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