Proton uptake associated with the reduction of the primary quinone Q(A) influences the binding site of the secondary quinone Q(B) in Rhodopseudomonasviridis photosynthetic reaction centers

Previously, two binding sites for the secondary quinone QB in the photosynt hetic reaction center (RC) from Rhodopseudomonas viridis were identified by X-ray crystallography, a 'proximal' binding site close to the non-heme iro n, and a 'distal' site, displaced by 4.2 Angstrom along the path of the iso prenoid tail [C.R.D. Lancaster and H. Michel, Structure 5 (1997) 1339-1359] . The quinone ring planes in the two sites differ by roughly a 180 degrees rotation around the isoprenoid tail. Here we present molecular dynamics sim ulations, which support the theory of a spontaneous transfer of Q(B) betwee n the distal site and the proximal site. In contrast to earlier computation al studies on RCs, the molecular dynamics simulations of Q(B) migration res ulted in a proximal Q(B) binding pattern identical to that of the crystallo graphic findings. Also, we demonstrate that the preference towards the prox imal Q(B) location is not necessarily attributed to reduction of Q(B) to th e semiquinone, but already to the preceding reduction of the primary quinon e Q(A) and resulting protonation changes in the protein. Energy mapping of the Q(B) binding pocket indicates that the quinone ring rotation required f or completion of the transfer between the two sites is improbable at the di stal or proximal binding sites due to high potential barriers, but may be p ossible at a newly identified position near the distal binding site. (C) 20 01 Elsevier Science B.V. All rights reserved.