Oliveira, ASF; Ciccotti, G; Haider, S; Mulholland, AJ; (2021) Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems. European Physical Journal B , 94 , Article 144. 10.1140/epjb/s10051-021-00157-0.

Preview

Text Oliveira2021_Article_DynamicalNonequilibriumMolecul.pdf - Published Version Download (2MB) | Preview

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 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.

Download activity - last month

Export as XMLJSONCSV

Download activity - last 12 months

Export as CSVJSONXML

Downloads by country - last 12 months

Export as JSONCSVXML

Archive Staff Only

View Item