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 inclusion of structural relaxation was achieved by alternating energy minimization with the calculation of protonation pattern in an iterative manner until consistency of minimized structure and protonation pattern was reached. We applied this method to the bacterial photosynthetic reaction center (bRC) of Rps. viridis and could show that the relaxation procedure accounts for the nuclear polarization and therefore allows one to lower the dielectric constant for the protein from the typically chosen value of epsilon(p) = 4 to a value of epsilon(p) = 2 without fundamentally changing the results. Owing to the lower dielectric shielding at epsilon(p) = 2, the charges of the titratable groups interact more strongly, which leads to sampling problems during Monte Carlo titration. We solved this problem by introducing triple moves in addition to the conventional single and double moves. We also present a new method that considers ensembles of protein conformations for the calculation of protonation patterns. Our method was successfully applied to calculate the redox potential differences of the quinones in the bRC using the relaxed structures for the different redox states of the quinones.