On the basis of x-ray diffraction data to a resolution of 2.9 angstroms, atomic models of most protein components of the bovine cytochrome bc1 complex were built, including core 1, core 2, cytochrome b, subunit 6, subunit 7, a carboxyl-terminal fragment of cytochrome c1, and an amino-terminal fragment of the iron-sulfur protein. The positions of the four iron centers within the bc1 complex and the binding sites of the two specific respiratory inhibitors antimycin A and myxothiazol were identified. The membrane-spanning region of each bc1 complex monomer consists of 13 transmembrane helices, eight of which belong to cytochrome b. Closely interacting monomers are arranged as symmetric dimers and form cavities through which the inhibitor binding pockets can be accessed. The proteins core 1 and core 2 are structurally similar to each other and consist of two domains of roughly equal size and identical folding topology.

We Ubiquinol-cytochrome-c oxidoreductase (cytochrome bc1 complex; EC 1.10.2.2) is a segment of the respiratory chain in mitochondria and of the photosynthetic apparatus of purple bacteria. It catalyzes electron transfer (ET) from ubiquinol to cytochrome c, coupled to proton transport across a membrane (from the matrix space to the intermembrane space of mitochondria; from the cytoplasm to the periplasm of purple bacteria). The resulting electrochemical proton gradient drives ATP synthesis and transport processes (1, 2). Essential for the function of the bc1 complex are the three redox proteins cytochrome b, cytochrome c1, and the iron-sulfur protein (ISP). Two b-type hemes (b L and b H ) are attached to cytochrome b, one c-type heme is bound to cytochrome c1, and a Rieske-type iron-sulfur center (FeS) is bound to ISP (2). Whereas some bacterial bc1 complexes consist of only those redox subunits (3), their mitochondrial counterparts contain up to 8 additional protein subunits whose precise functions in the complex are largely unknown (4).The protonmotive Q cycle model (2, 5, 6) best explains experimental results on the ET pathway through the four redox centers of the bc1 complex. It postulates two separate ubiquinone binding sites, called Q o and Q i . In bc1 complexes of the inner membrane of mitochondria, Q o is located near the membrane surface facing the intermembrane space, and Q i is near the membrane surface facing the matrix space. The Q cycle model requires bifurcated electron flow from ubiquinol bound in the Q o site: The first electron of ubiquinol is sequentially transferred to the ISP, cytochrome c1, and eventually to the soluble cytochrome c. Protons are released into the intermembrane space, generating a ubisemiquinone anion in the Q o site. The second electron is transferred to hemes b L and b H and to a ubiquinone or a ubisemiquinone anion in the Q i site. The fully reduced quinone in the Q i site picks up two protons from the matrix space and moves to the Q o site for recycling.The discovery of different types of specific ET inhibitors of the bc1 complex was crucial for the development of this Q cycle hypothesis. The two major types of bc1 inhibitors are called Q o or Q i inhibitors, depending on their action in the cytochrome bc1 complex (7,8). All Q i inhibitors target specifically the ET path from heme b L to ubiquinone͞ubisemiquinone in the Q i site; they do not share common structural motifs. Q o inhibitors block binding of quinol to the Q o site and ET through this site. They can be classified further on the basis of common structural motifs and of their effects on the absorption spectrum of heme b L and on the electron paramagnetic resonance (EPR) spectrum and redox potential of the FeS (7). One Q o inhibitor subtype shares a methoxyacrylate (MOA) group (examples: myxothiazol, MOA-stilbene), another subtype resembles a hydroxyquinone molecule (example: 5-undecyl-6-hydroxy-4,7-dioxobenzothiazol or UHDBT), and a third subtype has a chromone group as the common motif (example: stigma...

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