Molecular dynamics simulations of bovine rhodopsin: influence of protonation states and different membrane-mimicking environments

Abstract

G-protein coupled receptors (GPCRs) are a protein family of outstanding pharmaceutical interest. GPCR homology models, based on the crystal structure of bovine rhodopsin, have been shown to be valuable tools in the drug-design process. The initial model is often refined by molecular dynamics (MD) simulations, a procedure that has been recently discussed controversially. We therefore analyzed MD simulations of bovine rhodopsin in order to identify contacts that could serve as constraints in the simulation of homology models. Additionally, the effect of an N-terminal truncation, the nature of the membrane mimic, the influence of varying protonation states of buried residues and the importance of internal water molecules was analyzed. All simulations were carried out using the program-package GROMACS. While N-terminal truncation negatively influenced the overall protein stability, a stable simulation was possible in both solvent environments. As regards the protonation state of titratable sites, the experimental data could be reproduced by the program UHBD (University of Houston Brownian Dynamics), suggesting its application for studying homology models of GPCRs. A high flexibility was observed for internal water molecules at some sites. Finally, interhelical hydrogen-bonding interactions could be derived, which can now serve as constraints in the simulations of GPCR homology models.

Generation of a homology model of the human histamine H3 receptor for ligand docking and pharmacophore-based screening

“…In order to avoid model deterioration, which is frequently observed during completely unconstrained MD simulation, [47] conserved interhelical hydrogen bond contacts, which have been previously analysed in simulations of a model of bovine rhodopsin [35], were preserved via the incorporation of distance constraints during the simulations.…”

“…A CCl 4 /solvent box of the dimensions 8.56 · 6.45 · 9.01 nm was generated and the hH 3 R models were simulated without applying any constraints on the model. The generation and equilibration of the CCl 4 /solvent box, the insertion of the receptor into this box and the subsequent simulation of the receptor were carried out in analogy to the simulation of bovine rhodospin in a CCl 4 /solvent box (see [35] for details).…”

“…The insertion of the ligand receptor complex into this membrane mimic, details on equilibration and simulations are described in reference [35] for the analogue simulation of bovine rhodopsin. During the simulation of the FUB836/hH 3 R model the following interhelical hydrogen bond contacts were restrained by applying the following Fig.…”

Allosteric Interactions with Muscarinic Acetylcholine Receptors: Complex Role of the Conserved Tryptophan M2422Trp in a Critical Cluster of Amino Acids for Baseline Affinity, Subtype Selectivity, and Cooperativity

“…For this purpose, the model was embedded in a phospholipid bilayer with aqueous phases containing Na ϩ and Cl Ϫ as counter-ions both extraand intracellularly. Schlegel et al (2005) recently described this procedure. Position restraints were initially set on the ternary complex with a force of 5000 kJ ⅐ mol Ϫ1 ⅐ nm Ϫ2 to equilibrate the membrane and solvent molecules.…”

How a small change in retinal leads to G‐protein activation: Initial events suggested by molecular dynamics calculations

“…[44][45][46][47][48][49] Each of these studies has something of value to add to our understanding of the molecular nature of rhodopsin and its activation by light. Each group has made different choices with respect to membrane representation, length of simulation, size of simulation, and treatment of electrostatics.…”