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PEDS Advance Access published online on October 25, 2005
Protein Engineering Design and Selection, 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
Received July 11, 2005
Revised September 1, 2005
Accepted September 19, 2005

Article

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

Dmitri Mouradov 1, Ari Craven 1, Jade K. Forwood 1, Jack U. Flanagan 2, Raquel García-Castellanos 3, F. Xavier Gomis-Rüth 3, David A. Hume 4, Jennifer L. Martin 5, Bostjan Kobe 5, and Thomas Huber 6*

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

* To whom correspondence should be addressed.
Thomas Huber, E-mail: huber{at}maths.uq.edu.au


  Abstract

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.
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