Conformational rigidity in a lattice model of proteins.
It is shown in this paper that some simulations of protein folding in lattice models, which use an incorrect implementation of the Monte Carlo algorithm, do not converge towards thermal equilibrium. I developed a rigorous treatment for protein folding simulation on a lattice model relying on the introduction of a parameter standing for the rigidity of the conformations. Its properties are discussed and its role during the folding process is elucidated. The calculation of thermal properties of small chains living on a two-dimensional lattice is performed and a Bortz-Kalos-Lebowitz scheme is implemented in the presented method in order to study kinetics of chains at very low temperature. The coefficients of the Arrhenius law obtained with this algorithm are found to be in excellent agreement with the value of the main potential barrier of the system. Finally, a scenario of the mechanisms, including the rigidity parameters, that guide a protein towards its native structure, at medium temperature, is given.
Collet
Olivier
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Equipe de Dynamique des Assemblages Membranaires, UMR CNRS 7565, Faculté des Sciences, Université Henri Poincaré-Nancy 1,Vandoeuvre-lès-Nancy, France.
D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D007700:Kinetics; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009010:Monte Carlo Method; D016011:Normal Distribution; D011108:Polymers / Q000737:chemistry; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D013696:Temperature; D013816:Thermodynamics
D011108:Polymers; D011506:Proteins; D012997:Solvents