Approaches to ab initio molecular replacement of α-helical transmembrane proteins

Thomas, Jens M. H.; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J.

Approaches to ab initio molecular replacement of α-helical transmembrane proteins

Dateien

Thomas_2-tie4zyqlg9458.pdfGröße: 1.85 MBDownloads: 273

Datum

2017

Autor:innen

Thomas, Jens M. H.

Simkovic, Felix

Keegan, Ronan

Mayans, Olga

Zhang, Chengxin

Zhang, Yang

Rigden, Daniel J.

Open Access-Veröffentlichung

Open Access Hybrid

Sammlungen

Biologie

Publikationstyp

Zeitschriftenartikel

Publikationsstatus

Published

Erschienen in

Acta crystallographica Section D : Structural biology. 2017, 73(Pt 12), pp. 985-996. ISSN 2059-7983. eISSN 2059-7983. Available under: doi: 10.1107/S2059798317016436

Zusammenfassung

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

Fachgebiet (DDC)

570 Biowissenschaften, Biologie

Schlagwörter

transmembrane proteins; ab initio phasing; ab initio modelling; predicted contacts

Zitieren

ISO 690

THOMAS, Jens M. H., Felix SIMKOVIC, Ronan KEEGAN, Olga MAYANS, Chengxin ZHANG, Yang ZHANG, Daniel J. RIGDEN, 2017. Approaches to ab initio molecular replacement of α-helical transmembrane proteins. In: Acta crystallographica Section D : Structural biology. 2017, 73(Pt 12), pp. 985-996. ISSN 2059-7983. eISSN 2059-7983. Available under: doi: 10.1107/S2059798317016436

BibTex

@article{Thomas2017-12-01Appro-41301,
  year={2017},
  doi={10.1107/S2059798317016436},
  title={Approaches to ab initio molecular replacement of α-helical transmembrane proteins},
  number={Pt 12},
  volume={73},
  issn={2059-7983},
  journal={Acta crystallographica Section D : Structural biology},
  pages={985--996},
  author={Thomas, Jens M. H. and Simkovic, Felix and Keegan, Ronan and Mayans, Olga and Zhang, Chengxin and Zhang, Yang 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/123456789/41301">
    <dc:creator>Zhang, Chengxin</dc:creator>
    <dc:creator>Mayans, Olga</dc:creator>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/41301/1/Thomas_2-tie4zyqlg9458.pdf"/>
    <dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/>
    <dc:contributor>Rigden, Daniel J.</dc:contributor>
    <dc:creator>Rigden, Daniel J.</dc:creator>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/41301"/>
    <dc:creator>Simkovic, Felix</dc:creator>
    <dc:language>eng</dc:language>
    <dc:contributor>Thomas, Jens M. H.</dc:contributor>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dc:contributor>Mayans, Olga</dc:contributor>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-02-13T12:23:39Z</dcterms:available>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/41301/1/Thomas_2-tie4zyqlg9458.pdf"/>
    <dc:contributor>Keegan, Ronan</dc:contributor>
    <dc:creator>Thomas, Jens M. H.</dc:creator>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dcterms:issued>2017-12-01</dcterms:issued>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2018-02-13T12:23:39Z</dc:date>
    <dc:contributor>Zhang, Yang</dc:contributor>
    <dc:rights>terms-of-use</dc:rights>
    <dcterms:abstract xml:lang="eng">α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.</dcterms:abstract>
    <dc:creator>Keegan, Ronan</dc:creator>
    <dc:creator>Zhang, Yang</dc:creator>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dcterms:title>Approaches to ab initio molecular replacement of α-helical transmembrane proteins</dcterms:title>
    <dc:contributor>Simkovic, Felix</dc:contributor>
    <dc:contributor>Zhang, Chengxin</dc:contributor>
  </rdf:Description>
</rdf:RDF>

Universitätsbibliographie

Ja