title: Atomic-level description of protein-lipid interactions using an accelerated membrane model.
abstract: Peripheral membrane proteins are structurally diverse proteins that are involved in fundamental cellular processes. Their activity of these proteins is frequently modulated through their interaction with cellular membranes, and as a result techniques to study the interfacial interaction between peripheral proteins and the membrane are in high demand. Due to the fluid nature of the membrane and the reversibility of protein-membrane interactions, the experimental study of these systems remains a challenging task. Molecular dynamics simulations offer a suitable approach to study protein-lipid interactions; however, the slow dynamics of the lipids often prevents sufficient sampling of specific membrane-protein interactions in atomistic simulations. To increase lipid dynamics while preserving the atomistic detail of protein-lipid interactions, in the highly mobile membrane-mimetic (HMMM) model the membrane core is replaced by an organic solvent, while short-tailed lipids provide a nearly complete representation of natural lipids at the organic solvent/water interface. Here, we present a brief introduction and a summary of recent applications of the HMMM to study different membrane proteins, complementing the experimental characterization of the presented systems, and we offer a perspective of future applications of the HMMM to study other classes of membrane proteins. This article is part of a Special Issue entitled: Membrane proteins edited by J.C. Gumbart and Sergei Noskov.
authors.affiliation: Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology. Electronic address: baylonc2@illinois.edu.
authors.forename: Javier L
authors.initials: JL
authors.lastname: Baylon
authors.affiliation: Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology. Electronic address: vermaas2@illinois.edu.
authors.forename: Josh V
authors.initials: JV
authors.lastname: Vermaas
authors.affiliation: Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology; College of Medicine. Electronic address: mmulle23@illinois.edu.
authors.forename: Melanie P
authors.initials: MP
authors.lastname: Muller
authors.affiliation: Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology; College of Medicine. Electronic address: marcar2@illinois.edu.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Arcario
authors.affiliation: Beckman Institute for Advanced Science and Technology; School of Chemical Sciences; Department of Chemistry; National Center for Supercomputing Applications. Electronic address: pogorelo@illinois.edu.
authors.forename: Taras V
authors.initials: TV
authors.lastname: Pogorelov
authors.affiliation: Center for Biophysics and Quantitative Biology; Beckman Institute for Advanced Science and Technology; College of Medicine; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801. Electronic address: emad@life.illinois.edu.
authors.forename: Emad
authors.initials: E
authors.lastname: Tajkhorshid
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D008051:Lipid Bilayers / Q000737:chemistry*; D008560:Membrane Fluidity; D008565:Membrane Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods
chemical_list: D008051:Lipid Bilayers; D008565:Membrane Proteins
keywords: Lipids; Membrane; Molecular dynamics; Peripheral proteins