A docking analysis of the statistical physics of protein–protein recognition
Bernauer, Julie; Poupon, Anne; Azé, Jérôme; Janin, Joël; Bernauer, Julie; Yeast Structural Genomics Laboratory, IBBMC UMR CNRS 8619, Bâtiment 430, Université Paris-Sud, 91405-Orsay, France; Poupon, Anne; Yeast Structural Genomics Laboratory, IBBMC UMR CNRS 8619, Bâtiment 430, Université Paris-Sud, 91405-Orsay, France; Azé, Jérôme; Laboratoire de Recherche en Informatique, Bâtiment 490, Université Paris-Sud, 91405-Orsay, France; Janin, Joël; Laboratoire d'Enzymologie et Biochimie Structurales, UPR 9063 CNRS, 91198-Gif-sur-Yvette, France
Журнал:
Physical Biology
Дата:
2005-06-01
Аннотация:
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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