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Lipid-Protein Interactions pp 435–455Cite as

The Simulation Approach to Lipid–Protein Interactions

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 974))

Abstract

The interactions between lipids and proteins are crucial for a range of biological processes, from the folding and stability of membrane proteins to signaling and metabolism facilitated by lipid-binding proteins. However, high-resolution structural details concerning functional lipid/protein interactions are scarce due to barriers in both experimental isolation of native lipid-bound complexes and subsequent biophysical characterization. The molecular dynamics (MD) simulation approach provides a means to complement available structural data, yielding dynamic, structural, and thermodynamic data for a protein embedded within a physiologically realistic, modelled lipid environment. In this chapter, we provide a guide to current methods for setting up and running simulations of membrane proteins and soluble, lipid-binding proteins, using standard atomistically detailed representations, as well as simplified, coarse-grained models. In addition, we outline recent studies that illustrate the power of the simulation approach in the context of biologically relevant lipid/protein interactions.

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Authors and Affiliations

  1. Department of Chemistry, Unilever Centre for Molecular Informatics, University of Cambridge, Cambridge, UK

    Teresa Paramo & Peter J. Bond

  2. Theoretische Molekulare Biophysik, Max Planck Institute of Biophysics, Frankfurt am Main, Germany

    Diana Garzón

  3. School of Chemistry, University of Southampton, Highfield, Southampton, UK

    Daniel A. Holdbrook & Syma Khalid

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  1. Teresa Paramo
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  2. Diana Garzón
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  3. Daniel A. Holdbrook
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  4. Syma Khalid
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  5. Peter J. Bond
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Correspondence to Peter J. Bond .

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Editors and Affiliations

  1. Institut für Biologie, Abteilung Biophysik, Universität Kassel, Heinrich-Plett-Straße 40, Kassel, 34132, Germany

    Jörg H. Kleinschmidt

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Paramo, T., Garzón, D., Holdbrook, D.A., Khalid, S., Bond, P.J. (2013). The Simulation Approach to Lipid–Protein Interactions. In: Kleinschmidt, J. (eds) Lipid-Protein Interactions. Methods in Molecular Biology, vol 974. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-275-9_19

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  • DOI: https://doi.org/10.1007/978-1-62703-275-9_19

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-274-2

  • Online ISBN: 978-1-62703-275-9

  • eBook Packages: Springer Protocols

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