The chain of dihedral angles: How does it rotate in condensed media?

Shaitan, K.V.

Автор: Shaitan K.V.
Журнал: Journal of Bioenergetics and Biomembranes
Год издания: 2018
Издательство: Springer/Plenum Publishers
Местоположение издательства: New York, USA
DOI: 10.1007/s10863-018-9775-7
Аннотация: The mechanics of the conformational motions of chain molecules (peptides, lipids, etc.) in viscous medium are considered. We demonstrate that very complex representative point trajectory in the torsion angles’ configuration space can be described in terms of simple geometrical representations. This approach leads to clear physical picture for collective conformational dynamics and understanding of MD simulation effects. Let us consider the next variables: 1) - the energy-dissipation (ED) rate, - viscous friction coefficient, - the velocity of i-node of the chain (i=1,2,...N). 2) - the rate of change of the potential energy (PE). In the case of the viscous medium (water, etc.) inertial terms are negligible. Thermal fluctuations can be taken into account. Due to conservation energy law we can obtain 3) Eqs. (1) and (3) can be rewritten in terms of standardized velocity components as follows: 1a) ; 3a) Eq. (1a) defines the hypersphere (HSP) of radius 1 with center at 0 in the space of the node velocities. Eq.3a defines the manyfold of HSPs with radius 1/2 and the centers “O” whose distances from the zero point are ½ as well. The center “O” of HSP (3a) rotates around zero point inside HSP (1a) due to conformational dynamics of the chain molecule. The contact point of HSPs (1a) and (3a) moves on the surface of HSP (1a). Time dependence of the contact point coordinates specify the trajectory of the representative point. Two extremal principles for the relaxation of the stressed conformation states can be formulated [1]. The first is – «The rate of PE decrease is maximal at every moment in time». The second is – «The rate of ED is minimal at a given rate of PE decreasing». In the asymptotic limit N>>1 there exists a very useful rule for molecular chain conformation dynamics in viscous medium: “Dihedral angles’ rotations occur in such a way that the average energy dissipation rate is uniformly distributed over all nodes of the molecular chain”. It demonstrates the collective effects for the rotations along the dihedral angles of the chain in a viscous medium, which arise from the action of friction forces only. The work was supported by the RFBR (№ 18-504-12045). 1. Shaitan K.V. Variational Principles in the Mechanics of Conformational Motions of Macromolecules in a Viscous Medium. Biophysics (Moscow), 2018, Vol. 63, No. 1, pp. 1–9. doi: 10.1134/S0006350918010165
Добавил в систему: Шайтан Константин Вольдемарович

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The chain of dihedral angles: How does it rotate in condensed media?статья Электронная публикация

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