The Topology of the Energy Landscapes of Macromolecules in the Torsion Angle Space and the Principle of the Minimum Energy Dissipation Rate in Conformational Relaxation

Shaitan, K.V.

Автор: Shaitan K.V.
Журнал: Biophysics
Том: 62
Номер: 6
Год издания: 2017
Издательство: Maik Nauka/Interperiodica Publishing
Местоположение издательства: Russian Federation
Первая страница: 892
Последняя страница: 899
DOI: 10.1134/S0006350917060227
Аннотация: Abstract⎯This article discusses some basic problems of structural biology and molecular dynamics simulation methods that need to be taken into account when considering, the protein folding problem, and prediction of 3D-structures for biopolymers. A multidimensional Fourier series expansions were formulated for the energy landscapes of the systems with conformational mobility, These energy landscape representations are correct from the viewpoint of the topology of the macromolecule configuration spaces. The problem of the single global minimum on the energy landscape for proteins is discussed and is formulated in tems of phase rules for the component of Fourier expansions. This rule is formally similar to the problem of diffraction on a multidimensional cubic lattice. The calibration of biopolymer force fields and their correspondence to topologically correct energy landscapes are discussed. Equations of motion were obtained in a matrix form for the relaxation of a representative point position on a multidimensional potential energy surface. The solutions of the equations for conformational relaxation were shown to obey the principle of the minimum energy dissipation rate at a given relaxation rate of potential energy (or folding rate). Keywords: structural biology, molecular dynamics, supercomputer technologies, energy landscapes, topology of the energy surface, Morse theory, conformational mobility, functional dynamics of biopolymers, folding, principle of minimum energy dissipation rate DOI: 10.1134/S0006350917060227 Original Russian Text © K.V. Shaitan, 2017, published in Biofizika, 2017, Vol. 62, No. 6, pp. 1084–1092.
Добавил в систему: Шайтан Константин Вольдемарович

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The Topology of the Energy Landscapes of Macromolecules in the Torsion Angle Space and the Principle of the Minimum Energy Dissipation Rate in Conformational Relaxationстатья

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