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Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

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Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

Auteurs : Christophe Schmitz [Australie] ; Robert Vernon [États-Unis] ; Gottfried Otting [Australie] ; David Baker [États-Unis] ; Thomas Huber [Australie]

Source :

Journal of molecular biology [ 0022-2836 ] ; 2012.

RBID : PMC:3638895

Abstract

Paramagnetic metal ions generate pseudocontact shifts (PCSs) in nuclear magnetic resonance spectra that are manifested as easily measurable changes in chemical shifts. Metals can be incorporated into proteins through metal binding tags, and PCS data constitute powerful long-range restraints on the positions of nuclear spins relative to the coordinate system of the magnetic susceptibility anisotropy tensor (Δχ-tensor) of the metal ion. We show that three-dimensional structures of proteins can reliably be determined using PCS data from a single metal binding site combined with backbone chemical shifts. The program PCS-ROSETTA automatically determines the Δχ-tensor and metal position from the PCS data during the structure calculations, without any prior knowledge of the protein structure. The program can determine structures accurately for proteins of up to 150 residues, offering a powerful new approach to protein structure determination that relies exclusively on readily measurable backbone chemical shifts and easily discriminates between correctly and incorrectly folded conformations.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3638895

DOI: 10.1016/j.jmb.2011.12.056
PubMed: 22285518
PubMed Central: 3638895

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<author><name sortKey="Schmitz, Christophe" sort="Schmitz, Christophe" uniqKey="Schmitz C" first="Christophe" last="Schmitz">Christophe Schmitz</name>
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<series><title level="j">Journal of molecular biology</title>
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<front><div type="abstract" xml:lang="en"><p id="P1">Paramagnetic metal ions generate pseudocontact shifts (PCSs) in nuclear magnetic resonance spectra that are manifested as easily measurable changes in chemical shifts. Metals can be incorporated into proteins through metal binding tags, and PCS data constitute powerful long-range restraints on the positions of nuclear spins relative to the coordinate system of the magnetic susceptibility anisotropy tensor (Δ<italic>χ</italic>
-tensor) of the metal ion. We show that three-dimensional structures of proteins can reliably be determined using PCS data from a single metal binding site combined with backbone chemical shifts. The program PCS-ROSETTA automatically determines the Δ<italic>χ</italic>
-tensor and metal position from the PCS data during the structure calculations, without any prior knowledge of the protein structure. The program can determine structures accurately for proteins of up to 150 residues, offering a powerful new approach to protein structure determination that relies exclusively on readily measurable backbone chemical shifts and easily discriminates between correctly and incorrectly folded conformations.</p>
</div>
</front>
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<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">2985088R</journal-id>
<journal-id journal-id-type="pubmed-jr-id">4967</journal-id>
<journal-id journal-id-type="nlm-ta">J Mol Biol</journal-id>
<journal-id journal-id-type="iso-abbrev">J. Mol. Biol.</journal-id>
<journal-title-group><journal-title>Journal of molecular biology</journal-title>
</journal-title-group>
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<issn pub-type="epub">1089-8638</issn>
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<article-id pub-id-type="manuscript">NIHMS446743</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Protein Structure Determination from Pseudocontact Shifts Using ROSETTA</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Schmitz</surname>
<given-names>Christophe</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
<xref rid="FN2" ref-type="author-notes">†</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Vernon</surname>
<given-names>Robert</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref rid="FN2" ref-type="author-notes">†</xref>
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<contrib contrib-type="author"><name><surname>Otting</surname>
<given-names>Gottfried</given-names>
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<contrib contrib-type="author"><name><surname>Baker</surname>
<given-names>David</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref rid="FN1" ref-type="author-notes">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Huber</surname>
<given-names>Thomas</given-names>
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<xref ref-type="aff" rid="A3">3</xref>
<xref rid="FN1" ref-type="author-notes">*</xref>
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<aff id="A1"><label>1</label>
School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia</aff>
<aff id="A2"><label>2</label>
Department of Biochemistry, University of Washington, University of Washington, Seattle, WA 98195, USA</aff>
<aff id="A3"><label>3</label>
Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia</aff>
<author-notes><corresp id="FN1"><label>*</label>
Corresponding authors: <email>dabaker@u.washington.edu</email>
; <email>t.huber@uq.edu.au</email>
</corresp>
<fn id="FN2" fn-type="equal"><label>†</label>
<p>C.S. and R.V. contributed equally to this work.</p>
</fn>
<fn id="FN3" fn-type="present-address"><p>Present address: C. Schmitz, Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.</p>
</fn>
</author-notes>
<pub-date pub-type="nihms-submitted"><day>1</day>
<month>3</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>18</day>
<month>1</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="ppub"><day>9</day>
<month>3</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>29</day>
<month>4</month>
<year>2013</year>
</pub-date>
<volume>416</volume>
<issue>5</issue>
<fpage>668</fpage>
<lpage>677</lpage>
<permissions><copyright-statement>© 2011 Published by Elsevier Ltd.</copyright-statement>
<copyright-year>2011</copyright-year>
</permissions>
<abstract><p id="P1">Paramagnetic metal ions generate pseudocontact shifts (PCSs) in nuclear magnetic resonance spectra that are manifested as easily measurable changes in chemical shifts. Metals can be incorporated into proteins through metal binding tags, and PCS data constitute powerful long-range restraints on the positions of nuclear spins relative to the coordinate system of the magnetic susceptibility anisotropy tensor (Δ<italic>χ</italic>
-tensor) of the metal ion. We show that three-dimensional structures of proteins can reliably be determined using PCS data from a single metal binding site combined with backbone chemical shifts. The program PCS-ROSETTA automatically determines the Δ<italic>χ</italic>
-tensor and metal position from the PCS data during the structure calculations, without any prior knowledge of the protein structure. The program can determine structures accurately for proteins of up to 150 residues, offering a powerful new approach to protein structure determination that relies exclusively on readily measurable backbone chemical shifts and easily discriminates between correctly and incorrectly folded conformations.</p>
</abstract>
<kwd-group><kwd>pseudocontact shift</kwd>
<kwd>protein structure determination</kwd>
<kwd>NMR spectroscopy</kwd>
<kwd>PCS-ROSETTA</kwd>
<kwd>lanthanides</kwd>
</kwd-group>
<funding-group><award-group><funding-source country="United States">National Institute of General Medical Sciences : NIGMS</funding-source>
<award-id>R01 GM092802 || GM</award-id>
</award-group>
<award-group><funding-source country="United States">Howard Hughes Medical Institute : </funding-source>
<award-id> || HHMI_</award-id>
</award-group>
</funding-group>
</article-meta>
</front>
</pmc>
</record>

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Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

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