A STOCHASTIC-MODEL FOR THE COOPERATIVE RELAXATION OF PROTEINS, BASED ON A HIERARCHY OF INTERACTIONS BETWEEN AMINO ACIDIC RESIDUES

In this paper, a stochastic model for the cooperative relaxation of pr oteins, based on a hierarchic structure of the interactions between am ino acids is proposed. It relies on the arbitrary splitting of interac tions into two classes, strong and weak, and tests the preponderance o f one class over the other. The presented model generalizes a first on e valid for homogeneous interactions in the protein molecules previous ly studied by the authors. The time evolution of the system is studied as a function of five parameters, three of which are related to the c ooperativity. Moreover, different approximations of the discrete syste m to a diffusion process, and to a Poisson process are considered, acc ording to the magnitude of the parameters. A method for estimating the parameters from real data is proposed. Finally, numerical simulations and a comparison with the molecular dynamics of a real protein (Barna se) are reported.