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Hidden Symmetry Effects in the Dynamics of Linear Polymers and Biopolymersстатья Исследовательская статья
- Автор: Shaitan K.V.
- Журнал: Biophysics
- Том: 67
- Номер: 3
- Год издания: 2022
- Издательство: Maik Nauka/Interperiodica Publishing
- Местоположение издательства: Russian Federation
- Первая страница: 386
- Последняя страница: 405
- Переводные версии: Эффекты скрытой симметрии в динамике линейных полимеров и биополимеров
- DOI: 10.1134/S0006350922030204
- Аннотация: Abstract—The effects of two types of symmetry for linear polymers are considered: spatial symmetry with respect to translations and rotation of the macromolecule as a whole in a homogeneous viscous medium, and symmetry with respect to permutations of identical monomer units (or sections of the polymer chain with thesame chemical structure) in the chain. It is shown that, in a homogeneous viscous medium, for a macromolecule with rigid bonds during relaxation folding, the conservation law is obeyed—the sum of the rotation velocity vectors around torsion angles is equal to zero. Symmetry with respect to permutations of identicalmonomer units in the polymer chain under certain conditions leads to the formation of energy funnels withthe minimal frustration which correspond to helical or multihelical 3D-structures of polymer chain. In this case, there exist the deepest central funnel and less deep satellite funnels, which all are separated from each other by energy barriers. This topography of the energy funnel corresponds to a number of effects that are observed in the kinetics of protein folding (a volcano-like profile of the free energy surface, the sensitivity of protein refolding to denaturing steps, etc.). When calculating the topography of the free energy surface, thecharacteristic temperature parameter T0 arises and this is defined as potential energy gain due to chain foldingper one conformational degree of freedom. It is shown that at T > 0.26 T0, the spatial structure of the folded polymer is destroyed. The parameter T0 and the denaturation temperature in the system under consideration arise from the basic mathematical principles of the arrangement of energy landscapes in the configurationspace of torsion angles with the topology of a multidimensional torus and symmetry сonsiderations regarding the permutation of identical monomer units. At biopolymer denaturation temperatures, for example, on theorder of 60°C, this ratio leads to an estimate of the energy of nonvalent bonds of monomers on the order of 2.5 kcal/mol per one conformational degree of freedom, which is very similar to hydrogen bonds in aqueous medium. The two types of symmetries under study and their influence on the dynamics of macromolecules and the topography of the energy landscapes of linear polymers can occur simultaneously under certain conditions.The effects that come with it may provide additional information about the prebiological physicochemical evolution of macromolecules in association with the formation of a pool of linear polymers with unique spatial structures.Keywords: regularities in the dynamics of linear polymers in a viscous medium, energy landscapes of linear polymers and biopolymers, spatial structure of biopolymers, folding dynamics, minimum frustration principle for an energy funnel, problems of calibration of force fields, multidimensional Fourier series, free energyof biopolymers, critical temperature of denaturation, physicochemical molecular evolutionDOI: 10.1134/S0006350922030204
- Добавил в систему: Шайтан Константин Вольдемарович
Прикрепленные файлы
| № | Имя | Описание | Имя файла | Размер | Добавлен |
|---|---|---|---|---|---|
| 1. | Полный текст | пдф | BPHS386_dBRXSAO.pdf | 2,2 МБ | 24 августа 2022 [ShaitanKV] |