Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems

A. Sofia F. Oliveira (), Giovanni Ciccotti, Shozeb Haider and Adrian J. Mulholland ()
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A. Sofia F. Oliveira: University of Bristol
Giovanni Ciccotti: Institute for Applied Computing “Mauro Picone” (IAC), CNR
Shozeb Haider: University College London
Adrian J. Mulholland: University of Bristol

The European Physical Journal B: Condensed Matter and Complex Systems, 2021, vol. 94, issue 7, 1-12

Abstract: Abstract A dynamical approach to nonequilibrium molecular dynamics (D-NEMD), proposed in the 1970s by Ciccotti et al., is undergoing a renaissance and is having increasing impact in the study of biological macromolecules. This D-NEMD approach, combining MD simulations in stationary (in particular, equilibrium) and nonequilibrium conditions, allows for the determination of the time-dependent structural response of a system using the Kubo–Onsager relation. Besides providing a detailed picture of the system’s dynamic structural response to an external perturbation, this approach also has the advantage that the statistical significance of the response can be assessed. The D-NEMD approach has been used recently to identify a general mechanism of inter-domain signal propagation in nicotinic acetylcholine receptors, and allosteric effects in $$\upbeta $$ β -lactamase enzymes, for example. It complements equilibrium MD and is a very promising approach to identifying and analysing allosteric effects. Here, we review the D-NEMD approach and its application to biomolecular systems, including transporters, receptors, and enzymes. Graphic abstract

Date: 2021
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DOI: 10.1140/epjb/s10051-021-00157-0

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