title: Peripheral membrane proteins: Tying the knot between experiment and computation.
abstract: Experimental biology has contributed to answer questions about the morphology of a system and how molecules organize themselves to maintain a healthy functional cell. Single-molecule techniques, optical and magnetic experiments, and fluorescence microscopy have come a long way to probe structural and dynamical information at multiple scales. However, some details are simply too small or the processes are too short-lived to detect by experiments. Computational biology provides a bridge to understand experimental results at the molecular level, makes predictions that have not been seen in vivo, and motivates new fields of research. This review focuses on the advances on peripheral membrane proteins (PMPs) studies; what is known about their interaction with membranes, their role in cell biology, and some limitations that both experiment and computation still have to overcome to gain better structural and functional understanding of these PMPs. As many recent reviews have acknowledged, interdisciplinary efforts between experiment and computation are needed in order to have useful models that lead future directions in the study of PMPs. We present new results of a case study on a PMP that behaves as an intricate machine controlling lipid homeostasis between cellular organelles, Osh4 in yeast Saccharomyces cerevisiae. Molecular dynamics simulations were run to examine the interaction between the protein and membrane models that reflect the lipid diversity of the endoplasmic reticulum and trans-Golgi membranes. Our study is consistent with experimental data showing several residues that interact to smaller or larger extent with the bilayer upon stable binding (~200 ns into the trajectory). We identified PHE239 as a key residue stabilizing the protein-membrane interaction along with two other binding regions, the ALPS-like motif and the β6-β7 loops in the mouth region of the protein. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
authors.affiliation: Department of Chemical and Biomolecular Engineering, College Park, MD 20742, USA.
authors.forename: Viviana
authors.initials: V
authors.lastname: Monje-Galvan
authors.affiliation: Department of Chemical and Biomolecular Engineering, College Park, MD 20742, USA; Biophysics Program, University of Maryland, College Park, MD 20742, USA. Electronic address: jbklauda@umd.edu.
authors.forename: Jeffery B
authors.initials: JB
authors.lastname: Klauda
mesh_terms: D001665:Binding Sites; D002462:Cell Membrane / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D008051:Lipid Bilayers / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods; D011987:Receptors, Steroid / Q000737:chemistry / Q000648:ultrastructure; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000648:ultrastructure; D000098825:Oxysterol Binding Proteins
chemical_list: D008051:Lipid Bilayers; D008565:Membrane Proteins; D011987:Receptors, Steroid; D029701:Saccharomyces cerevisiae Proteins; C087901:KES1 protein, S cerevisiae; D000098825:Oxysterol Binding Proteins
keywords: Lipid transport proteins; Molecular dynamics; Osh4; Protein–lipid interactions