Efficient Sampling and Characterization of Free Energy Landscapes of Ion-Peptide Systems

Lade...
Vorschaubild
Dateien
Zu diesem Dokument gibt es keine Dateien.
Datum
2018
Herausgeber:innen
Kontakt
ISSN der Zeitschrift
Electronic ISSN
ISBN
Bibliografische Daten
Verlag
Schriftenreihe
Auflagebezeichnung
URI (zitierfähiger Link)
ArXiv-ID
Internationale Patentnummer
Angaben zur Forschungsförderung
Projekt
Open Access-Veröffentlichung
Core Facility der Universität Konstanz
Gesperrt bis
Titel in einer weiteren Sprache
Forschungsvorhaben
Organisationseinheiten
Zeitschriftenheft
Publikationstyp
Zeitschriftenartikel
Publikationsstatus
Published
Erschienen in
Journal of Chemical Theory and Computation : JCTC. 2018, 14(11), pp. 5476-5488. ISSN 1549-9618. eISSN 1549-9626. Available under: doi: 10.1021/acs.jctc.8b00560
Zusammenfassung

Proteins that influence nucleation, growth, or polymorph selection during biomineralization processes are often rich in glutamic- or aspartic acid. Here, the interactions between carboxylate side chains and ions lead to an interplay of peptide conformations and ion structuring in solution. Molecular dynamics simulations are an ideal tool to mechanistically investigate these processes. Unfortunately, the formation of strong ion-peptide contacts and ion bridges drastically impedes structural reorganization of ionic bonds and conformational transitions of the polymers. Thus, to obtain a complete thermodynamical picture of such systems, enhanced sampling techniques become necessary as well as the methods to characterize the conformational states of these partially disordered polymer-ion systems. Here, we propose a new set of Hamiltonian replica exchange (HRE) parameters for efficient simulations of peptide-ion systems, with an aspartic acid trimer in the presence of Ca2+ and Cl- ions as a test system. We introduce dimensionality reduction and clustering strategies to characterize the states of such a multicomponent system and to analyze the outcome of the proposed HRE with different reweighting methods.

Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
540 Chemie
Schlagwörter
Konferenz
Rezension
undefined / . - undefined, undefined
Zitieren
ISO 690LEMKE, Tobias, Christine PETER, Oleksandra KUKHARENKO, 2018. Efficient Sampling and Characterization of Free Energy Landscapes of Ion-Peptide Systems. In: Journal of Chemical Theory and Computation : JCTC. 2018, 14(11), pp. 5476-5488. ISSN 1549-9618. eISSN 1549-9626. Available under: doi: 10.1021/acs.jctc.8b00560
BibTex
@article{Lemke2018-11-13Effic-43519,
  year={2018},
  doi={10.1021/acs.jctc.8b00560},
  title={Efficient Sampling and Characterization of Free Energy Landscapes of Ion-Peptide Systems},
  number={11},
  volume={14},
  issn={1549-9618},
  journal={Journal of Chemical Theory and Computation : JCTC},
  pages={5476--5488},
  author={Lemke, Tobias and Peter, Christine and Kukharenko, Oleksandra}
}
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/123456789/43519">
    <dcterms:issued>2018-11-13</dcterms:issued>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dc:contributor>Kukharenko, Oleksandra</dc:contributor>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/29"/>
    <dcterms:title>Efficient Sampling and Characterization of Free Energy Landscapes of Ion-Peptide Systems</dcterms:title>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/43519"/>
    <dcterms:abstract xml:lang="eng">Proteins that influence nucleation, growth, or polymorph selection during biomineralization processes are often rich in glutamic- or aspartic acid. Here, the interactions between carboxylate side chains and ions lead to an interplay of peptide conformations and ion structuring in solution. Molecular dynamics simulations are an ideal tool to mechanistically investigate these processes. Unfortunately, the formation of strong ion-peptide contacts and ion bridges drastically impedes structural reorganization of ionic bonds and conformational transitions of the polymers. Thus, to obtain a complete thermodynamical picture of such systems, enhanced sampling techniques become necessary as well as the methods to characterize the conformational states of these partially disordered polymer-ion systems. Here, we propose a new set of Hamiltonian replica exchange (HRE) parameters for efficient simulations of peptide-ion systems, with an aspartic acid trimer in the presence of Ca&lt;sup&gt;2+&lt;/sup&gt; and Cl&lt;sup&gt;-&lt;/sup&gt; ions as a test system. We introduce dimensionality reduction and clustering strategies to characterize the states of such a multicomponent system and to analyze the outcome of the proposed HRE with different reweighting methods.</dcterms:abstract>
    <dc:contributor>Peter, Christine</dc:contributor>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dc:language>eng</dc:language>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-10-15T09:13:09Z</dcterms:available>
    <dc:creator>Kukharenko, Oleksandra</dc:creator>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/29"/>
    <dc:creator>Lemke, Tobias</dc:creator>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-10-15T09:13:09Z</dc:date>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/52"/>
    <dc:creator>Peter, Christine</dc:creator>
    <dc:contributor>Lemke, Tobias</dc:contributor>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/52"/>
  </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
Ja
Begutachtet
Ja
Diese Publikation teilen