Biopolym. Cell. 2004; 20(3):244-254.
http://dx.doi.org/10.7124/bc.0006AC
Molecular Biophysics
Clustering Monte Carlo simulations of the hierarchical protein folding on a simple lattice model
1Yesylevskyy S. O., 1, 2Demchenko A. P.
  1. Palladin Institute of Biochemistry, NAS of Ukraine
    9, Leontovycha Str., Kyiv, Ukraine, 01601
  2. TUBITAK - Genetics Engineering and Biotechnology Institute of Turkey
    41470 Gebze / Kocaeli, Turkey

Abstract

A role of specific collective motions and clustering behavior in protein folding was investigated using simple 2D lattice models. Two model peptides, which have the sequences of hierarchical and non-hierarchical design, were studied comparatively. Simulations were performed using three methods: Metropolis Monte Carlo with the local move set, Metropolis Monte Carlo with unspecific rigid rotations, and the Clustering Monte Carlo (CMC) algorithm that has been recently described by the authors. The latter was developed with particular aim to provide a realistic description of cluster dynamics. We present convincing evidence that the folding pathways and kinetics of hierarchically folding sequence are not adequately described in conventional MC simulations. In this case the account for cluster dynamics provided by CMC algorithm reveals important features of folding of hierarchically organized sequences. Our data suggest that the methods, which enable specific cluster motions, should be used for realistic description of hierarchical folding.
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