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Computer Simulations of Membrane Proteins

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Book cover Membrane Organization and Dynamics

Part of the book series: Springer Series in Biophysics ((BIOPHYSICS,volume 20))

Abstract

Developments in computational algorithms and structure-determination technologies have enabled molecular dynamics simulations to become a routine tool to investigate the structure and dynamics of biological membranes and membrane proteins in great detail. In this chapter, we provide an overview of atomistic molecular dynamics simulations and related methods, such as coarse-grain simulations and biased sampling methods, and illustrate using key examples how such methods have advanced our understanding in the field of membrane protein biophysics. We exemplify how MD simulations have provided insights into selective permeation mechanisms through lipid bilayers and ion channels, as well as conformational changes associated with transport in both G-protein coupled receptors and membrane transporters.

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Acknowledgements

C.J. thanks King’s College London for a Graduate Teaching Assistant (GTA) studentship. V.O. acknowledges a BBSRC-CASE studentship, in association with Pfizer Neusentis. C.D. acknowledges use of ARCHER, the UK National Supercomputing Service, the National Service for Computational Chemistry Software (NSCCS) and the Hartree Center. Research in the Domene group is supported by the Engineer and Physical Sciences Research Council (EPSRC) and the Biotechnology and Biological Sciences Research Council (BBSRC).

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  1. Department of Chemistry, King’s College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK

    Christian Jorgensen, Victoria Oakes & Carmen Domene

  2. Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK

    Carmen Domene

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    Amitabha Chattopadhyay

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Jorgensen, C., Oakes, V., Domene, C. (2017). Computer Simulations of Membrane Proteins. In: Chattopadhyay, A. (eds) Membrane Organization and Dynamics . Springer Series in Biophysics, vol 20. Springer, Cham. https://doi.org/10.1007/978-3-319-66601-3_15

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