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Issue 33, 2015
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Distance measures and evolution of polymer chains in their topological space

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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

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Publication details

The article was received on 16 Jun 2015, accepted on 07 Jul 2015 and first published on 20 Jul 2015


Article type: Paper
DOI: 10.1039/C5SM01482D
Citation: Soft Matter, 2015,11, 6576-6585
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    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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