ATP Synthase: Advantages of the Rotary Mechanism under Diverse Conditions

Abstract

ATP synthesis based on the proton-motive force (pmf) across mitochondrial and bacterial membranes is a key cellular function performed by the F-ATPase, a complex rotary machine. Although mechanistic details of the F-ATPase have drawn intensive scrutiny, it remains unknown whether the rotary process itself is merely a sufficient outcome of evolution or whether the elaborate rotary mechanism has advantages over other, arguably simpler, mechanisms. For example, ATP-hydrolyzing P-loop transporters can be reversed to perform ATP synthesis, suggesting a variety of potential synthesis mechanisms. The present work uses kinetic models, operating under fundamental biophysical constraints, to compare a rotary-like mechanism for ATP synthesis with a systematic enumeration of alternative mechanisms based on event-ordering; each is constrained to operate under the same H+/ATP ratio and thermodynamic conditions. The models are independent of structural details and rely solely on thermodynamic and kinetic principles. The resulting models qualitatively reproduce key kinetic characteristics of ATP synthase under physiological conditions, including the sigmoidal relationship between the rate of ATP synthesis and pmf. When the mechanisms are separately optimized to maximize the rate of ATP synthesis over a range of presumed physiological conditions, the performance of the rotary mechanism stands out significantly, particularly in the most challenging, energy-poor conditions. Although all the models are thermodynamically equivalent in using the same free energy per ATP synthesized, the rotary model possesses a kinetic advantage: its one-at-a-time transport of protons enables more ratchet-like progress and less delay-induced unbinding of protons on the driving (low-pH) side of the membrane. Our results suggest the rotary mechanism has a quantifiable intrinsic advantage that may have played a role in evolution.