Computing H/D-Exchange rates of single residues from data of proteolytic fragments

Lade...
Vorschaubild
Dateien
Karrenbauer etal.pdf
Karrenbauer etal.pdfGröße: 664.7 KBDownloads: 275
Datum
2010
Autor:innen
Althaus, Ernst
Canzar, Stefan
Ehrler, Carsten
Emmett, Mark R.
Marshall, Alan G.
Meyer-Bäse, Anke
Tipton, Jeremiah D.
Zhang, Hui-Min
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
Core Facility der Universität Konstanz
Gesperrt bis
Titel in einer weiteren Sprache
Forschungsvorhaben
Organisationseinheiten
Zeitschriftenheft
Publikationstyp
Zeitschriftenartikel
Publikationsstatus
Published
Erschienen in
Zusammenfassung

Background: Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/
Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex.
In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and
compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides
generated from the protease digest of the protein is related to the solvent accessibility of amide protons within
the original protein construct.
Results: In this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on
combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data
of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue
resolution.
Conclusions: With our new method it is possible to automatically determine deuterium exchange with higher
spatial resolution than the level of digested fragments.

Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
004 Informatik
Schlagwörter
Konferenz
Rezension
undefined / . - undefined, undefined
Zitieren
ISO 690ALTHAUS, Ernst, Stefan CANZAR, Carsten EHRLER, Mark R. EMMETT, Andreas KARRENBAUER, Alan G. MARSHALL, Anke MEYER-BÄSE, Jeremiah D. TIPTON, Hui-Min ZHANG, 2010. Computing H/D-Exchange rates of single residues from data of proteolytic fragments. In: BMC Bioinformatics. 2010, 11(1), 424. eISSN 1471-2105. Available under: doi: 10.1186/1471-2105-11-424
BibTex
@article{Althaus2010Compu-17267,
  year={2010},
  doi={10.1186/1471-2105-11-424},
  title={Computing H/D-Exchange rates of single residues from data of proteolytic fragments},
  number={1},
  volume={11},
  journal={BMC Bioinformatics},
  author={Althaus, Ernst and Canzar, Stefan and Ehrler, Carsten and Emmett, Mark R. and Karrenbauer, Andreas and Marshall, Alan G. and Meyer-Bäse, Anke and Tipton, Jeremiah D. and Zhang, Hui-Min},
  note={Article Number: 424}
}
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/123456789/17267">
    <dc:contributor>Zhang, Hui-Min</dc:contributor>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/17267/1/Karrenbauer%20etal.pdf"/>
    <dc:creator>Emmett, Mark R.</dc:creator>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/17267/1/Karrenbauer%20etal.pdf"/>
    <dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dc:creator>Marshall, Alan G.</dc:creator>
    <dc:contributor>Ehrler, Carsten</dc:contributor>
    <dc:creator>Canzar, Stefan</dc:creator>
    <dcterms:issued>2010</dcterms:issued>
    <dc:contributor>Meyer-Bäse, Anke</dc:contributor>
    <dc:contributor>Canzar, Stefan</dc:contributor>
    <dc:creator>Tipton, Jeremiah D.</dc:creator>
    <dc:creator>Karrenbauer, Andreas</dc:creator>
    <dc:language>eng</dc:language>
    <dc:contributor>Althaus, Ernst</dc:contributor>
    <dcterms:abstract xml:lang="eng">Background: Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/&lt;br /&gt;Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex.&lt;br /&gt;In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and&lt;br /&gt;compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides&lt;br /&gt;generated from the protease digest of the protein is related to the solvent accessibility of amide protons within&lt;br /&gt;the original protein construct.&lt;br /&gt;Results: In this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on&lt;br /&gt;combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data&lt;br /&gt;of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue&lt;br /&gt;resolution.&lt;br /&gt;Conclusions: With our new method it is possible to automatically determine deuterium exchange with higher&lt;br /&gt;spatial resolution than the level of digested fragments.</dcterms:abstract>
    <dc:contributor>Tipton, Jeremiah D.</dc:contributor>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dc:contributor>Karrenbauer, Andreas</dc:contributor>
    <dc:creator>Zhang, Hui-Min</dc:creator>
    <dc:contributor>Emmett, Mark R.</dc:contributor>
    <dc:creator>Ehrler, Carsten</dc:creator>
    <dc:rights>terms-of-use</dc:rights>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2011-12-01T12:54:23Z</dc:date>
    <bibo:uri rdf:resource="http://kops.uni-konstanz.de/handle/123456789/17267"/>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/52"/>
    <dc:creator>Althaus, Ernst</dc:creator>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/52"/>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/>
    <dc:contributor>Marshall, Alan G.</dc:contributor>
    <dc:creator>Meyer-Bäse, Anke</dc:creator>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2011-12-01T12:54:23Z</dcterms:available>
    <dcterms:bibliographicCitation>First publ. in: BMC Bioinformatics ; 11 (2010). - 424</dcterms:bibliographicCitation>
    <dcterms:title>Computing H/D-Exchange rates of single residues from data of proteolytic fragments</dcterms:title>
  </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
Diese Publikation teilen