Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex:: A new crystal structure reveals an altered intramolecular hydrogen-bonding pattern

Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc(1) complex. Structure-activity relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pK(a) for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl 0 of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc(1) complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc(1) complex at 2.28 A resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cytochrome b, and the formylamino OH-bonds via a water molecule to Lys227. A strong density, the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alpha A helix. (c) 2005 Elsevier Ltd. All rights reserved.