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

Author

Listed:
  • A. Sofia F. Oliveira

    (University of Bristol
    BrisSynBio, Life Sciences Building)

  • Giovanni Ciccotti

    (Institute for Applied Computing “Mauro Picone” (IAC), CNR
    University College of Dublin, UCD-Belfield
    Università di Roma La Sapienza)

  • Shozeb Haider

    (University College London)

  • Adrian J. Mulholland

    (University of Bristol)

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

Suggested Citation

  • A. Sofia F. Oliveira & Giovanni Ciccotti & Shozeb Haider & Adrian J. Mulholland, 2021. "Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 94(7), pages 1-12, July.
    • Handle: RePEc:spr:eurphb:v:94:y:2021:i:7:d:10.1140_epjb_s10051-021-00157-0
    DOI: 10.1140/epjb/s10051-021-00157-0
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    1. U. Maskos & B. E. Molles & S. Pons & M. Besson & B. P. Guiard & J.-P. Guilloux & A. Evrard & P. Cazala & A. Cormier & M. Mameli-Engvall & N. Dufour & I. Cloëz-Tayarani & A.-P. Bemelmans & J. Mallet & , 2005. "Nicotine reinforcement and cognition restored by targeted expression of nicotinic receptors," Nature, Nature, vol. 436(7047), pages 103-107, July.
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