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Molecular Dynamics of Membrane Peptides and Proteins: Principles and Comparison to Experimental Data

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Membrane Protein Structure Determination

Part of the book series: Methods in Molecular Biology ((MIMB,volume 654))

Abstract

Molecular dynamics (MD) simulation is a standard tool used to assess the motion of biomolecules at atomic resolution. It requires a so-called “force field” that allows the evaluation of an empirical energy from the 3D coordinates of the atoms in the system. In this chapter, the application of MD simulations to membrane proteins and peptides is described with a particular emphasis on the comparison of MD results to experimental data. Such a comparison can be used either for (1) validating the results of a simulation, (2) interpreting an experiment at the atomic level, or (3) calibrating the force field. This last step is particularly important for the use of MD as a predictive tool. As an illustration, a comparison of 2H NMR experiments to MD simulations of a transmembrane peptide is presented and discussed.

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  1. Equipe de Bioinformatique Génomique et Moléculaire, INSERM UMR-S726, Institut National de Transfusion Sanguine, Université Paris Diderot – Paris 7, Paris, France

    Patrick F. J. Fuchs

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Correspondence to Patrick F. J. Fuchs .

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  1. , Université Paris Diderot - Paris 7, INSERM U773/CRB3, rue Henri Huchard 16, Paris, 75018, France

    Jean-Jacques Lacapère

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Fuchs, P.F.J. (2010). Molecular Dynamics of Membrane Peptides and Proteins: Principles and Comparison to Experimental Data. In: Lacapère, JJ. (eds) Membrane Protein Structure Determination. Methods in Molecular Biology, vol 654. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-762-4_21

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  • DOI: https://doi.org/10.1007/978-1-60761-762-4_21

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-761-7

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