Conformational Motion Correlations in the Formation of Polypeptide Secondary Structure in a Viscous Medium

Shaitan, K.V.; Popelenskii, F.Y.; Armeev, G.A.

Авторы: Shaitan K.V., Popelenskii F.Yu, Armeev G.A.
Журнал: Biophysics
Том: 62
Номер: 3
Год издания: 2017
Издательство: Maik Nauka/Interperiodica Publishing
Местоположение издательства: Russian Federation
Первая страница: 348
Последняя страница: 355
DOI: 10.1134/S0006350917030186
Аннотация: Abstract—The Langevin dynamics method and statistical correlation analysis were used to study the α-helical structure folding dynamics of the (Ala)50, (AlaGly)25, and (AlaGly)75 polypeptides depending on the viscosity of the medium. Friction forces that arise when the effective viscosity of the medium is similar to the viscosity of water were found to result in strong correlations between the backbone torsion angles. The polypeptides under study folded mainly to produce α-helical structures. A structure of two contacting α-helices that were approximately equal in length and had a loop between them was observed for a longer chain of 150 residues. A method to visualize the correlation matrix of the dihedral angles of a polypeptide chain was developed for analyzing the effects of the dynamic correlation of conformational degrees of freedom. The analysis of the dynamics of the correlation matrix showed that rotations involving angles of the same type (φ–φ and ψ–ψ) occur predominantly in one direction. Rotations invoving different angles (φ–ψ) occur predominantly in opposite directions, so that the total macromolecule does not rotate. A significant reduction in the effective viscosity of the medium disrupts the correlation and makes the rotations stochastic, thus distorting the formation of the regular (helical) structure. The effects of correlated conformational motions are consequences of viscous friction forces. This conclusion agrees with our previous results that outlined the principle of the minimum rate of energy dissipation and the equipartition of energy dissipation rate between conformational degrees of freedom. Keywords: polypeptides, secondary structure, conformational dynamics, folding, correlation matrices for dihedral angles, correlation analysis of conformational motions in polypeptides, principle of minimum energy dissipation rate, viscosity effects DOI: 10.1134/S0006350917030186 Перевод статьи:БИОФИЗИКА, 2017, том 62, вып. 3, c. 443–451
Добавил в систему: Шайтан Константин Вольдемарович

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Conformational Motion Correlations in the Formation of Polypeptide Secondary Structure in a Viscous Mediumстатья

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