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Abstract

Based on new Rhodopseudomonas (Rp.) viridis reaction center (RC) coordinates with a reliable structure of the secondary acceptor quinone (Q_B) site, a continuum dielectric model and finite difference technique have been used to identify clusters of electrostatically interacting ionizable residues. Twenty-three residues within a distance of 25 A from Q_B (Q_B cluster) have been shown to be strongly electrostatically coupled to Q_B, either directly or indirectly. An analogous cluster of 24 residues is found to interact with Q_A (Q_A cluster). Both clusters extend to the cytoplasmic surface in at least two directions. However, the Q_B cluster differs from the Q_A cluster in that it has a surplus of acidic residues, more strong electrostatic interactions, is less solvated, and experiences a strong positive electrostatic field arising from the polypeptide backbone. Consequently, upon reduction of QA or Q_B, it is the Q_B cluster, and not the Q_A cluster, which is responsible for substoichiometric proton uptake at neutral pH. The bulk of the changes in the Q_B cluster are calculated to be due to the protonation of a tightly coupled cluster of the three Glu residues (L212, H177, and M234) within the Q_B cluster. If the lifetime of the doubly reduced state Q_B^2- is long enough, Asp M43 and Ser L223 are predicted to also become protonated. The calculated complex titration behavior of the strongly interacting residues of the Q_B cluster and the resulting electrostatic response to electron transfer may be a common feature in proton-transferring membrane protein complexes.