Serveur d'exploration Covid (26 mars)

Attention, ce site est en cours de développement !
Attention, site généré par des moyens informatiques à partir de corpus bruts.
Les informations ne sont donc pas validées.

Consistent blind protein structure generation from NMR chemical shift data

Identifieur interne : 000728 ( Pmc/Corpus ); précédent : 000727; suivant : 000729

Consistent blind protein structure generation from NMR chemical shift data

Auteurs : Yang Shen ; Oliver Lange ; Frank Delaglio ; Paolo Rossi ; James M. Aramini ; Gaohua Liu ; Alexander Eletsky ; Yibing Wu ; Kiran K. Singarapu ; Alexander Lemak ; Alexandr Ignatchenko ; Cheryl H. Arrowsmith ; Thomas Szyperski ; Gaetano T. Montelione ; David Baker ; Ad Bax

Source :

RBID : PMC:2290745

Abstract

Protein NMR chemical shifts are highly sensitive to local structure. A robust protocol is described that exploits this relation for de novo protein structure generation, using as input experimental parameters the 13Cα, 13Cβ, 13C′, 15N, 1Hα and 1HN NMR chemical shifts. These shifts are generally available at the early stage of the traditional NMR structure determination process, before the collection and analysis of structural restraints. The chemical shift based structure determination protocol uses an empirically optimized procedure to select protein fragments from the Protein Data Bank, in conjunction with the standard ROSETTA Monte Carlo assembly and relaxation methods. Evaluation of 16 proteins, varying in size from 56 to 129 residues, yielded full-atom models that have 0.7–1.8 Å root mean square deviations for the backbone atoms relative to the experimentally determined x-ray or NMR structures. The strategy also has been successfully applied in a blind manner to nine protein targets with molecular masses up to 15.4 kDa, whose conventional NMR structure determination was conducted in parallel by the Northeast Structural Genomics Consortium. This protocol potentially provides a new direction for high-throughput NMR structure determination.


