title: 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.
authors.affiliation: Department of Pharmaceutical Chemistry, Heinrich-Heine University of Düsseldorf, Universitätsstrasse 1, Geb. 26.23/O2, 40225 Düsseldorf, Germany.
authors.forename: Birgit
authors.initials: B
authors.lastname: Schlegel
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Sippl
authors.forename: Hans-Dieter
authors.initials: HD
authors.lastname: Höltje
mesh_terms: D015060:1,2-Dipalmitoylphosphatidylcholine; D000595:Amino Acid Sequence; D000818:Animals; D001224:Aspartic Acid / Q000737:chemistry; D002251:Carbon Tetrachloride; D002417:Cattle; D002462:Cell Membrane / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D018698:Glutamic Acid / Q000737:chemistry; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011522:Protons; D012243:Rhodopsin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012984:Software; D040681:Structural Homology, Protein; D014867:Water / Q000737:chemistry / Q000378:metabolism
chemical_list: D011522:Protons; D014867:Water; D015060:1,2-Dipalmitoylphosphatidylcholine; D001224:Aspartic Acid; D018698:Glutamic Acid; D012243:Rhodopsin; D002251:Carbon Tetrachloride