title: The simulation approach to lipid-protein interactions.
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.
authors: Department of Chemistry, Unilever Centre for Molecular Informatics, University of Cambridge, Cambridge, UK.
authors: Teresa
authors: T
authors: Paramo
authors: Diana
authors: D
authors: Garzón
authors: Daniel A
authors: DA
authors: Holdbrook
authors: Syma
authors: S
authors: Khalid
authors: Peter J
authors: PJ
authors: Bond
mesh_terms: D000465:Algorithms; D008051:Lipid Bilayers / Q000378:metabolism; D050356:Lipid Metabolism; D008565:Membrane Proteins / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding
chemical_list: D008051:Lipid Bilayers; D008565:Membrane Proteins