In this paper, a stochastic model for the cooperative relaxation of proteins, based on a hierarchic structure of the interactions between amino acids is proposed. It relies on the arbitrary splitting of interactions into two classes, strong and weak, and tests the preponderance of one class over the other. The presented model generalizes a first one valid for homogeneous interactions in the protein molecules previously 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 cooperativity. Moreover, different approximations of the discrete system to a diffusion process, and to a Poisson process are considered, according 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 (Barnase) are reported.

Abundo, M.r., Accardi, L., Stella, L., Rosato, N. (1998). A stochastic model for the cooperative relaxation of proteins, based on a hierarchy of interactions between amino acidic residues. MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES, 8(2), 327-358 [10.1142/S0218202598000147].

A stochastic model for the cooperative relaxation of proteins, based on a hierarchy of interactions between amino acidic residues

ABUNDO, MARIO ROSOLINO;ACCARDI, LUIGI;STELLA, LORENZO;ROSATO, NICOLA
1998-01-01

Abstract

In this paper, a stochastic model for the cooperative relaxation of proteins, based on a hierarchic structure of the interactions between amino acids is proposed. It relies on the arbitrary splitting of interactions into two classes, strong and weak, and tests the preponderance of one class over the other. The presented model generalizes a first one valid for homogeneous interactions in the protein molecules previously 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 cooperativity. Moreover, different approximations of the discrete system to a diffusion process, and to a Poisson process are considered, according 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 (Barnase) are reported.
1998
Pubblicato
Rilevanza internazionale
Articolo
Sì, ma tipo non specificato
Settore MAT/06 - PROBABILITA' E STATISTICA MATEMATICA
English
Con Impact Factor ISI
MOLECULAR-DYNAMICS SIMULATIONS
Abundo, M.r., Accardi, L., Stella, L., Rosato, N. (1998). A stochastic model for the cooperative relaxation of proteins, based on a hierarchy of interactions between amino acidic residues. MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES, 8(2), 327-358 [10.1142/S0218202598000147].
Abundo, Mr; Accardi, L; Stella, L; Rosato, N
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2108/23401
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