Journal
EUROPEAN PHYSICAL JOURNAL B
Volume 94, Issue 7, Pages -Publisher
SPRINGER
DOI: 10.1140/epjb/s10051-021-00157-0
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Funding
- EPSRC [EP/M022609/1]
- BBSRC/EPSRC Synthetic Biology Research Centre- ASFO [BB/L01386X/1]
- National Institutes of Health (USA) [RO1AI063517]
- Astra Zeneca-EPSRC
- EPSRC [EP/M022609/1] Funding Source: UKRI
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The D-NEMD approach combines molecular dynamics simulations under equilibrium and nonequilibrium conditions to determine the dynamic structural response of a system, and assess the statistical significance of the response. It has been recently applied to identify different mechanisms in biological macromolecular systems, making it a promising research approach.
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 beta-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.
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