Url:
DOI: 10.1073/pnas.0800256105
PubMed: 18326625
PubMed Central: 2290745

Links to Exploration step

PMC:2290745

Le document en format XML

<record>
<TEI>
<teiHeader>
<fileDesc>
<titleStmt>
<title xml:lang="en">Consistent blind protein structure generation from NMR chemical shift data</title>
<author>
<name sortKey="Shen, Yang" sort="Shen, Yang" uniqKey="Shen Y" first="Yang" last="Shen">Yang Shen</name>
<affiliation>
<nlm:aff id="aff1">*Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Lange, Oliver" sort="Lange, Oliver" uniqKey="Lange O" first="Oliver" last="Lange">Oliver Lange</name>
<affiliation>
<nlm:aff id="aff2">Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Delaglio, Frank" sort="Delaglio, Frank" uniqKey="Delaglio F" first="Frank" last="Delaglio">Frank Delaglio</name>
<affiliation>
<nlm:aff id="aff1">*Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Rossi, Paolo" sort="Rossi, Paolo" uniqKey="Rossi P" first="Paolo" last="Rossi">Paolo Rossi</name>
<affiliation>
<nlm:aff id="aff3">Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, and Robert Wood Johnson Medical School, Piscataway, NJ 08854;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Aramini, James M" sort="Aramini, James M" uniqKey="Aramini J" first="James M." last="Aramini">James M. Aramini</name>
<affiliation>
<nlm:aff id="aff3">Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, and Robert Wood Johnson Medical School, Piscataway, NJ 08854;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Liu, Gaohua" sort="Liu, Gaohua" uniqKey="Liu G" first="Gaohua" last="Liu">Gaohua Liu</name>
<affiliation>
<nlm:aff id="aff3">Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, and Robert Wood Johnson Medical School, Piscataway, NJ 08854;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Eletsky, Alexander" sort="Eletsky, Alexander" uniqKey="Eletsky A" first="Alexander" last="Eletsky">Alexander Eletsky</name>
<affiliation>
<nlm:aff wicri:cut="; and" id="aff4">Departments of Chemistry and Structural Biology and Northeast Structural Genomics Consortium, University at Buffalo, State University of New York, Buffalo, NY 14260</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Wu, Yibing" sort="Wu, Yibing" uniqKey="Wu Y" first="Yibing" last="Wu">Yibing Wu</name>
<affiliation>
<nlm:aff wicri:cut="; and" id="aff4">Departments of Chemistry and Structural Biology and Northeast Structural Genomics Consortium, University at Buffalo, State University of New York, Buffalo, NY 14260</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Singarapu, Kiran K" sort="Singarapu, Kiran K" uniqKey="Singarapu K" first="Kiran K." last="Singarapu">Kiran K. Singarapu</name>
<affiliation>
<nlm:aff wicri:cut="; and" id="aff4">Departments of Chemistry and Structural Biology and Northeast Structural Genomics Consortium, University at Buffalo, State University of New York, Buffalo, NY 14260</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Lemak, Alexander" sort="Lemak, Alexander" uniqKey="Lemak A" first="Alexander" last="Lemak">Alexander Lemak</name>
<affiliation>
<nlm:aff id="aff5">Ontario Cancer Institute, Department of Medical Biophysics, and Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G IL5</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Ignatchenko, Alexandr" sort="Ignatchenko, Alexandr" uniqKey="Ignatchenko A" first="Alexandr" last="Ignatchenko">Alexandr Ignatchenko</name>
<affiliation>
<nlm:aff id="aff5">Ontario Cancer Institute, Department of Medical Biophysics, and Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G IL5</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Arrowsmith, Cheryl H" sort="Arrowsmith, Cheryl H" uniqKey="Arrowsmith C" first="Cheryl H." last="Arrowsmith">Cheryl H. Arrowsmith</name>
<affiliation>
<nlm:aff id="aff5">Ontario Cancer Institute, Department of Medical Biophysics, and Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G IL5</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Szyperski, Thomas" sort="Szyperski, Thomas" uniqKey="Szyperski T" first="Thomas" last="Szyperski">Thomas Szyperski</name>
<affiliation>
<nlm:aff wicri:cut="; and" id="aff4">Departments of Chemistry and Structural Biology and Northeast Structural Genomics Consortium, University at Buffalo, State University of New York, Buffalo, NY 14260</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Montelione, Gaetano T" sort="Montelione, Gaetano T" uniqKey="Montelione G" first="Gaetano T." last="Montelione">Gaetano T. Montelione</name>
<affiliation>
<nlm:aff id="aff3">Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, and Robert Wood Johnson Medical School, Piscataway, NJ 08854;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Baker, David" sort="Baker, David" uniqKey="Baker D" first="David" last="Baker">David Baker</name>
<affiliation>
<nlm:aff id="aff2">Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Bax, Ad" sort="Bax, Ad" uniqKey="Bax A" first="Ad" last="Bax">Ad Bax</name>
