Coarse grained description of the protein folding

Details Coarse grained description of the protein folding Coarse grained description of the protein folding

1998-06-15

arxiv.org/abs/cond-mat/9806178v1

Phys. Rev. E 58, 3589 (1998)

Physics

Condensed Matter

Statistical Mechanics

REVTeX, 9 pages, 15 EPS figures, to appear in Phys. Rev. E

Scientific paper

10.1103/PhysRevE.58.3589

We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of the effective states. The first method is based on the steepest descent mapping of states to underlying local energy minima and the other involves an additional projection to maximally compact conformations. Both methods generate connectivity patterns that allow to distinguish between the good and bad folders. Connectivity graphs corresponding to the folding funnel have few loops and are thus tree-like. The Arrhenius law for the median folding time of a 16-monomer sequence is established and the corresponding barrier is related to easily identifiable kinetic trap states.

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