pK(a) calculations along a bacteriorhodopsin molecular dynamics trajectory

Electrostatic calculations of pK(a-values) are reported along a 400 ps molecular dynamics trajectory of bacteriorhodopsin. The sensitivity of calculated pK(a) values to a number of structural factors and factors related to the modelling of the electrostatics are also studied. The results are very sensitive to the choice of internal dielectric constant of the protein (in the interval 2-4). Moreover it is important to include internal water molecules and to average over a long enough portion ( approximately 100 ps) of an equilibrium molecular dynamics trajectory. The internal waters are necessary to get an ion-counter ion complex with the Schiff base and Arg 82 protonated and the aspartic groups (85 and 212) deprotonated. The fluctuations along the MD-trajectory do not change the protonation state of internal residues at neutral pH. However, at other pH values the averaging along a trajectory maybe crucial to get correct protonation states. A relationship is found between the arginine group 82, the aspartic group 85 and the glutamate group 204. Glu 204 is protonated in the ground state but the pK(a) value decreases towards deprotonation when the chromophore isomerizes into the cis state.