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PEDS Advance Access originally published online on October 25, 2005
Protein Engineering Design and Selection 2006 19(1):9-16; doi:10.1093/protein/gzi070
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

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

Dmitri Mouradov1, Ari Craven1, Jade K. Forwood1, Jack U. Flanagan2,3, Raquel García-Castellanos5, F.Xavier Gomis-Rüth5, David A. Hume1,2,3,4, Jennifer L. Martin1,2, Bostjan Kobe1,2 and Thomas Huber1,6,7

1School of Molecular and Microbial Sciences, 2Institute for Molecular Bioscience, 3Cooperative Research Centre for Chronic Inflammatory Diseases, 4ARC Special Research Centre for Functional and Applied Genomics and 6Advanced Computational Modelling Centre, Department of Mathematics, The University of Queensland, Brisbane, Queensland 4072, Australia and 5Institut de Biologia Molecular de Barcelona, Centre d'Investigació i Desenvolupament, Consell Superior d'Investigacions Científiques, c/Jordi Girona 18–26, E-08034 Barcelona, Spain

7 To whom correspondence should be addressed, at the Advanced Computational Modelling Centre, Department of Mathematics. E-mail: huber{at}maths.uq.edu.au

We 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 x 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 C{alpha} 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.

Keywords: chemical cross-linking/latexin–carboxypeptidaseA/mass spectrometry/molecular docking/protein complex structure

Received July 11, 2005; revised September 1, 2005; accepted September 19, 2005.

Edited by Andrej Sali


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