CALCULATION OF PROTONATION PATTERNS IN PROTEINS WITH STRUCTURAL RELAXATION AND MOLECULAR ENSEMBLES - APPLICATION TO THE PHOTOSYNTHETIC REACTION-CENTER

The conventional method to determine protonation patterns of proteins was extended by explicit consideration of structural relaxation. The i nclusion of structural relaxation was achieved by alternating energy m inimization with the calculation of protonation pattern in an iterativ e manner until consistency of minimized structure and protonation patt ern was reached. We applied this method to the bacterial photosyntheti c reaction center (bRC) of Rps. viridis and could show that the relaxa tion procedure accounts for the nuclear polarization and therefore all ows one to lower the dielectric constant for the protein from the typi cally chosen value of epsilon(p) = 4 to a value of epsilon(p) = 2 with out fundamentally changing the results. Owing to the lower dielectric shielding at epsilon(p) = 2, the charges of the titratable groups inte ract more strongly, which leads to sampling problems during Monte Carl o titration. We solved this problem by introducing triple moves in add ition to the conventional single and double moves. We also present a n ew method that considers ensembles of protein conformations for the ca lculation of protonation patterns. Our method was successfully applied to calculate the redox potential differences of the quinones in the b RC using the relaxed structures for the different redox states of the quinones.