Phosphorus Chemistry at the Roots of Bioenergetics: Ligand Permutation as the Molecular Basis of the Mechanism of ATP Synthesis/Hydrolysis by FOF1-ATP Synthase

Abstract

The integration of phosphorus chemistry with the mechanism of ATP synthesis/hydrolysis requires dynamical information during ATP turnover and catalysis. Oxygen exchange reactions occurring at β-catalytic sites of the FOF1-ATP synthase/F1-ATPase imprint a unique record of molecular events during the catalytic cycle of ATP synthesis/hydrolysis. They have been shown to provide valuable time-resolved information on enzyme catalysis during ATP synthesis and ATP hydrolysis. The present work conducts new experiments on oxygen exchange catalyzed by submitochondrial particles designed to (i) measure the relative rates of Pi–ATP, Pi–HOH, and ATP–HOH isotope exchanges; (ii) probe the effect of ADP removal on the extent of inhibition of the exchanges, and (iii) test their uncoupler sensitivity/resistance. The objectives have been realized based on new experiments on submitochondrial particles, which show that both the Pi–HOH and ATP–HOH exchanges occur at a considerably higher rate relative to the Pi–ATP exchange, an observation that cannot be explained by previous mechanisms. A unifying explanation of the kinetic data that rationalizes these observations is given. The experimental results in (ii) show that ADP removal does not inhibit the intermediate Pi–HOH exchange when ATP and submitochondrial particles are incubated, and that the nucleotide requirement of the intermediate Pi–HOH exchange is adequately met by ATP, but not by ADP. These results contradicts the central postulate in Boyer’s binding change mechanism of reversible catalysis at a F1 catalytic site with Keq~1 that predicts an absolute requirement of ADP for the occurrence of the Pi–HOH exchange. The prominent intermediate Pi–HOH exchange occurring under hydrolytic conditions is shown to be best explained by Nath’s torsional mechanism of energy transduction and ATP synthesis/hydrolysis, which postulates an essentially irreversible cleavage of ATP by mitochondria/particles, independent from a reversible formation of ATP from ADP and Pi. The explanation within the torsional mechanism is also shown to rationalize the relative insensitivity of the intermediate Pi–HOH exchange to uncouplers observed in the experiments in (iii) compared to the Pi–ATP and ATP–HOH exchanges. This is shown to lead to new concepts and perspectives based on ligand displacement/substitution and ligand permutation for the elucidation of the oxygen exchange reactions within the framework of fundamental phosphorus chemistry. Fast mechanisms that realize the rotation/twist, tilt, permutation and switch of ligands, as well as inversion at the γ-phosphorus synchronously and simultaneously and in a concerted manner, have been proposed, and their stereochemical consequences have been analyzed. These considerations take us beyond the binding change mechanism of ATP synthesis/hydrolysis in bioenergetics.

Editorial: Functions, working mechanisms, and regulation of rotary ATPases and Ductin proteins

“…Connecting the regulation of their rotation-coupled catalysis-transport cycle with the various associated biological functions requires a detailed understanding of the enzymes’ rotary mechanism. Despite recent progress with developing new and alternative models [see, e.g., Frasch et al (2022) ; Kishikawa et al (2022) ; Nakano et al (2023) ; Nath (2023) ], a full understanding of the biological functions of these enzymes is limited by the fact that measuring the proton-transfer and rotation rates of rotary ATPases in the cellular context still represents a significant challenge. For instance, the native rotation rate of a chemically intact enzyme could be measured so far only using indirect methods ( Ferencz et al, 2013 ; Ferencz et al, 2017 ; Petrovszki et al, 2021 ).…”

The relationship between dietary phosphorus and peripheral neuropathy in the general population of the United States: A preliminary research

“…Additionally, phosphorus may influence the occurrence of PN by regulating the function of neuronal cell membranes and affecting neural signal transmission. Conversely, insufficient dietary phosphorus intake may also have negative effects on the nervous system, as phosphorus plays a crucial role in maintaining cell membrane structure, ATP synthesis, and other processes vital for normal neuronal function [18].…”