A docking analysis of the statistical physics of protein-protein recognition.

Abstract : We describe protein-protein recognition within the frame of the random energy model of statistical physics. We simulate, by docking the component proteins, the process of association of two proteins that form a complex. We obtain the energy spectrum of a set of protein-protein complexes of known three-dimensional structure by performing docking in random orientations and scoring the models thus generated. We use a coarse protein representation where each amino acid residue is replaced by its Voronoï cell, and derive a scoring function by applying the evolutionary learning program ROGER to a set of parameters measured on that representation. Taking the scores of the docking models to be interaction energies, we obtain energy spectra for the complexes and fit them to a Gaussian distribution, from which we derive physical parameters such as a glass transition temperature and a specificity transition temperature.
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Submitted on : Thursday, November 12, 2009 - 7:49:16 PM
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Julie Bernauer, Anne Poupon, Jérôme Azé, Joël Janin. A docking analysis of the statistical physics of protein-protein recognition.. Physical Biology, Institute of Physics: Hybrid Open Access, 2005, 2 (2), pp.S17-23. ⟨http://www.iop.org/EJ/article/1478-3975/2/2/S02/ph5_2_s02.pdf⟩. ⟨10.1088/1478-3975/2/2/S02⟩. ⟨inria-00431699⟩



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