Formation of collective conformational degrees of freedom during macromolecular chain folding dynamics in a viscous medium

Abstract

Computational methods were used to study the dynamics of the formation of the collective conformational degrees of freedom in the relaxation folding of a model biopolymer chain of 50 nodes in a viscous medium; the model has been described previously. Collective conformational motions of the nodes were shown to arise due to friction forces in a viscous medium. The collective motions have several typical forms, including a wave of differently directed motions of chain nodes that propagates from one end of the chain to another (like a soliton) in response to a pertubation in terminal group position. Individual nodes located at the middle of the chain make approximately equal contributions to the total energy dissipation rate. The end nodes contribute approximately 2–4 times more than internal nodes to the total energy dissipation. The results of numerical experiments are consistent with the theoretical concept developed earlier to describe the dynamics of linear macromolecular chains in a viscous medium in the limit of a very large number of nodes.