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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Structure and Dynamics of the Aβ<sub>21–30</sub> Peptide from the Interplay of NMR Experiments and Molecular Simulations</title><author><name sortKey="Fawzi, Nicolas L" sort="Fawzi, Nicolas L" uniqKey="Fawzi N" first="Nicolas L." last="Fawzi">Nicolas L. Fawzi</name><affiliation><nlm:aff id="A1">UCSF/UC Berkeley Joint Graduate Group in Bioengineering, Berkeley, California 94720</nlm:aff></affiliation></author><author><name sortKey="Phillips, Aaron H" sort="Phillips, Aaron H" uniqKey="Phillips A" first="Aaron H." last="Phillips">Aaron H. Phillips</name><affiliation><nlm:aff id="A2">Department of Chemistry, University of California, Berkeley, California 94720</nlm:aff></affiliation></author><author><name sortKey="Ruscio, Jory Z" sort="Ruscio, Jory Z" uniqKey="Ruscio J" first="Jory Z." last="Ruscio">Jory Z. Ruscio</name><affiliation><nlm:aff id="A3">Department of Bioengineering, University of California, Berkeley, California 94720</nlm:aff></affiliation></author><author><name sortKey="Doucleff, Michaeleen" sort="Doucleff, Michaeleen" uniqKey="Doucleff M" first="Michaeleen" last="Doucleff">Michaeleen Doucleff</name><affiliation><nlm:aff id="A2">Department of Chemistry, University of California, Berkeley, California 94720</nlm:aff></affiliation></author><author><name sortKey="Wemmer, David E" sort="Wemmer, David E" uniqKey="Wemmer D" first="David E." last="Wemmer">David E. Wemmer</name><affiliation><nlm:aff id="A2">Department of Chemistry, University of California, Berkeley, California 94720</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720</nlm:aff></affiliation></author><author><name sortKey="Head Gordon, Teresa" sort="Head Gordon, Teresa" uniqKey="Head Gordon T" first="Teresa" last="Head-Gordon">Teresa Head-Gordon</name><affiliation><nlm:aff id="A1">UCSF/UC Berkeley Joint Graduate Group in Bioengineering, Berkeley, California 94720</nlm:aff></affiliation><affiliation><nlm:aff id="A3">Department of Bioengineering, University of California, Berkeley, California 94720</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18412346</idno><idno type="pmc">3474854</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3474854</idno><idno type="RBID">PMC:3474854</idno><idno type="doi">10.1021/ja710366c</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000447</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Structure and Dynamics of the Aβ<sub>21–30</sub> Peptide from the Interplay of NMR Experiments and Molecular Simulations</title><author><name sortKey="Fawzi, Nicolas L" sort="Fawzi, Nicolas L" uniqKey="Fawzi N" first="Nicolas L." last="Fawzi">Nicolas L. Fawzi</name><affiliation><nlm:aff id="A1">UCSF/UC Berkeley Joint Graduate Group in Bioengineering, Berkeley, California 94720</nlm:aff></affiliation></author><author><name sortKey="Phillips, Aaron H" sort="Phillips, Aaron H" uniqKey="Phillips A" first="Aaron H." last="Phillips">Aaron H. Phillips</name><affiliation><nlm:aff id="A2">Department of Chemistry, University of California, Berkeley, California 94720</nlm:aff></affiliation></author><author><name sortKey="Ruscio, Jory Z" sort="Ruscio, Jory Z" uniqKey="Ruscio J" first="Jory Z." last="Ruscio">Jory Z. Ruscio</name><affiliation><nlm:aff id="A3">Department of Bioengineering, University of California, Berkeley, California 94720</nlm:aff></affiliation></author><author><name sortKey="Doucleff, Michaeleen" sort="Doucleff, Michaeleen" uniqKey="Doucleff M" first="Michaeleen" last="Doucleff">Michaeleen Doucleff</name><affiliation><nlm:aff id="A2">Department of Chemistry, University of California, Berkeley, California 94720</nlm:aff></affiliation></author><author><name sortKey="Wemmer, David E" sort="Wemmer, David E" uniqKey="Wemmer D" first="David E." last="Wemmer">David E. Wemmer</name><affiliation><nlm:aff id="A2">Department of Chemistry, University of California, Berkeley, California 94720</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720</nlm:aff></affiliation></author><author><name sortKey="Head Gordon, Teresa" sort="Head Gordon, Teresa" uniqKey="Head Gordon