Simulation on mechanochemical coupling of rotary biomotors F₁ and V₁

The F₁-ATPase and V₁-ATPase are rotary biomotors. Alignment of their amino acid sequences, which originate from bovine heart mitochondria (1BMF) and Enterococcus hirae (3VR6), respectively, demonstrates that the segment forming the ATP catalytic pocket is highly conserved. Single-molecule experiments, however, have revealed subtle differences in efficiency between the F₁ and V₁ motors. Here, we perform both atomistic and coarse-grained molecular dynamics simulations to investigate the mechanochemical coupling and coordination in F₁ and V₁ ATPase. Our results show that the correlation between conformational changes in F₁ is stronger than that in V₁, indicating that the mechanochemical coupling in F₁ is tighter than in V₁. Moreover, the unidirectional rotation of F₁ is more processive than that of V₁, which accounts for the higher efficiency observed in F₁ and explains the occasional backward steps detected in single-molecule experiments on V₁.