Bacteriorhodopsin in a periodic boundary water-vacuum-water box as an example towards stable molecular dynamics simulations of G-protein coupled receptors

This study presents an optimised set-up for molecular dynamics (MD) simulat ions of G-protein coupled receptors (GPCR). Such simulations are complicate d because(1) the experimental template structure for GPCRs (bovine rhodopsi n) is of low resolution, (2) the receptor surroundings are irregular (water exposed loops vs, lipid exposed transmembrane regions) and (3) the protona tion and solvation states of the inner core receptor residues are unknown. We compared various simulations of the experimentally derived and refined e lectron density structure of the seven helical transmembrane protein bacter iorhodopsin (bR) under different MD conditions using AMBER 4.1, Our results demonstrate that the optimal MD set-up with minimal computational effort i s a periodic boundary (PB) box containing two water shells solvating the ex tra- and intracellular loops separated by a vacuum layer surrounding the he lical transmembrane (TM) regions. It was found that the vacuum layer and wa ter layers are stable under periodic boundary conditions during at least 1 ns of MD simulation. In this set-up the bR structure is stable without any restraints. The average bR structure during the last 500 ps of the MD run h as an excellent RMSD value relative to the original bR structure (RMSD = 1. 66 Angstrom for the C alpha atoms within the TM domains) and shows a very h igh helical stability within the TM regions (88.8% helix), The use of this MD set-up for simulations of GPCRs is discussed.