Structural Analysis of Respirasomes in Electron Transfer Pathway of Acidithiobacillus ferrooxidans: A Computer-Aided Molecular Designing Study

Acidithiobacillus ferrooxidans obtains its metabolic energy by reducing extracellular ferrous iron with either downhill or uphill electron transfer pathway. The downhill electron transfer pathway has been substantially explored in recent years to underpin the mechanism of iron respiration but, there exists a wide gap in our present understanding on how these proteins are organized as a supercomplex and what sort of atomic level interactions governs their stability in the iron respiratory chain. In the present study, we aimed at unraveling the structural basis of supermolecular association of respirasomes using protein threading, protein-protein docking, and molecular dynamics (MD) simulation protocols. Our results revealed that Phe312 of outer membrane cytochrome c plays a crucial role in diffusing electrons from heme C group to Asp73 of rusticyanin. In line with the previous experimental results, His143 of rusticyanin was found to have a stable interaction with Glu121 of periplasmic cytochrome c4. Cytochrome c4 interacts with subunit B of cytochrome c oxidase through Lys146 and Thr148 of the conserved hydrophobic/aromatic motif 145-WKWTFSY-151 to attain stability during simulation. Phe468 of cytochrome c oxidase was found indispensable for stabilizing heme aa3 during MD simulation. Taken together, we conclude that the molecular interactions of charged and hydrophobic amino acids present on the surface of each respirasome form a hypothetical electron wire in the iron respiratory supercomplex of A. ferrooxidans.