The Effect of the Viscosity of the Medium on the Molecular Dynamics of the Formation of Secondary Structure of (AlaGly)25 and (AlaGly)75 Polypeptides

Erendjenova, A.A.; Armeev, G.A.; Shaitan, K.V.

Авторы: Erendjenova A.A., Armeev G.A., Shaitan K.V.
Журнал: Biophysics
Том: 65
Номер: 5
Год издания: 2020
Издательство: Maik Nauka/Interperiodica Publishing
Местоположение издательства: Russian Federation
Первая страница: 731
Последняя страница: 735
DOI: 10.1134/S000635092005005X
Аннотация: Abstract—Folding of model polypeptide sequences consisting of 50 and 150 amino-acid residues with the alanineand glycine repeat was explored using Langevin dynamics techniques at different values of the viscosityof a virtual medium. The starting conformations corresponded to a totally extended chain structure. Thechange in the dissipative properties of the medium was simulated under varying parameters of the Langevinthermostat. It is shown that there is a sufficiently high and threshold sensitivity of the result of chain foldingto the viscosity of the medium. The folding of the considered polypeptide sequences when the viscosity of themedium is already on the order of viscosity of liquefied gases occurs mainly in alpha-helical conformations.With a decrease in the effective viscosity of the medium below the critical value, disordered structures areformed. It is noteworthy that in a virtual environment energy effects are not an unambiguous criterion fordetermining conformation as a result of folding of the polypeptide chain. The observed effects of viscosity,which lead to the correlation of conformational motions due to the action of dissipative forces and the selectionof possible conformational relaxation paths of the chain, directly affect the folding result in accordancewith the predictions of the analytic theory.Keywords: molecular dynamics, polypeptides, folding, viscosity, secondary structure, potential energy surfaceDOI: 10.1134/S000635092005005XПеревод русской публикации в журнале Биофизика
Добавил в систему: Шайтан Константин Вольдемарович

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The Effect of the Viscosity of the Medium on the Molecular Dynamics of the Formation of Secondary Structure of (AlaGly)25 and (AlaGly)75 Polypeptidesстатья Исследовательская статья

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