T" first="Teresa" last="Head-Gordon">Teresa Head-Gordon</name><affiliation><nlm:aff id="A1">UCSF/UC Berkeley Joint Graduate Group in Bioengineering, Berkeley, California 94720</nlm:aff></affiliation><affiliation><nlm:aff id="A3">Department of Bioengineering, University of California, Berkeley, California 94720</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720</nlm:aff></affiliation></author></analytic><series><title level="j">Journal of the American Chemical Society</title><idno type="ISSN">0002-7863</idno><idno type="eISSN">1520-5126</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 id="P1">We combine molecular dynamics simulations and new high-field NMR experiments to describe the solution structure of the Aβ<sub>21–30</sub> peptide fragment that may be relevant for understanding structural mechanisms related to Alzheimer’s disease. By using two different empirical force-field combinations, we provide predictions of the three-bond scalar coupling constants (<sup>3</sup>J<sub>H<sup>N</sup>H<sup>α</sup></sub>), chemical-shift values, <sup>13</sup>C relaxation parameters, and rotating-frame nuclear Overhauser effect spectroscopy (ROESY) crosspeaks that can then be compared directly to the same observables measured in the corresponding NMR experiment of Aβ<sub>21–30</sub>. We find robust prediction of the <sup>13</sup>C relaxation parameters and medium-range ROESY crosspeaks by using new generation TIP4P-Ew water and Amber ff99SB protein force fields, in which the NMR validates that the simulation yields both a structurally and dynamically correct ensemble over the entire Aβ<sub>21–30</sub> peptide. Analysis of the simulated ensemble shows that all medium-range ROE restraints are not satisfied simultaneously and demonstrates the structural diversity of the Aβ<sub>21–30</sub> conformations more completely than when determined from the experimental medium-range ROE restraints alone. We find that the structural ensemble of the Aβ<sub>21–30</sub> peptide involves a majority population (~60%) of unstructured conformers, lacking any secondary structure or persistent hydrogen-bonding networks. However, the remaining minority population contains a substantial percentage of conformers with a β-turn centered at Val24 and Gly25, as well as evidence of the Asp23 to Lys28 salt bridge important to the fibril structure. This study sets the stage for robust theoretical work on Aβ<sub>1–40</sub> and Aβ<sub>1–42</sub>, for which collection of detailed NMR data on the monomer will be more challenging because of aggregation and fibril formation on experimental timescales at physiological conditions. In addition, we believe that the interplay of modern molecular simulation and high-quality NMR experiments has reached a fruitful stage for characterizing structural ensembles of disordered peptides and proteins in general.</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">7503056</journal-id><journal-id journal-id-type="pubmed-jr-id">4435</journal-id><journal-id journal-id-type="nlm-ta">J Am Chem Soc</journal-id><journal-id journal-id-type="iso-abbrev">J. Am. Chem. Soc.</journal-id><journal-title-group><journal-title>Journal of the American Chemical Society</journal-title></journal-title-group><issn pub-type="ppub">0002-7863</issn><issn pub-type="epub">1520-5126</issn></journal-meta><article-meta><article-id pub-id-type="pmid">18412346</article-id><article-id pub-id-type="pmc">3474854</article-id><article-id pub-id-type="doi">10.1021/ja710366c</article-id><article-id pub-id-type="manuscript">NIHMS375011</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Structure and Dynamics of the Aβ<sub>21–30</sub> Peptide from the Interplay of NMR Experiments and Molecular Simulations</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Fawzi</surname><given-names>Nicolas L.</given-names></name><xref ref-type="aff" rid="A1">†</xref></contrib><contrib contrib-type="author"><name><surname>Phillips</surname><given-names>Aaron H.</given-names></name><xref ref-type="aff" rid="A2">‡</xref></contrib><contrib contrib-type="author"><name><surname>Ruscio</surname><given-names>Jory Z.