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Bioinformatics Advance Access published online on May 5, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl178
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received February 28, 2006
Revised April 17, 2006
Accepted May 3, 2006

Article

PROXIMO - a new algorithm to model protein complexes using data from Radical Probe Mass Spectrometry (RP-MS)

Sebastien K. Gerega 1 and Kevin M. Downard 1 *

1 School of Molecular & Microbial Biosciences, The University of Sydney, Australia

* To whom correspondence should be addressed.
Kevin M. Downard, E-mail: kdownard{at}usyd.edu.au


  Abstract

The design and implementation of a new algorithm, known as PROXIMO for protein oxidation interface modeller, is described to predict the structure of protein complexes using data generated in Radical Probe Mass Spectrometry (RP-MS) experiments. Photochemical radiolysis and discharge sources can be used to effect RP-MS in which hydroxyl radicals are formed directly from the bulk solvent on millisecond timescales and react with surface accessible residues in footprinting-like experiments. The algorithm utilises a geometric surface fitting routine to predict likely structures for protein complexes. These structures are scored based on a correlation between the measured solvent accessibility of oxidisable residue side chains and oxidation shielding data obtained by RP-MS.

The algorithm has been implemented to predict structures for the ribonuclease S-protein-peptide and calmodulin-melittin complexes using RP-MS data generated in this laboratory. The former is in close agreement with the high-resolution experimental structure available.

Associate Editor: Martin Bishop
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