A docking analysis of the statistical physics of protein-protein recognition.
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.
Bernauer
Julie
J
Yeast Structural Genomics Laboratory, IBBMC UMR CNRS 8619, Bâtiment 430, Université Paris-Sud, 91405-Orsay, France.
Poupon
Anne
A
Azé
Jérôme
J
Janin
Joël
J
D001703:Biophysics / Q000379:methods*; D002468:Cell Physiological Phenomena; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D030562:Databases, Protein; D005898:Glass; D015233:Models, Statistical; D008968:Molecular Conformation; D016011:Normal Distribution; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D013696:Temperature