Acta Physica Polonica B

Vol. 38, No. 5, May 2007, page 1899


Thermodynamic Properties of Polypeptide Chains. Parallel Tempering Monte Carlo Simulations

A. Sikorski, D. Gront

A coarse-grained model of polypeptide chains was designed and studied. The chains consisted of united atoms located at the position of alpha carbons and the coordinates of these atoms were restricted to a [310] type lattice. Two kinds of amino acids residues were defined: hydrophilic and hydrophobic ones. The sequence of the residues was assumed to be characteristic for \alpha -helical proteins (the helical septet). The force field used consisted of the long-range contact potential between residues and the local potential preferring conformational states, which were characteristic for \alpha -helices. In order to study the thermodynamics of our model we employed the Multi-histogram method combined with the Parallel Tempering (the Replica Exchange) Monte Carlo sampling scheme. The optimal set of temperatures for the Parallel Tempering simulations was found by an iterative procedure. The influence of the temperature and the force field on the properties of coil-to-globule transition was studied. It was shown that this method can give more precise results when compared to Metropolis and Replica Exchange methods.

PACS numbers: 02.50.Ng, 02.70.Tt, 87.15.Aa



 
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