</given-names></name><xref ref-type="aff" rid="A3">§</xref></contrib><contrib contrib-type="author"><name><surname>Doucleff</surname><given-names>Michaeleen</given-names></name><xref ref-type="aff" rid="A2">‡</xref></contrib><contrib contrib-type="author"><name><surname>Wemmer</surname><given-names>David E.</given-names></name><xref ref-type="aff" rid="A2">‡</xref><xref ref-type="aff" rid="A4">‖</xref></contrib><contrib contrib-type="author"><name><surname>Head-Gordon</surname><given-names>Teresa</given-names></name><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="aff" rid="A1">†</xref><xref ref-type="aff" rid="A3">§</xref><xref ref-type="aff" rid="A4">‖</xref></contrib></contrib-group><aff id="A1"><label>†</label>UCSF/UC Berkeley Joint Graduate Group in Bioengineering, Berkeley, California 94720</aff><aff id="A2"><label>‡</label>Department of Chemistry, University of California, Berkeley, California 94720</aff><aff id="A3"><label>§</label>Department of Bioengineering, University of California, Berkeley, California 94720</aff><aff id="A4"><label>‖</label>Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720</aff><author-notes><corresp id="cor1"><email>tlhead-gordon@lbl.gov</email></corresp></author-notes><pub-date pub-type="nihms-submitted"><day>4</day><month>5</month><year>2012</year></pub-date><pub-date pub-type="epub"><day>16</day><month>4</month><year>2008</year></pub-date><pub-date pub-type="ppub"><day>14</day><month>5</month><year>2008</year></pub-date><pub-date pub-type="pmc-release"><day>17</day><month>10</month><year>2012</year></pub-date><volume>130</volume><issue>19</issue><fpage>6145</fpage><lpage>6158</lpage><permissions><copyright-statement>© 2008 American Chemical Society</copyright-statement><copyright-year>2008</copyright-year></permissions><abstract><p id="P1">We combine molecular dynamics simulations and new high-field NMR experiments to describe the solution structure of the Aβ<sub>21–30</sub> peptide fragment that may be relevant for understanding structural mechanisms related to Alzheimer’s disease. By using two different empirical force-field combinations, we provide predictions of the three-bond scalar coupling constants (<sup>3</sup>J<sub>H<sup>N</sup>H<sup>α</sup></sub>), chemical-shift values, <sup>13</sup>C relaxation parameters, and rotating-frame nuclear Overhauser effect spectroscopy (ROESY) crosspeaks that can then be compared directly to the same observables measured in the corresponding NMR experiment of Aβ<sub>21–30</sub>. We find robust prediction of the <sup>13</sup>C relaxation parameters and medium-range ROESY crosspeaks by using new generation TIP4P-Ew water and Amber ff99SB protein force fields, in which the NMR validates that the simulation yields both a structurally and dynamically correct ensemble over the entire Aβ<sub>21–30</sub> peptide. Analysis of the simulated ensemble shows that all medium-range ROE restraints are not satisfied simultaneously and demonstrates the structural diversity of the Aβ<sub>21–30</sub> conformations more completely than when determined from the experimental medium-range ROE restraints alone. We find that the structural ensemble of the Aβ<sub>21–30</sub> peptide involves a majority population (~60%) of unstructured conformers, lacking any secondary structure or persistent hydrogen-bonding networks. However, the remaining minority population contains a substantial percentage of conformers with a β-turn centered at Val24 and Gly25, as well as evidence of the Asp23 to Lys28 salt bridge important to the fibril structure. This study sets the stage for robust theoretical work on Aβ<sub>1–40</sub> and Aβ<sub>1–42</sub>, for which collection of detailed NMR data on the monomer will be more challenging because of aggregation and fibril formation on experimental timescales at physiological conditions. In addition, we believe that the interplay of modern molecular simulation and high-quality NMR experiments has reached a fruitful stage for characterizing structural ensembles of disordered peptides and proteins in general.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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