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Lipid Membranes for Membrane Proteins

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Molecular Modeling of Proteins

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

Abstract

The molecular dynamics (MD) simulation of membrane proteins requires the setup of an accurate representation of lipid bilayers. This chapter describes the setup of a lipid bilayer system from scratch using generally available tools, starting with a definition of the lipid molecule POPE, generation of a lipid bilayer, energy minimization, MD simulation, and data analysis. The data analysis includes the calculation of area and volume per lipid, deuterium order parameters, self-diffusion constant, and the electron density profile.

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Acknowledgements

This work was supported by the School of Life and Medical Sciences, University of Hertfordshire and has made use of the University of Hertfordshire Science and Technology Research Institute high-performance computing facility. I thank all research groups that made their tools and programs available to the research community.

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Authors and Affiliations

  1. School of Life and Medical Sciences, University of Hertfordshire, College Lane, AL10 9AB, Hatfield, Hertfordshire, UK

    Andreas Kukol

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  1. Andreas Kukol
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Correspondence to Andreas Kukol .

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Editors and Affiliations

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

    Andreas Kukol

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Kukol, A. (2015). Lipid Membranes for 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_4

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  • DOI: https://doi.org/10.1007/978-1-4939-1465-4_4

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1464-7

  • Online ISBN: 978-1-4939-1465-4

  • eBook Packages: Springer Protocols

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