Routine phasing of coiled-coil protein crystal structures with AMPLE

Lade...
Vorschaubild
Dateien
Thomas_0-349937.pdf
Thomas_0-349937.pdfGröße: 664.87 KBDownloads: 182
Datum
2015
Autor:innen
Thomas, Jens M. H.
Keegan, Ronan M.
Bibby, Jaclyn
Winn, Martyn D.
Rigden, Daniel J.
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 Gold
Sammlungen
Core Facility der Universität Konstanz
Gesperrt bis
Titel in einer weiteren Sprache
Forschungsvorhaben
Organisationseinheiten
Zeitschriftenheft
Publikationstyp
Zeitschriftenartikel
Publikationsstatus
Published
Erschienen in
IUCrJ. 2015, 2(2), pp. 198-206. eISSN 2052-2525. Available under: doi: 10.1107/S2052252515002080
Zusammenfassung

Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallo-graphic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
570 Biowissenschaften, Biologie
Schlagwörter
Konferenz
Rezension
undefined / . - undefined, undefined
Zitieren
ISO 690THOMAS, Jens M. H., Ronan M. KEEGAN, Jaclyn BIBBY, Martyn D. WINN, Olga MAYANS, Daniel J. RIGDEN, 2015. Routine phasing of coiled-coil protein crystal structures with AMPLE. In: IUCrJ. 2015, 2(2), pp. 198-206. eISSN 2052-2525. Available under: doi: 10.1107/S2052252515002080
BibTex
@article{Thomas2015-03-01Routi-34958,
  year={2015},
  doi={10.1107/S2052252515002080},
  title={Routine phasing of coiled-coil protein crystal structures with AMPLE},
  number={2},
  volume={2},
  journal={IUCrJ},
  pages={198--206},
  author={Thomas, Jens M. H. and Keegan, Ronan M. and Bibby, Jaclyn and Winn, Martyn D. and Mayans, Olga and Rigden, Daniel J.}
}
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/123456789/34958">
    <dc:creator>Thomas, Jens M. H.</dc:creator>
    <dc:rights>terms-of-use</dc:rights>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2016-08-05T13:33:01Z</dcterms:available>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/34958/3/Thomas_0-349937.pdf"/>
    <dcterms:title>Routine phasing of coiled-coil protein crystal structures with AMPLE</dcterms:title>
    <dcterms:abstract xml:lang="eng">Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallo-graphic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.</dcterms:abstract>
    <dc:creator>Rigden, Daniel J.</dc:creator>
    <dc:contributor>Winn, Martyn D.</dc:contributor>
    <dcterms:issued>2015-03-01</dcterms:issued>
    <dc:creator>Bibby, Jaclyn</dc:creator>
    <dc:creator>Mayans, Olga</dc:creator>
    <dc:contributor>Mayans, Olga</dc:contributor>
    <dc:contributor>Rigden, Daniel J.</dc:contributor>
    <dc:contributor>Bibby, Jaclyn</dc:contributor>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/34958"/>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/34958/3/Thomas_0-349937.pdf"/>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dc:contributor>Keegan, Ronan M.</dc:contributor>
    <dc:creator>Winn, Martyn D.</dc:creator>
    <dc:contributor>Thomas, Jens M. H.</dc:contributor>
    <dc:creator>Keegan, Ronan M.</dc:creator>
    <dc:language>eng</dc:language>
    <dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2016-08-05T13:33:01Z</dc:date>
  </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