8144</lpage><page-range>8139-8144</page-range><self-uri content-type="pdf" xlink:type="simple" xlink:href="pnas.1112143109.pdf"></self-uri><abstract><p>Using a single-trajectory-based tempering method with a high-temperature dihedral bias, we repeatedly folded four helical proteins [<italic>α</italic><sub>3</sub>D (PDB ID: 2A3D, 73 residues), <italic>α</italic><sub>3</sub>W (1LQ7, 67 residues), Fap1-NR<sub><italic>α</italic></sub> (2KUB, 81 residues) and S-836 (2JUA, 102 residues)] and some of the mutants in explicit solvent within several microseconds. The lowest root-mean-square deviations of backbone atoms from the experimentally determined structures were 1.9, 1.4, 1.0, and 2.1 Å, respectively. Cluster analyses of folding trajectories showed the native conformation usually occupied the most populated cluster. The simulation protocol can be applied to large-scale simulations of other helical proteins on commonly accessible computing platforms.</p></abstract><kwd-group><kwd>enhanced sampling</kwd><kwd>molecular dynamics</kwd><kwd>packing chirality</kwd><kwd>protein folding</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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