Molecular dynamics of membrane peptides and proteins: principles and comparison to experimental data.
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 (2)H NMR experiments to MD simulations of a transmembrane peptide is presented and discussed.
Fuchs
Patrick F J
PF
Equipe de Bioinformatique Génomique et Moléculaire, INSERM UMR-S726, Institut National de Transfusion Sanguine, Université Paris Diderot - Paris 7, Paris, France. patrick.fuchs@univ-paris-diderot.fr
D009682:Magnetic Resonance Spectroscopy; D008565:Membrane Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D012984:Software
D008565:Membrane Proteins; D010455:Peptides