title: Molecular mechanism of membrane binding of the GRP1 PH domain.
abstract: The pleckstrin homology (PH) domain of the general receptor of phosphoinositides 1 (GRP1) protein selectively binds to a rare signaling phospholipid, phosphatidylinositol (3,4,5)-trisphosphate (PIP3), in the membrane. The specific PIP3 lipid docking of GRP1 PH domain is essential to protein cellular function and is believed to occur in a stepwise process, electrostatic-driven membrane association followed by the specific PIP3 binding. By a combination of all-atom molecular dynamics (MD) simulations, coarse-grained analysis, electron paramagnetic resonance (EPR) membrane docking geometry, and fluorescence resonance energy transfer (FRET) kinetic studies, we have investigated the search and bind process in the GRP1 PH domain at the molecular scale. We simulated the two membrane binding states of the GRP1 PH domain in the PIP3 search process, before and after the GRP1 PH domain docks with the PIP3 lipid. Our results suggest that the background anionic phosphatidylserine lipids, which constitute around one-fifth of the membrane by composition, play a critical role in the initial stages of recruiting protein to the membrane surface through non-specific electrostatic interactions. Our data also reveal a previously unseen transient membrane association mechanism that is proposed to enable a two-dimensional "hopping" search of the membrane surface for the rare PIP3 target lipid. We further modeled the PIP3-bound membrane-protein system using the EPR membrane docking structure for the MD simulations, quantitatively validating the EPR membrane docking structure and augmenting our understanding of the binding interface with atomic-level detail. Several observations and hypotheses reached from our MD simulations are also supported by experimental kinetic studies.
authors.affiliation: Department of Chemistry, Institute of Biophysical Dynamics, James Franck Institute, and Computation Institute, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Chun-Liang
authors.initials: CL
authors.lastname: Lai
authors.forename: Anand
authors.initials: A
authors.lastname: Srivastava
authors.forename: Carissa
authors.initials: C
authors.lastname: Pilling
authors.forename: Anna R
authors.initials: AR
authors.lastname: Chase
authors.forename: Joseph J
authors.initials: JJ
authors.lastname: Falke
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Voth
mesh_terms: D001798:Blood Proteins / Q000737:chemistry / Q000378:metabolism; D002462:Cell Membrane / Q000378:metabolism; D007700:Kinetics; D008051:Lipid Bilayers / Q000737:chemistry* / Q000378:metabolism*; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D018129:Phosphatidylinositol Phosphates / Q000737:chemistry / Q000378:metabolism; D010718:Phosphatidylserines / Q000737:chemistry / Q000378:metabolism; D010743:Phospholipids / Q000737:chemistry / Q000378:metabolism; D010750:Phosphoproteins / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D018160:Receptors, Cytoplasmic and Nuclear / Q000737:chemistry* / Q000378:metabolism*; D055672:Static Electricity
chemical_list: D001798:Blood Proteins; D008051:Lipid Bilayers; D008565:Membrane Proteins; D018129:Phosphatidylinositol Phosphates; D010718:Phosphatidylserines; D010743:Phospholipids; D010750:Phosphoproteins; D018160:Receptors, Cytoplasmic and Nuclear; C040985:phosphatidylinositol receptors; C039077:platelet protein P47
keywords: CG; ENTH; EPR; Epsin N-terminal homology; FRET; GRP1; MD; PDB; PH; PIP(2); PIP(3); PS; Protein Data Bank; RMSF; anionic lipids; coarse-grained; electron paramagnetic resonance; fluorescence resonance energy transfer; general receptor of phosphoinositides 1; membrane targeting; molecular dynamics; peripheral membrane protein; phosphatidylinositol (3,4,5)-trisphosphate; phosphatidylinositol (4,5)-bisphosphate; phosphatidylinositol-3,4,5-trisphosphate or PIP(3); phosphatidylserine; pleckstrin homology; pleckstrin homology domain; root-mean-square fluctuation