Multiscale Modeling and Simulation Approaches to Lipid–Protein Interactions

Huber, Roland G., Carpenter, Timothy S., Dube, Namita, Holdbrook, Daniel A., Ingólfsson, Helgi I., Irvine, William A., Marzinek, Jan K., Samsudin, Firdaus, Allison, Jane R., Khalid, Syma and Bond, Peter J. (2019) Multiscale Modeling and Simulation Approaches to Lipid–Protein Interactions. In, Kleinschmidt, J. (ed.) Methods in Molecular Biology. (Methods in Molecular Biology, 2003) New York, NY. Humana New York, pp. 1-30. (doi:10.1007/978-1-4939-9512-7_1).

Abstract

Lipid membranes play a crucial role in living systems by compartmentalizing biological processes and forming a barrier between these processes and the environment. Naturally, a large apparatus of biomolecules is responsible for construction, maintenance, transport, and degradation of these lipid barriers. Additional classes of biomolecules are tasked with transport of specific substances or transduction of signals from the environment across lipid membranes. In this article, we intend to describe a set of techniques that enable one to build accurate models of lipid systems and their associated proteins, and to simulate their dynamics over a variety of time and length scales. We discuss the methods and challenges that allow us to derive structural, mechanistic, and thermodynamic information from these models. We also show how these models have recently been applied in research to study some of the most complex lipid–protein systems to date, including bacterial and viral envelopes, neuronal membranes, and mammalian signaling systems.

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Contributors

Author: Firdaus Samsudin

Author: Syma Khalid

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