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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model</title><author><name sortKey="Chen, Mingchen" sort="Chen, Mingchen" uniqKey="Chen M" first="Mingchen" last="Chen">Mingchen Chen</name><affiliation><nlm:aff id="A1"><italic>Center for Theoretical Biological Physics</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A2"><italic>Department of Bioengineering, Rice University</italic></nlm:aff></affiliation></author><author><name sortKey="Lin, Xingcheng" sort="Lin, Xingcheng" uniqKey="Lin X" first="Xingcheng" last="Lin">Xingcheng Lin</name><affiliation><nlm:aff id="A1"><italic>Center for Theoretical Biological Physics</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A3">Department of Physics and Astronomy, Rice University</nlm:aff></affiliation></author><author><name sortKey="Zheng, Weihua" sort="Zheng, Weihua" uniqKey="Zheng W" first="Weihua" last="Zheng">Weihua Zheng</name><affiliation><nlm:aff id="A1"><italic>Center for Theoretical Biological Physics</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A4"><italic>Department of Chemistry, Rice University</italic></nlm:aff></affiliation></author><author><name sortKey="Onuchic, Jose N" sort="Onuchic, Jose N" uniqKey="Onuchic J" first="José N." last="Onuchic">José N. Onuchic</name><affiliation><nlm:aff id="A1"><italic>Center for Theoretical Biological Physics</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A3">Department of Physics and Astronomy, Rice University</nlm:aff></affiliation><affiliation><nlm:aff id="A4"><italic>Department of Chemistry, Rice University</italic></nlm:aff></affiliation></author><author><name sortKey="Wolynes, Peter G" sort="Wolynes, Peter G" uniqKey="Wolynes P" first="Peter G." last="Wolynes">Peter G. Wolynes</name><affiliation><nlm:aff id="A1"><italic>Center for Theoretical Biological Physics</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A4"><italic>Department of Chemistry, Rice University</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A3">Department of Physics and Astronomy, Rice University</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27148634</idno><idno type="pmc">5001898</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001898</idno><idno type="RBID">PMC:5001898</idno><idno type="doi">10.1021/acs.jpcb.6b02451</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000430</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model</title><author><name sortKey="Chen, Mingchen" sort="Chen, Mingchen" uniqKey="Chen M" first="Mingchen" last="Chen">Mingchen Chen</name><affiliation><nlm:aff id="A1"><italic>Center for Theoretical Biological Physics</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A2"><italic>Department of Bioengineering, Rice University</italic></nlm:aff></affiliation></author><author><name sortKey="Lin, Xingcheng" sort="Lin, Xingcheng" uniqKey="Lin X" first="Xingcheng" last="Lin">Xingcheng Lin</name><affiliation><nlm:aff id="A1"><italic>Center for Theoretical Biological Physics</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A3">Department of Physics and Astronomy, Rice University</nlm:aff></affiliation></author><author><name sortKey="Zheng, Weihua" sort="Zheng, Weihua" uniqKey="Zheng W" first="Weihua" last="Zheng">Weihua Zheng</name><affiliation><nlm:aff id="A1"><italic>Center for Theoretical Biological Physics</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A4"><italic>Department of Chemistry, Rice University</italic></nlm:aff></affiliation></author><author><name sortKey="Onuchic, Jose N" sort="Onuchic, Jose N" uniqKey="Onuchic J" first="José N." last="Onuchic">José N. Onuchic</name><affiliation><nlm:aff id="A1"><italic>Center for Theoretical Biological Physics</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A3">Department of Physics and Astronomy, Rice University</nlm:aff></affiliation><affiliation><nlm:aff id="A4"><italic>Department of Chemistry, Rice University</italic></nlm:aff></affiliation></author><author><name sortKey="Wolynes, Peter G" sort="Wolynes, Peter G" uniqKey="Wolynes P" first="Peter G." last="Wolynes">Peter G. Wolynes</name><affiliation><nlm:aff id="A1"><italic>Center for Theoretical Biological Physics</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A4"><italic>Department of Chemistry, Rice University</italic></nlm:aff></affiliation><affiliation><nlm:aff id="A3">Department of Physics and Astronomy, Rice University</nlm:aff></affiliation></author></analytic><series><title level="j">The journal of physical chemistry. B</title><idno type="ISSN">1520-6106</idno><idno type="eISSN">1520-5207</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequence that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six alpha-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground-up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.</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>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101157530</journal-id><journal-id journal-id-type="pubmed-jr-id">30073</journal-id><journal-id journal-id-type="nlm-ta">J Phys Chem B</journal-id><journal-id journal-id-type="iso-abbrev">J Phys Chem B</journal-id><journal-title-group><journal-title>The journal of physical chemistry. B</journal-title></journal-title-group><issn pub-type="ppub">1520-6106</issn><issn pub-type="epub">1520-5207</issn></journal-meta><article-meta><article-id pub-id-type="pmid">27148634</article-id><article-id pub-id-type="pmc">5001898</article-id><article-id pub-id-type="doi">10.1021/acs.jpcb.6b02451</article-id><article-id pub-id-type="manuscript">NIHMS785138</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Mingchen</given-names></name><xref ref-type="aff" rid="A1">†</xref><xref ref-type="aff" rid="A2">‡</xref></contrib><contrib contrib-type="author"><name><surname>Lin</surname><given-names>Xingcheng</given-names></name><xref ref-type="aff" rid="A1">†</xref><xref ref-type="aff" rid="A3">¶</xref></contrib><contrib contrib-type="author"><name><surname>Zheng</surname><given-names>Weihua</given-names></name><xref ref-type="aff" rid="A1">†</xref><xref ref-type="aff" rid="A4">§</xref></contrib><contrib contrib-type="author"><name><surname>Onuchic</surname><given-names>José N.</given-names></name><xref ref-type="aff" rid="A1">†</xref><xref ref-type="aff" rid="A3">¶</xref><xref ref-type="aff" rid="A4">§</xref></contrib><contrib contrib-type="author"><name><surname>Wolynes</surname><given-names>Peter G.</given-names></name><xref ref-type="corresp" rid="CR1">∗</xref><xref ref-type="aff" rid="A1">†</xref><xref ref-type="aff" rid="A4">§</xref><xref ref-type="aff" rid="A3">¶</xref></contrib></contrib-group><aff id="A1"><label>†</label><italic>Center for Theoretical Biological Physics</italic></aff><aff id="A2"><label>‡</label><italic>Department of Bioengineering, Rice University</italic></aff><aff id="A3"><label>¶</label>Department of Physics and Astronomy, Rice University</aff><aff id="A4"><label>§</label><italic>Department of Chemistry, Rice University</italic></aff><author-notes><corresp id="CR1"><email>pwolynes@rice.edu</email> Phone: (713)348-4101</corresp></author-notes><pub-date pub-type="nihms-submitted"><day>11</day><month>5</month><year>2016</year></pub-date><pub-date pub-type="epub"><day>13</day><month>5</month><year>2016</year></pub-date><pub-date pub-type="ppub"><day>25</day><month>8</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>26</day><month>8</month><year>2016</year></pub-date><volume>120</volume><issue>33</issue><fpage>8557</fpage><lpage>8565</lpage><pmc-comment>elocation-id from pubmed: 10.1021/acs.jpcb.6b02451</pmc-comment>
<abstract><p id="P1">The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequence that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six alpha-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground-up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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