Issue 33, 2015

Distance measures and evolution of polymer chains in their topological space

Abstract

Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational transitions that are associated with changes in molecular topology. For folded linear biomolecules, arrangement of intramolecular contacts is identified as a key topological property, termed as circuit topology. Distance measures are proposed as reaction coordinates to represent progress along a pathway from initial topology to final topology. Certain topological classes are shown to be more accessible from a random topology. We study dynamic stability and pathway degeneracy associated with a topological reaction and found that off-pathways might seriously hamper evolution to desired topologies. Finally we present an algorithm for estimating the number of intermediate topologies visited during a topological reaction. The results of this study are relevant to, among others, structural studies of RNA and proteins, analysis of topologically associated domains in chromosomes, and molecular evolution.

Graphical abstract: Distance measures and evolution of polymer chains in their topological space

Supplementary files

Article information

Article type
Paper
Submitted
16 Jun 2015
Accepted
07 Jul 2015
First published
20 Jul 2015

Soft Matter, 2015,11, 6576-6585

Distance measures and evolution of polymer chains in their topological space

A. Mashaghi and A. Ramezanpour, Soft Matter, 2015, 11, 6576 DOI: 10.1039/C5SM01482D

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