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Exploring biomolecular energy landscapes

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Abstract

The potential energy landscape perspective provides both a conceptual and a computational framework for predicting, understanding and designing molecular properties. In this Feature Article, we highlight some recent advances that greatly facilitate structure prediction and analysis of global thermodynamics and kinetics in proteins and nucleic acids. The geometry optimisation procedures, on which these calculations are based, can be accelerated significantly using local rigidification of selected degrees of freedom, and through implementations on graphics processing units. Results of progressive local rigidification are first summarised for trpzip1, including a systematic analysis of the heat capacity and rearrangement rates. Benchmarks for all the essential optimisation procedures are then provided for a variety of proteins. Applications are then illustrated from a study of how mutation affects the energy landscape for a coiled-coil protein, and for transitions in helix morphology for a DNA duplex. Both systems exhibit an intrinsically multifunnel landscape, with the potential to act as biomolecular switches.

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Publication details

The article was received on 29 Mar 2017, accepted on 02 May 2017 and first published on 02 May 2017


Article type: Feature Article
DOI: 10.1039/C7CC02413D
Citation: Chem. Commun., 2017, Advance Article
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    Exploring biomolecular energy landscapes

    J. A. Joseph, K. Röder, D. Chakraborty, R. G. Mantell and D. J. Wales, Chem. Commun., 2017, Advance Article , DOI: 10.1039/C7CC02413D

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