The ubiquinol cytochrome c oxidoreductase (cytochrome bc1 complex) plays a central role in electron transport chains of bacteria, mitochondria and chloroplasts, converting redox free energy into a proton gradient used to drive the cell's metabolism through ATP synthesis. This complex catalyzes the oxidation of ubiquinol in the membrane, the reduction of cytochrome c and the translocation of protons across the membrane [97]. All bc1 complexes contain three essential sub-units to which the prosthetic groups are bound: a cytochrome (cyt) b with high- and low-potential hemes bH and bL, an iron sulfur protein (ISP) containing a 2Fe2S center, and a cytochrome c1 with another heme group. The catalytic mechanism involves two catalytic sites for oxidation (Oo site) or reduction (Oi site) of the quinones. The crystal structures of several mitochondrial bc1 complexes with and without an inhibitor (stigmatellin) bound at the Oo site became available during the past year [98, 99]. In the structure with stigmatellin bound, part of the ISP domain is turned with respect to its position in the structure without the inhibitor [99]. This suggests that the electron transfer path from the Oo site to cyt c1 involves a substantial movement of the ISP. Our collaborator, A. R. Crofts, provided us with crystal structures of chicken heart mitochondria bc1 complexes, with and without the inhibitor bound at the Oo site [99]. Comparison of these two structures revealed the axis of rotation of the iron sulfur protein (ISP) mobile head and the angle of rotation. We have prepared two systems consisting of the cytochrome b, cytochrome c1 and ISP domains of the two structures for equilibration. We investigate the mechanism governing the rotation of the ISP head by means of Steered Molecular Dynamic (SMD) simulations [3-8, 100]. In the simulations, external forces have to be applied to the ISP to provide an appropriate torque inducing the rotation. We are mainly interested in revealing the geometrical constraints imposed on the movement of the ISP head by the other sub-units of the bc1 complex. We will simulate the rotation of the ISP head in the presence of cyt b and cyt c1 sub-units by using SMD to induce the rotation. This simulation will provide the information on whether the motion of the ISP head is unconstrained or it involves molecular interactions that may induce or prevent the rotation. The latter case may indicate mutations that alter the rate of the catalytic reaction.
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