The Relaxation Model of Ideal Folding in a Homogeneous Viscous Medium
Shaitan, K.V.
Biofizika 60(5): 843-852
2015
ISSN/ISBN: 0006-3029 PMID: 26591594 Document Number: 684970
The problem of 3D biopolymer structure formation is investigated by the methods of a theory of stochastic dynamics. The variational principle for. elementary displacement and velocity of conformational movements and its implications for the folding process of the polymer chain in a viscous medium are formulated. The result is a most smooth decrease in potential energy during conformational relaxation of the system (a timid mountain-skier principle), which is in consistence with the Onsager principle for kinetics in weakly nonequilibrium systems. The model is in accordance with the results of molecular simulations of the similar systems. The relationship between the structure of the multidimensional potential energy surface and folding kinetics is discussed. The model of a parabolic energy funnel formed by non-bonded interactions is developed. The folding kinetics in the parabolic model of energy funnel is almost close to exponential law.