Abstract
We review foundations of biomolecular simulations that enable the study of membrane protein models with a particular focus on structure–function relationships and opportunities for drug design. A range of broadly used methods is presented comprising homology modeling, normal mode analysis, molecular dynamics simulations, and free energy calculations. These methods are illustrated with examples on several membrane protein systems, in particular ligand-gated ion channels such as the P2X receptors, the N-methyl-d-aspartate (NMDA) receptors, and the Cys-loop family of pentameric ion channels.
An erratum to this chapter can be found at http://dx.doi.org/10.1007/978-1-4939-0662-8_15
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Acknowledgments
M.B. thanks the French Agency for Research for funding (Grant ANR-07-CIS7-003-01). This work was supported by the “Initiative d’Excellence” program from the French State (Grant “DYNAMO”, ANR-11-LABX-0011). Benoist Laurent and Samuel Murail are acknowledged for contribution to several figures.
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Hénin, J., Baaden, M., Taly, A. (2014). Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins. In: Mus-Veteau, I. (eds) Membrane Proteins Production for Structural Analysis. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-0662-8_13
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