Amino acid protonation states determine binding sites of the secondary ubiquinone and its anion in the Rhodobacter sphaeroides photosynthetic reaction center

Molecular dynamics simulations of native ubiquinone-10 binding in the photo synthetic reaction center of Rhodobacter sphaeroides are presented that sup port the theory that the neutral and radical anionic quinones Q(B) and Q(B) (.-) bind in different locations. The differences in binding are attribute d to differing protonation states of the nearby amino acids GLUL212?, and A SP L213. Q(B) binding at the ''dark-adapted" Q(B) Site observed by Stowell et al. is most consistent with protonation of GLUL212. Q(B) (.-) binding at the experimentally observed "light-adapted'' Q(B)(.-) Site is consistent o nly with protonation of both GLU L212, and ASP L313. The experimentally est ablished pH dependence of electron-transfer rate, combined with our MD resu lts, implies that protonation of ASP L213 must occur before electron transf er. Additionally, the molecular dynamics results suggest that movement of t he semiquinone anion Q(B) (.-) between sites (for different amino acid prot onation states) is spontaneous near room temperature and cannot by itself a ccount for the higher of two experimentally observed activation energies fo r electron transfer from Q(A) to Q(B).