Conformationally linked interaction in the cytochrome bc1 complex between inhibitors of the Q o site and the Rieske iron–sulfur protein

Abstract

The modified Q cycle mechanism accounts for the proton and charge translocation stoichiometry of the bc 1 complex, and is now widely accepted. However the mechanism by which the requisite bifurcation of electron flow at the Q o site reaction is enforced is not clear. One of several proposals involves conformational gating of the docking of the Rieske ISP at the Q o site, controlled by the stage of the reaction cycle. Effects of different Q o-site inhibitors on the position of the ISP seen in crystals may reflect the same conformational mechanism, in which case understanding how different inhibitors control the position of the ISP may be a key to understanding the enforcement of bifurcation at the Q o site ( Table 1). Here we examine the available structures of cytochrome bc 1 with different Q o-site inhibitors and different ISP positions to look for clues to this mechanism. The effect of ISP removal on binding affinity of the inhibitors stigmatellin and famoxadone suggest a “mutual stabilization” of inhibitor binding and ISP docking, however this thermodynamic observation sheds little light on the mechanism. The cd 1 helix of cytochrome b moves in such a way as to accommodate docking when inhibitors favoring docking are bound, but it is impossible with the current structures to say whether this movement of α-cd 1 is a cause or result of ISP docking. One component of the movement of the linker between E and F helices also correlates with the type of inhibitor and ISP position, and seems to be related to the H-bonding pattern of Y279 of cytochrome b. An H-bond from Y279 to the ISP, and its possible modulation by movement of F275 in the presence of famoxadone and related inhibitors, or its competition with an alternate H-bond to I269 of cytochrome b that may be destabilized by bound famoxadone, suggest other possible mechanisms. This article is part of a Special Issue entitled: Allosteric cooperativity in respiratory proteins.