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Issue 41, 2014
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Circuit topology of self-interacting chains: implications for folding and unfolding dynamics

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Abstract

Understanding the relationship between molecular structure and folding is a central problem in disciplines ranging from biology to polymer physics and DNA origami. Topology can be a powerful tool to address this question. For a folded linear chain, the arrangement of intra-chain contacts is a topological property because rearranging the contacts requires discontinuous deformations. Conversely, the topology is preserved when continuously stretching the chain while maintaining the contact arrangement. Here we investigate how the folding and unfolding of linear chains with binary contacts is guided by the topology of contact arrangements. We formalize the topology by describing the relations between any two contacts in the structure, which for a linear chain can either be in parallel, in series, or crossing each other. We show that even when other determinants of folding rate such as contact order and size are kept constant, this ‘circuit’ topology determines folding kinetics. In particular, we find that the folding rate increases with the fractions of parallel and crossed relations. Moreover, we show how circuit topology constrains the conformational phase space explored during folding and unfolding: the number of forbidden unfolding transitions is found to increase with the fraction of parallel relations and to decrease with the fraction of series relations. Finally, we find that circuit topology influences whether distinct intermediate states are present, with crossed contacts being the key factor. The approach presented here can be more generally applied to questions on molecular dynamics, evolutionary biology, molecular engineering, and single-molecule biophysics.

Graphical abstract: Circuit topology of self-interacting chains: implications for folding and unfolding dynamics

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Publication details

The article was received on 30 Jul 2014, accepted on 08 Sep 2014 and first published on 17 Sep 2014


Article type: Paper
DOI: 10.1039/C4CP03402C
Citation: Phys. Chem. Chem. Phys., 2014,16, 22537-22544
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    Circuit topology of self-interacting chains: implications for folding and unfolding dynamics

    A. Mugler, S. J. Tans and A. Mashaghi, Phys. Chem. Chem. Phys., 2014, 16, 22537
    DOI: 10.1039/C4CP03402C

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