<affiliation>
<nlm:aff id="aff1">*Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892;</nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt>
<idno type="wicri:source">PMC</idno>
<idno type="pmid">18326625</idno>
<idno type="pmc">2290745</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2290745</idno>
<idno type="RBID">PMC:2290745</idno>
<idno type="doi">10.1073/pnas.0800256105</idno>
<date when="2008">2008</date>
<idno type="wicri:Area/Pmc/Corpus">000728</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000728</idno>
</publicationStmt>
<sourceDesc>
<biblStruct>
<analytic>
<title xml:lang="en" level="a" type="main">Consistent blind protein structure generation from NMR chemical shift data</title>
<author>
<name sortKey="Shen, Yang" sort="Shen, Yang" uniqKey="Shen Y" first="Yang" last="Shen">Yang Shen</name>
<affiliation>
<nlm:aff id="aff1">*Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Lange, Oliver" sort="Lange, Oliver" uniqKey="Lange O" first="Oliver" last="Lange">Oliver Lange</name>
<affiliation>
<nlm:aff id="aff2">Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Delaglio, Frank" sort="Delaglio, Frank" uniqKey="Delaglio F" first="Frank" last="Delaglio">Frank Delaglio</name>
<affiliation>
<nlm:aff id="aff1">*Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Rossi, Paolo" sort="Rossi, Paolo" uniqKey="Rossi P" first="Paolo" last="Rossi">Paolo Rossi</name>
<affiliation>
<nlm:aff id="aff3">Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, and Robert Wood Johnson Medical School, Piscataway, NJ 08854;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Aramini, James M" sort="Aramini, James M" uniqKey="Aramini J" first="James M." last="Aramini">James M. Aramini</name>
<affiliation>
<nlm:aff id="aff3">Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, and Robert Wood Johnson Medical School, Piscataway, NJ 08854;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Liu, Gaohua" sort="Liu, Gaohua" uniqKey="Liu G" first="Gaohua" last="Liu">Gaohua Liu</name>
<affiliation>
<nlm:aff id="aff3">Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, and Robert Wood Johnson Medical School, Piscataway, NJ 08854;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Eletsky, Alexander" sort="Eletsky, Alexander" uniqKey="Eletsky A" first="Alexander" last="Eletsky">Alexander Eletsky</name>
<affiliation>
<nlm:aff wicri:cut="; and" id="aff4">Departments of Chemistry and Structural Biology and Northeast Structural Genomics Consortium, University at Buffalo, State University of New York, Buffalo, NY 14260</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Wu, Yibing" sort="Wu, Yibing" uniqKey="Wu Y" first="Yibing" last="Wu">Yibing Wu</name>
<affiliation>
<nlm:aff wicri:cut="; and" id="aff4">Departments of Chemistry and Structural Biology and Northeast Structural Genomics Consortium, University at Buffalo, State University of New York, Buffalo, NY 14260</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Singarapu, Kiran K" sort="Singarapu, Kiran K" uniqKey="Singarapu K" first="Kiran K." last="Singarapu">Kiran K. Singarapu</name>
<affiliation>
<nlm:aff wicri:cut="; and" id="aff4">Departments of Chemistry and Structural Biology and Northeast Structural Genomics Consortium, University at Buffalo, State University of New York, Buffalo, NY 14260</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Lemak, Alexander" sort="Lemak, Alexander" uniqKey="Lemak A" first="Alexander" last="Lemak">Alexander Lemak</name>
<affiliation>
<nlm:aff id="aff5">Ontario Cancer Institute, Department of Medical Biophysics, and Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G IL5</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Ignatchenko, Alexandr" sort="Ignatchenko, Alexandr" uniqKey="Ignatchenko A" first="Alexandr" last="Ignatchenko">Alexandr Ignatchenko</name>
<affiliation>
<nlm:aff id="aff5">Ontario Cancer Institute, Department of Medical Biophysics, and Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G IL5</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Arrowsmith, Cheryl H" sort="Arrowsmith, Cheryl H" uniqKey="Arrowsmith C" first="Cheryl H." last="Arrowsmith">Cheryl H. Arrowsmith</name>
<affiliation>
<nlm:aff id="aff5">Ontario Cancer Institute, Department of Medical Biophysics, and Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G IL5</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Szyperski, Thomas" sort="Szyperski, Thomas" uniqKey="Szyperski T" first="Thomas" last="Szyperski">Thomas Szyperski</name>
<affiliation>
<nlm:aff wicri:cut="; and" id="aff4">Departments of Chemistry and Structural Biology and Northeast Structural Genomics Consortium, University at Buffalo, State University of New York, Buffalo, NY 14260</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Montelione, Gaetano T" sort="Montelione, Gaetano T" uniqKey="Montelione G" first="Gaetano T." last="Montelione">Gaetano T. Montelione</name>
