Energetics of quinone-dependent electron and proton transfers in Rhodobacter sphaeroides photosynthetic reaction centers.

Proteins bind redox cofactors, modifying their electrochemistry and affinity by specific interactions of the binding site with each cofactor redox state. Photosynthetic reaction centers from Rhodobacter sphaeroides have three ubiquinone-binding sites, Q(A), and proximal and distal Q(B) sites. Ubiquinones, which can be doubly reduced and bind 2 protons, have 9 redox states. However, only Q and Q(-) are seen in the Q(A) site and Q, Q(-), and QH(2) in the proximal Q(B) site. The distal Q(B) function is uncertain. Multiple conformation continuum electrostatics (MCCE) was used to compare the ubiquinone electrochemical midpoints (E(m)) and pK(a) values at these three sites. At pH 7, the Q(A)/Q(A)(-) E(m) is -40 mV and proximal Q(B)/Q(B)(-) -10 mV in agreement with the experimental values (assuming a solution ubiquinone E(m) of -145 mV). Q(B) reduction requires changes in nearby residue protonation and SerL223 reorientation. The distal Q(B)/Q(B)(-) E(m) is a much more unfavorable -260 mV. Q(A) and proximal Q(B) sites generally stabilize species with a -1 charge, while the distal Q(B) site prefers binding neutral species. In each site, the dianion is destabilized because favorable interactions with the residues and backbone increase with charge (q), while the unfavorable loss of solvation energy increases with q(2). Therefore, proton binding before a second reduction, forming QH and then QH(-), is always preferred to forming the dianion (Q(-)(2)). The final product QH(2) is higher in energy at the proximal Q(B) site than in solution; therefore, it binds poorly, favoring release. In contrast, QH(2) binds more tightly than Q at the distal Q(B) site.