Issue 28, 2017

Topology of internally constrained polymer chains


Linear chains with intra-chain contacts can adopt different topologies and allow transitions between them, but it remains unclear how this process can be controlled. This question is important to systems ranging from proteins to chromosomes, which can adopt different conformations that are key to their function and toxicity. Here, we investigate how the topological dynamics of a simple linear chain is affected by interactions with a binding partner, using Monte Carlo and Molecular Dynamics simulations. We show that two point contacts with a binding partner are sufficient to accelerate or decelerate the formation of particular topologies within linear chains. Computed ‘‘folding-time landscapes” that detail the folding time within the topology space show that such contacts deform these landscapes and hence alter the occupation probability of topological states. The results provide a mechanism by which chain topologies can be controlled externally, which opens up the possibility of regulating topological dynamics and the formation of more complex topologies. The findings may have important implications for understanding the mechanism of chaperone action as well as genome architecture and evolution.

Graphical abstract: Topology of internally constrained polymer chains

Supplementary files

Article information

Article type
03 Apr 2017
31 May 2017
First published
05 Jul 2017
This article is Open Access
Creative Commons BY license

Phys. Chem. Chem. Phys., 2017,19, 18389-18393

Topology of internally constrained polymer chains

M. Heidari, V. Satarifard, S. J. Tans, M. R. Ejtehadi, S. Mashaghi and A. Mashaghi, Phys. Chem. Chem. Phys., 2017, 19, 18389 DOI: 10.1039/C7CP02145C

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