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dc.contributor.author
Kahraman, Abdullah
dc.contributor.author
Herzog, Franz
dc.contributor.author
Leitner, Alexander
dc.contributor.author
Rosenberger, George
dc.contributor.author
Aebersold, Ruedi
dc.contributor.author
Malmström, Lars
dc.date.accessioned
2018-09-13T08:52:21Z
dc.date.available
2017-06-10T22:06:32Z
dc.date.available
2018-09-13T08:52:21Z
dc.date.issued
2013-09-17
dc.identifier.issn
1932-6203
dc.identifier.other
10.1371/journal.pone.0073411
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/72574
dc.identifier.doi
10.3929/ethz-b-000072574
dc.description.abstract
Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
Public Library of Science
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/3.0/
dc.title
Cross-Link Guided Molecular Modeling with ROSETTA
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 3.0 Unported
ethz.journal.title
PLoS ONE
ethz.journal.volume
8
en_US
ethz.journal.issue
9
en_US
ethz.journal.abbreviated
PLoS ONE
ethz.pages.start
e73411
en_US
ethz.size
15 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.nebis
006206116
ethz.publication.place
San Francisco, CA, USA
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::02538 - Institut für Molekulare Systembiologie / Institute for Molecular Systems Biology::03663 - Aebersold, Rudolf (emeritus) / Aebersold, Rudolf (emeritus)
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::02538 - Institut für Molekulare Systembiologie / Institute for Molecular Systems Biology::03663 - Aebersold, Rudolf (emeritus) / Aebersold, Rudolf (emeritus)
ethz.date.deposited
2017-06-10T22:07:04Z
ethz.source
ECIT
ethz.identifier.importid
imp5936510d7fbce44783
ethz.ecitpid
pub:115031
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-07-15T08:27:00Z
ethz.rosetta.lastUpdated
2021-02-15T01:44:45Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
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