Why Do Proteins Fold into Unique 3D Structures? And Other Questions

Shaitan, K.V.

Автор: Shaitan K.V.
Журнал: Russian Journal of Physical Chemistry B
Том: 17
Номер: 3
Год издания: 2023
Издательство: Maik Nauka/Interperiodica Publishing
Местоположение издательства: Russian Federation
Первая страница: 550
Последняя страница: 570
Переводные версии: ПОЧЕМУ БЕЛОК СВОРАЧИВАЕТСЯ В УНИКАЛЬНУЮ 3D-СТРУКТУРУ? И НЕ ТОЛЬКО ЭТО…
DOI: 10.1134/S1990793123030259
Аннотация: Abstract—The article briefly reviews the history of the development of ideas about the dynamics of proteinsand other biopolymers and notes the significant contribution of V.I. Goldansky in organizing and conductingthese studies in Russia. The modern development of earlier ideas about the dynamics of biopolymers and proteinfolding is discussed. It is shown that folding is not an isolated problem and is related to the fundamentaldynamic properties of linear polymers in the condensed phase. Analytical methods using approaches basedon multidimensional geometry show that the viscosity of the medium is one of the most important factorsthat determines the rules for the movement of a representative point along the ultramultidimensional potentialenergy surface (PES). These rules lead to the concentration of trajectories in those regions of the configurationspace of a macromolecule that correspond to relatively smooth PES regions, which is important forunderstanding the reasons for the stability of the results of calculations of large systems using the moleculardynamics (MD) method, despite the fundamental inaccuracy in determining the available force fields. Thisarticle also briefly describes a new approach to determine and study the properties of a multidimensionalPES, which is based on the features of the topology of the configuration space of linear polymers (and biopolymers),symmetry with respect to permutations of identical chain links, and Morse theory for studying thetopography of multidimensional surfaces. Under certain conditions, this approach gives observable analyticalresults for the topography of the PES and the free energy surface (FES) of a macromolecule and makes it possibleto relate the rather heterogeneous results of experiments on protein folding from a unified point of view.At the same time, a new formulation appears for a number of fundamental and controversial issues related tothe physical laws of the formation of living systems. In particular, a connection is traced between the temperatureregime on the planet and the chemical realization of the energy of nonvalent interactions in a macromolecule,which are necessary for the formation of unique spatial structures of biopolymers.Keywords: protein dynamics, potential energy surface, energy landscapes, symmetry and viscosity, proteinfolding and refolding, polymer molecular dynamics, force fields, arrow of physicochemical molecular evolution
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Why Do Proteins Fold into Unique 3D Structures? And Other Questionsстатья

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