title: Molecular dynamics of bacteriorhodopsin.
abstract: A model of bacteriorhodopsin (bR), with a retinal chromophore attached, has been derived for a molecular dynamics simulation. A method for determining atomic coordinates of several ill-defined strands was developed using a structure prediction algorithm based on a sequential Kalman filter technique. The completed structure was minimized using the GROMOS force field. The structure was then heated to 293 K and run for 500 ps at constant temperature. A comparison with the energy-minimized structure showed a slow increase in the all-atom RMS deviation over the first 200 ps, leveling off to approximately 2.4 A relative to the starting structure. The final structure yielded a backbone-atom RMS deviation from the crystallographic structure of 2.8 A. The residue neighbors of the chromophore atoms were followed as a function of time. The set of persistent near-residue neighbors supports the theory that differences in pKa values control access to the Schiff base proton, rather than formation of a counterion complex.
authors.affiliation: Materials Directorate, Wright Laboratory (USAF), Wright-Patterson Air Force Base, Ohio 45433-7702, USA.
authors.forename: J A
authors.initials: JA
authors.lastname: Lupo
authors.forename: R
authors.initials: R
authors.lastname: Pachter
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D001436:Bacteriorhodopsins / Q000235:genetics*; D003196:Computer Graphics; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D001436:Bacteriorhodopsins