Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations

Lade...
Vorschaubild
Dateien
Peter_2-r7aq7nuv14ws0.pdf
Peter_2-r7aq7nuv14ws0.pdfGröße: 1.07 MBDownloads: 215
Datum
2001
Autor:innen
Daura, Xavier
van Gunsteren, Wilfred F.
Herausgeber:innen
Kontakt
ISSN der Zeitschrift
Electronic ISSN
ISBN
Bibliografische Daten
Verlag
Schriftenreihe
Auflagebezeichnung
ArXiv-ID
Internationale Patentnummer
Angaben zur Forschungsförderung
Projekt
Open Access-Veröffentlichung
Open Access Green
Sammlungen
Core Facility der Universität Konstanz
Gesperrt bis
Titel in einer weiteren Sprache
Forschungsvorhaben
Organisationseinheiten
Zeitschriftenheft
Publikationstyp
Zeitschriftenartikel
Publikationsstatus
Published
Erschienen in
Journal of Biomolecular NMR. 2001, 20(4), pp. 297-310. ISSN 0925-2738. eISSN 1573-5001. Available under: doi: 10.1023/A:1011241030461
Zusammenfassung

Comparatively small molecules such as peptides can show a high internal mobility with transitions between several conformational minima and sometimes coupling between rotational and internal degrees of freedom. In those cases the interpretation of NMR relaxation data is difficult and the use of standard methods for structure determination is questionable. On the other hand, in the case of those system sizes, the timescale of both rotational and internal motions is accessible by molecular dynamics (MD) simulations using explicit solvent. Thus a comparison of distance averages (〈r−6〉−1/6 or 〈r−3〉1/3) over the MD trajectory with NOE (or ROE) derived distances is no longer necessary, the (back)calculation of the complete spectra becomes possible. In the present study we use two 200 ns trajectories of a heptapeptide of β-amino acids in methanol at two different temperatures to obtain theoretical ROESY spectra by calculating the exact spectral densities for the interproton vectors and the full relaxation matrix. Those data are then compared with the experimental ones. This analysis permits to test some of the assumptions and approximations that generally have to be made to interpret NMR spectra, and to make a more reliable prediction of the conformational equilibrium that leads to the experimental spectrum.

Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
540 Chemie
Schlagwörter
Konferenz
Rezension
undefined / . - undefined, undefined
Zitieren
ISO 690PETER, Christine, Xavier DAURA, Wilfred F. VAN GUNSTEREN, 2001. Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations. In: Journal of Biomolecular NMR. 2001, 20(4), pp. 297-310. ISSN 0925-2738. eISSN 1573-5001. Available under: doi: 10.1023/A:1011241030461
BibTex
@article{Peter2001Calcu-40251,
  year={2001},
  doi={10.1023/A:1011241030461},
  title={Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations},
  number={4},
  volume={20},
  issn={0925-2738},
  journal={Journal of Biomolecular NMR},
  pages={297--310},
  author={Peter, Christine and Daura, Xavier and van Gunsteren, Wilfred F.}
}
RDF
<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/40251">
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/29"/>
    <dcterms:title>Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations</dcterms:title>
    <dcterms:issued>2001</dcterms:issued>
    <dc:creator>van Gunsteren, Wilfred F.</dc:creator>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dc:language>eng</dc:language>
    <dc:contributor>Daura, Xavier</dc:contributor>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-10-05T14:21:17Z</dc:date>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/40251/1/Peter_2-r7aq7nuv14ws0.pdf"/>
    <dc:creator>Peter, Christine</dc:creator>
    <dc:contributor>van Gunsteren, Wilfred F.</dc:contributor>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-10-05T14:21:17Z</dcterms:available>
    <dc:rights>terms-of-use</dc:rights>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/40251"/>
    <dcterms:abstract xml:lang="eng">Comparatively small molecules such as peptides can show a high internal mobility with transitions between several conformational minima and sometimes coupling between rotational and internal degrees of freedom. In those cases the interpretation of NMR relaxation data is difficult and the use of standard methods for structure determination is questionable. On the other hand, in the case of those system sizes, the timescale of both rotational and internal motions is accessible by molecular dynamics (MD) simulations using explicit solvent. Thus a comparison of distance averages (〈r−6〉−1/6 or 〈r−3〉1/3) over the MD trajectory with NOE (or ROE) derived distances is no longer necessary, the (back)calculation of the complete spectra becomes possible. In the present study we use two 200 ns trajectories of a heptapeptide of β-amino acids in methanol at two different temperatures to obtain theoretical ROESY spectra by calculating the exact spectral densities for the interproton vectors and the full relaxation matrix. Those data are then compared with the experimental ones. This analysis permits to test some of the assumptions and approximations that generally have to be made to interpret NMR spectra, and to make a more reliable prediction of the conformational equilibrium that leads to the experimental spectrum.</dcterms:abstract>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/29"/>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/40251/1/Peter_2-r7aq7nuv14ws0.pdf"/>
    <dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/>
    <dc:contributor>Peter, Christine</dc:contributor>
    <dc:creator>Daura, Xavier</dc:creator>
  </rdf:Description>
</rdf:RDF>
Interner Vermerk
xmlui.Submission.submit.DescribeStep.inputForms.label.kops_note_fromSubmitter
Kontakt
URL der Originalveröffentl.
Prüfdatum der URL
Prüfungsdatum der Dissertation
Finanzierungsart
Kommentar zur Publikation
Allianzlizenz
Corresponding Authors der Uni Konstanz vorhanden
Internationale Co-Autor:innen
Universitätsbibliographie
Nein
Begutachtet
Diese Publikation teilen