<affiliation>
<nlm:aff id="aff3">Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, and Robert Wood Johnson Medical School, Piscataway, NJ 08854;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Baker, David" sort="Baker, David" uniqKey="Baker D" first="David" last="Baker">David Baker</name>
<affiliation>
<nlm:aff id="aff2">Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195;</nlm:aff>
</affiliation>
</author>
<author>
<name sortKey="Bax, Ad" sort="Bax, Ad" uniqKey="Bax A" first="Ad" last="Bax">Ad Bax</name>
<affiliation>
<nlm:aff id="aff1">*Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892;</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="2008">2008</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass></textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<p>Protein NMR chemical shifts are highly sensitive to local structure. A robust protocol is described that exploits this relation for
<italic>de novo</italic>
protein structure generation, using as input experimental parameters the
<sup>13</sup>
C
<sup>α</sup>
,
<sup>13</sup>
C
<sup>β</sup>
,
<sup>13</sup>
C′,
<sup>15</sup>
N,
<sup>1</sup>
H
<sup>α</sup>
and
<sup>1</sup>
H
<sup>N</sup>
NMR chemical shifts. These shifts are generally available at the early stage of the traditional NMR structure determination process, before the collection and analysis of structural restraints. The chemical shift based structure determination protocol uses an empirically optimized procedure to select protein fragments from the Protein Data Bank, in conjunction with the standard ROSETTA Monte Carlo assembly and relaxation methods. Evaluation of 16 proteins, varying in size from 56 to 129 residues, yielded full-atom models that have 0.7–1.8 Å root mean square deviations for the backbone atoms relative to the experimentally determined x-ray or NMR structures. The strategy also has been successfully applied in a blind manner to nine protein targets with molecular masses up to 15.4 kDa, whose conventional NMR structure determination was conducted in parallel by the Northeast Structural Genomics Consortium. This protocol potentially provides a new direction for high-throughput NMR structure determination.</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="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">18326625</article-id>
<article-id pub-id-type="pmc">2290745</article-id>
<article-id pub-id-type="publisher-id">9596</article-id>
<article-id pub-id-type="doi">10.1073/pnas.0800256105</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Biological Sciences</subject>
<subj-group>
<subject>Biophysics</subject>
</subj-group>
</subj-group>
<series-title>From the Cover</series-title>
</article-categories>
<title-group>
<article-title>Consistent blind protein structure generation from NMR chemical shift data</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Shen</surname>
<given-names>Yang</given-names>
</name>
<xref ref-type="aff" rid="aff1">*</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Lange</surname>
<given-names>Oliver</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup></sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Delaglio</surname>
<given-names>Frank</given-names>
</name>
<xref ref-type="aff" rid="aff1">*</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Rossi</surname>
<given-names>Paolo</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup></sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Aramini</surname>
<given-names>James M.</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup></sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Liu</surname>
<given-names>Gaohua</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup></sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Eletsky</surname>
<given-names>Alexander</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>§</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wu</surname>
<given-names>Yibing</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>§</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Singarapu</surname>
<given-names>Kiran K.</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>§</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Lemak</surname>
<given-names>Alexander</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup></sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Ignatchenko</surname>
<given-names>Alexandr</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup></sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Arrowsmith</surname>
<given-names>Cheryl H.</given-names>
</name>
<xref ref-type="aff" rid="aff5">
<sup></sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Szyperski</surname>
<given-names>Thomas</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>§</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Montelione</surname>
