X-RAY CRYSTALLOGRAPHIC STUDIES ON SPECIFIC INHIBITORS OF MITOCHONDRIAL BC1 COMPLEX. Hoeon Kim, Di Xia, Johann Deisenhofer1, Chang-An Yu, Anatoly Kachurin and Linda Yu2, HHMI and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, TX 752351, Oklahoma State University, Stillwater, OK 740782
Mitochondrial or prokaryotic bcl complexes contain four redox centers, whose electron flow are affected by various specific inhibitors. These inhibitors usually interact with the complex with high affinity and specificity, and they can be class)fied into several groups based on points of action in the electron transfer pathway and chemical structures.
A series of co-crystals of the bcl complex with different types of inhibitors were grown and analyzed by the difference Fourier technique, using available phase information of the native system. In difference maps calculated with experimental MIR phases up to 3.5 Å, electron density for inhibitors were identified with high confidence in at least two co-crystal systems; antimycin-A and UHDBT (undecylhydroxydioxobenzothiazole).
In the case of antimycin-A, the difference map showed a single density peak exceeding the 20 sigma level. This strong density is probably due to the high binding constant of the inhibitor to the complex. The density for the inhibitor is located very close to the putative highpotential heme of cytochrome b. Moreover, there is also a significant negative density that could be a ubiquinone molecule present in the native structure but displaced upon antimycin-A binding. Displacement of ubiquinone would explain the inhibitory function of antimycin-A.
In the case of UHDBT, which blocks electron transfer between ubiquinone and iron-sulfur center, the density of the highest peak (10 sigma level) overlaps partially with that of the putative iron-sulfur cluster.
The density of these inhibitors became significantly better after combination of experimental phases with model phases. This allowed to confidently build inhibitor structures into the density.