title: Towards realistic description of collective motions in the lattice protein folding models.
abstract: Collective motions and the formation of clusters of residues play an important role in the folding of real proteins. However, existing Monte Carlo (MC) techniques of the protein folding simulations based on highly popular lattice models provide only a schematic representation of collective motions, which is rather far from physical reality. The Clustering Monte Carlo (CMC) algorithm was developed with particular aim to provide a realistic description of collective motions on the lattice. CMC allows modeling the cluster dynamics and the effects of the solvent viscosity, which is impossible in conventional algorithms. In this study two 2D lattice peptides, with the ground states of hierarchical and non-hierarchical design, were investigated comparatively using three methods: Metropolis MC with the local move set, Metropolis MC with unspecific rigid rotations and the CMC algorithm. We present evidence that the folding pathways and kinetics of hierarchically folding clustered sequence are not adequately described in conventional MC simulations, and the account for cluster dynamics provided by CMC allows to capture essential features of the folding process. Our data suggest that the methods, which enable specific cluster motions, such as CMC, should be used for a more realistic description of protein folding.
authors.affiliation: A.V. Palladin Institute of Biochemistry, Leontovicha Street 9, Kiev 01030, Ukraine.
authors.forename: S O
authors.initials: SO
authors.lastname: Yesylevskyy
authors.forename: A P
authors.initials: AP
authors.lastname: Demchenko
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D008958:Models, Molecular; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D013816:Thermodynamics
chemical_list: D010455:Peptides