<given-names>Gaetano T.</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup></sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Baker</surname>
<given-names>David</given-names>
</name>
<xref ref-type="aff" rid="aff2">
<sup></sup>
</xref>
<xref ref-type="corresp" rid="cor1">
<sup></sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Bax</surname>
<given-names>Ad</given-names>
</name>
<xref ref-type="aff" rid="aff1">*</xref>
<xref ref-type="corresp" rid="cor1">
<sup></sup>
</xref>
</contrib>
<aff id="aff1">*Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892;</aff>
<aff id="aff2">
<sup></sup>
Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195;</aff>
<aff id="aff3">
<sup></sup>
Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, and Robert Wood Johnson Medical School, Piscataway, NJ 08854;</aff>
<aff id="aff4">
<sup>§</sup>
Departments of Chemistry and Structural Biology and Northeast Structural Genomics Consortium, University at Buffalo, State University of New York, Buffalo, NY 14260; and</aff>
<aff id="aff5">
<sup></sup>
Ontario Cancer Institute, Department of Medical Biophysics, and Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada M5G IL5</aff>
</contrib-group>
<author-notes>
<corresp id="cor1">
<sup></sup>
To whom correspondence may be addressed. Email:
<email>dabaker@u.washington.edu</email>
or
<email>bax@nih.gov</email>
</corresp>
<fn fn-type="con">
<p>Contributed by Ad Bax, January 10, 2008</p>
</fn>
<fn fn-type="con">
<p>Author contributions: Y.S., D.B., and A.B. designed research; Y.S. and O.L. performed research; F.D. contributed new reagents/analytic tools; Y.S., P.R., J.M.A., G.L., A.E., Y.W., K.K.S., A.L., and A.I. analyzed data; and Y.S., C.H.A., T.S., G.T.M., D.B., and A.B. wrote the paper.</p>
</fn>
<fn fn-type="conflict">
<p>The authors declare no conflict of interest.</p>
</fn>
</author-notes>
<pub-date pub-type="ppub">
<day>25</day>
<month>3</month>
<year>2008</year>
</pub-date>
<pub-date pub-type="epub">
<day>7</day>
<month>3</month>
<year>2008</year>
</pub-date>
<volume>105</volume>
<issue>12</issue>
<fpage>4685</fpage>
<lpage>4690</lpage>
<history>
<date date-type="received">
<day>14</day>
<month>12</month>
<year>2007</year>
</date>
</history>
<permissions>
<copyright-statement>© 2008 by The National Academy of Sciences of the USA</copyright-statement>
</permissions>
<self-uri xlink:title="pdf" xlink:type="simple" xlink:href="zpq01208004685.pdf"></self-uri>
<abstract>
<p>Protein NMR chemical shifts are highly sensitive to local structure. A robust protocol is described that exploits this relation for
<italic>de novo</italic>
protein structure generation, using as input experimental parameters the
<sup>13</sup>
C
<sup>α</sup>
,
<sup>13</sup>
C
<sup>β</sup>
,
<sup>13</sup>
C′,
<sup>15</sup>
N,
<sup>1</sup>
H
<sup>α</sup>
and
<sup>1</sup>
H
<sup>N</sup>
NMR chemical shifts. These shifts are generally available at the early stage of the traditional NMR structure determination process, before the collection and analysis of structural restraints. The chemical shift based structure determination protocol uses an empirically optimized procedure to select protein fragments from the Protein Data Bank, in conjunction with the standard ROSETTA Monte Carlo assembly and relaxation methods. Evaluation of 16 proteins, varying in size from 56 to 129 residues, yielded full-atom models that have 0.7–1.8 Å root mean square deviations for the backbone atoms relative to the experimentally determined x-ray or NMR structures. The strategy also has been successfully applied in a blind manner to nine protein targets with molecular masses up to 15.4 kDa, whose conventional NMR structure determination was conducted in parallel by the Northeast Structural Genomics Consortium. This protocol potentially provides a new direction for high-throughput NMR structure determination.</p>
</abstract>
<kwd-group>
<kwd>molecular fragment replacement</kwd>
<kwd>protein structure prediction</kwd>
<kwd>ROSETTA</kwd>
<kwd>structural genomics</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV2/Data/Pmc/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000728 | SxmlIndent | more

Ou

HfdSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd -nk 000728 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Wicri/Sante
   |area=    CovidV2
   |flux=    Pmc
   |étape=   Corpus
   |type=    RBID
   |clé=     PMC:2290745
   |texte=   Consistent blind protein structure generation from NMR chemical shift data
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/RBID.i   -Sk "pubmed:18326625" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd   \
       | NlmPubMed2Wicri -a CovidV2 

Wicri

This area was generated with Dilib version V0.6.33.
Data generation: Sat Mar 28 17:51:24 2020. Site generation: Sun Jan 31 15:35:48 2021