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Molecular Dynamics Simulations of Membrane Proteins

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Molecular Modeling of Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1215))

Abstract

Membrane protein structures are underrepresented in the Protein Data Bank (PDB) due to difficulties associated with expression and crystallization. As such, it is one area where computational studies, particularly Molecular Dynamics (MD) simulations, can provide useful additional information. Recently, there has been substantial progress in the simulation of lipid bilayers and membrane proteins embedded within them. Initial efforts at simulating membrane proteins embedded within a lipid bilayer were relatively slow and interactive processes, but recent advances now mean that the setup and running of membrane protein simulations is somewhat more straightforward, though not without its problems. In this chapter, we outline practical methods for setting up and running MD simulations of a membrane protein embedded within a lipid bilayer and discuss methodologies that are likely to contribute future improvements.

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Acknowledgements

We thank the Leverhulme Trust and Unilever for support and Dr Jorge Pikunic for the BtuB coordinates and useful discussions.

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Author notes

  1. Peter J. Bond

    Present address: Department of Chemistry, The Unilever Centre for Molecular Science Informatics, Lensfield Road, Cambridge, CB2 1EW, UK

Authors and Affiliations

  1. Department of Biochemistry, The University of Oxford, South Parks Road, Oxford, OX1 3QU, UK

    Philip C. Biggin

  2. Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore, Singapore

    Peter J. Bond

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Correspondence to Philip C. Biggin .

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  1. University of Hertfordshire, Hatfield, Hertfordshire, United Kingdom

    Andreas Kukol

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Biggin, P.C., Bond, P.J. (2015). Molecular Dynamics Simulations of Membrane Proteins. In: Kukol, A. (eds) Molecular Modeling of Proteins. Methods in Molecular Biology, vol 1215. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1465-4_5

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