How does nitrous oxide reductase interact with its electron donors?—A docking study

Abstract

Electron transfer reactions are crucial for respiration and denitrification. In this article, we analyze the interaction of nitrous oxide reductase with its electron donors cytochrome c₅₅₀ and pseudoazurin. Our docking protocol comprises generation of candidate complexes followed by a selection step based on the distance of the donor and acceptor groups in each partner protein. Finally, the structures of the candidate complexes were optimized using a force field calculation, together with a second distance filtering step. The prediction power of this protocol was studied using the crystal structure of the cytochrome c₂/photosynthetic reaction center of Rhodobacter sphaeroides as a reference. The results suggest that both cytochrome c₅₅₀ and pseudoazurin bind at the same hydrophobic surface patch residing near the Cu_A center of nitrous oxide reductase. The central, well‐conserved interaction surface of the donors is hydrophobic, but it is surrounded by numerous lysine side‐chains, which interact electrostatically with analogously positioned side‐chain carboxylates of the acceptor. The prediction output is an ensemble of energetically similar structures that are rotationally related to each other. While such an ensemble may reflect incomplete prediction power of the docking protocol, it may also manifest a biological situation where there are multiple ways of forming a productive electron transfer complex. Analyses of the predicted structures and the conservation pattern of the amino acid residues suggest the existence of specific electron transfer pathways to and from the Cu_A center of nitrous oxide reductase. Proteins 2005.