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Title

Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking

AuthorsMouradov, Dmitri; Craven, Ari; Forwood, Jade Kenneth; Flanagan, Jack U.; García-Castellanos, Raquel; Gomis-Rüth, F. Xavier ; Hume, David A.; Martin, Jennifer Lynn; Kobe, Bostjan; Huber, Thomas
KeywordsMass spectrometry
Molecular docking
Protein complex structure
Latexin-carboxypeptidaseA
Chemical cross-linking
Issue DateJan-2006
PublisherOxford University Press
CitationProtein Engineering, Design and Selection 19(1): 9-16 (2006)
AbstractWe have determined the three-dimensional structure of the protein complex between latexin and carboxypeptidase A using a combination of chemical cross-linking, mass spectrometry and molecular docking. The locations of three intermolecular cross-links were identified using mass spectrometry and these constraints were used in combination with a speed-optimised docking algorithm allowing us to evaluate more than 3 × 1011 possible conformations. While cross-links represent only limited structural constraints, the combination of only three experimental cross-links with very basic molecular docking was sufficient to determine the complex structure. The crystal structure of the complex between latexin and carboxypeptidase A4 determined recently allowed us to assess the success of this structure determination approach. Our structure was shown to be within 4 Å r.m.s. deviation of Cα atoms of the crystal structure. The study demonstrates that cross-linking in combination with mass spectrometry can lead to efficient and accurate structural modelling of protein complexes. © The Author 2005. Published by Oxford University Press. All rights reserved.
Publisher version (URL)http://dx.doi.org/10.1093/protein/gzi070
URIhttp://hdl.handle.net/10261/104427
DOI10.1093/protein/gzi070
Identifiersdoi: 10.1093/protein/gzi070
issn: 1741-0126
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