A Self-Assembled Respiratory Chain that Catalyzes NADH Oxidation by Ubiquinone-10 Cycling between Complex I and the Alternative Oxidase

Complex I is a crucial respiratory enzyme that conserves the energy from NADH oxidation by ubiquinone‐10 (Q₁₀) in proton transport across a membrane. Studies of its energy transduction mechanism are hindered by the extreme hydrophobicity of Q₁₀, and they have so far relied on native membranes with many components or on hydrophilic Q₁₀ analogues that partition into membranes and undergo side reactions. Herein, we present a self‐assembled system without these limitations: proteoliposomes containing mammalian complex I, Q₁₀, and a quinol oxidase (the alternative oxidase, AOX) to recycle Q₁₀H₂ to Q₁₀. AOX is present in excess, so complex I is completely rate determining and the Q₁₀ pool is kept oxidized under steady‐state catalysis. The system was used to measure a fully‐defined K_M value for Q₁₀. The strategy is suitable for any enzyme with a hydrophobic quinone/quinol substrate, and could be used to characterize hydrophobic inhibitors with potential applications as pharmaceuticals, pesticides, or fungicides.

Unraveling the heater: new insights into the structure of the alternative oxidase

The alternative oxidase is a membrane-bound ubiquinol oxidase found in the majority of plants as well as many fungi and protists, including pathogenic organisms such as Trypanosoma brucei. It catalyzes a cyanide- and antimycin-A-resistant oxidation of ubiquinol and the reduction of oxygen to water, short-circuiting the mitochondrial electron-transport chain prior to proton translocation by complexes III and IV, thereby dramatically reducing ATP formation. In plants, it plays a key role in cellular metabolism, thermogenesis, and energy homeostasis and is generally considered to be a major stress-induced protein. We describe recent advances in our understanding of this protein's structure following the recent successful crystallization of the alternative oxidase from T. brucei. We focus on the nature of the active site and ubiquinol-binding channels and propose a mechanism for the reduction of oxygen to water based on these structural insights. We also consider the regulation of activity at the posttranslational and retrograde levels and highlight challenges for future research.

All-atom molecular dynamics simulations reveal significant differences in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc1 complexes

Antimycin A is the most frequently used specific and powerful inhibitor of the mitochondrial respiratory chain. We used all-atom molecular dynamics (MD) simulations to study the dynamic aspects of the interaction of antimycin A with the Q(i) site of the bacterial and bovine bc(1) complexes embedded in a membrane. The MD simulations revealed considerable conformational flexibility of antimycin and significant mobility of antimycin, as a whole, inside the Q(i) pocket. We conclude that many of the differences in antimycin binding observed in high-resolution x-ray structures may have a dynamic origin and result from fluctuations of protein and antimycin between multiple conformational states of similar energy separated by low activation barriers, as well as from the mobility of antimycin within the Q(i) pocket. The MD simulations also revealed a significant difference in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc(1) complexes. The strong hydrogen bond between antimycin and conserved Asp-228 (bovine numeration) was observed to be frequently broken in the bacterial bc(1) complex and only rarely in the bovine bc(1) complex. In addition, the distances between antimycin and conserved His-201 and Lys-227 were consistently larger in the bacterial bc(1) complex. The observed differences could be responsible for a weaker interaction of antimycin with the bacterial bc(1) complex.

Molecular basis for the enantioselective binding of a novel class of cytochrome bc1 complex inhibitors

The recently solved co-crystal structures of mitochondrial cytochrome bc1 complex with inhibitors have provided an important structural framework for the elucidation of modes of binding of various bc1 complex inhibitors. N-Phenyl triazolones, a novel class of bc1 complex ubiquinol oxidation (Qo)-site inhibitors, were found to exhibit atropisomerism; in few cases, the atropisomers were resolved and shown to express different biological activities. However, the underlying mechanism for such differential binding of the enantiomers to bc1 complex is unknown. Here molecular docking is used to examine the binding modes of the N-phenyl triazolones fungicides. Our docking studies allow the molecular basis for the enantioselective binding of atropisomeric triazolones to be elucidated. Furthermore, the mode of binding of azoxystrobin has also been clarified.

A motif for quinone binding sites in respiratory and photosynthetic systems

Many of the membrane-bound protein complexes of respiratory and photosynthetic systems are reactive with quinones. To date, no clear structural relationship between sites that bind quinone has been defined, apart from that in the homologous family of "type II" photosynthetic reaction centres. We show here that a structural element containing a weak sequence motif is common to the Q(A) and Q(B) sites of bacterial reaction centres and the Q(i) site of the mitochondrial bc(1) complex. Analyses of sequence databases indicate that this element may also be present in the PsaA/B subunits of photosystem I, in the ND4 and ND5 subunits of complex I and, possibly, in the mitochondrial alternative quinol oxidase. This represents a first step in the structural classification of quinone binding sites.

Complex I inhibitors as insecticides and acaricides

Structurally diverse synthetic insecticides and acaricides had been shown to inhibit the proton-translocating NADH:ubiquinone oxidoreductase (complex I) activity. In addition, secondary metabolites from microbial and plant sources known to act on complex I exhibited biological activity against agricultural and environmental insect pests. Mechanistic studies indicated that these compounds interfered with ubiquinone reduction most likely at the same site(s) as the classical complex I inhibitors rotenone and piericidin A. Two approaches to characterize the mechanism of insecticidal/acaricidal complex I inhibitors were followed: enzyme kinetic studies and binding studies with radiolabeled inhibitors. Enzyme kinetic experiments were sometimes controversially interpreted regarding a competitive or non-competitive inhibitor mechanism with respect to the electron acceptor. In general, radioligand binding data with submitochondrial membranes were in line with the enzymological results but due to methodological drawbacks, saturation kinetic analyses were impossible. The main problems underlying many studies of inhibitor interaction with complex I were (i) the use of membrane-bound enzyme preparations and (ii) the physicochemical properties of the amphiphilic inhibitors with their strong tendency to accumulate in the membrane phase. A more recent approach to characterize inhbibitor interaction sites in complex I was the isolation of piericidin-resistant mutants of photosynthetic bacteria which produce a simpler homologue of mitochondrial NADH:Q oxidoreductase.