Proton uptake associated with the reduction of the primary quinone QA influences the binding site of the secondary quinone QB in Rhodopseudomonas viridis photosynthetic reaction centers

Previously, two binding sites for the secondary quinone QB in the photosynthetic reaction center (RC) from Rhodopseudomonas viridis were identified by X-ray crystallography, a 'proximal' binding site close to the non-heme iron, and a 'distal' site, displaced by 4.2 Angstrom along the path of the isoprenoid 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 simulations, which support the theory of a spontaneous transfer of Q(B) between the distal site and the proximal site. In contrast to earlier computational studies on RCs, the molecular dynamics simulations of Q(B) migration resulted in a proximal Q(B) binding pattern identical to that of the crystallographic findings. Also, we demonstrate that the preference towards the proximal Q(B) location is not necessarily attributed to reduction of Q(B) to the semiquinone, but already to the preceding reduction of the primary quinone Q(A) and resulting protonation changes in the protein. Energy mapping of the Q(B) binding pocket indicates that the quinone ring rotation required for completion of the transfer between the two sites is improbable at the distal or proximal binding sites due to high potential barriers, but may be possible at a newly identified position near the distal binding site. (C) 2001 Elsevier Science B.V. All rights reserved.