SummaryAfter a brief history of the proposals for the mechanism of the ATP synthase, the main experimental arguments for a rotational mechanism of catalysis are analyzed and on the basis of this analysis it is concluded that no evidence has been provided for rotation as an obligatory element of the catalytic mechanism. On the other hand, the experimental evidence in favor of a two-sites catalytic mechanism, derived from various approaches and not compatible with a three-sites rotary mechanism, appear to be very solid. Finally a brief characterization of the various nucleotide binding sites is provided and a suggestion is made how the enzyme has evolutionarily developed from a rotating machine into an asymmetrical device for energy conservation.IUBMB Life, 55: 473-481, 2003 Keywords ATP synthase; binding change mechanism; rotary mechanism; dual-site mechanism; nucleotide binding sites; kinetic analysis; crosslinking.
A BRIEF HISTORY OF THE PROPOSED MECHANISM OF CATALYSIS OF THE ATP SYNTHASEAfter the development of a reliable isolation procedure for mitochondrial F 1 in the early seventies (1) the groups of Slater and Penefsky discovered the presence of tightly bound nucleotides in isolated MF 1 (2-4). At the same time Boyer and colleagues developed, on the basis of 18 O exchange experiments with coupled SMP, the concept of a near equilibrium between ATP + water and ADP + Pi at a tight catalytic site, the required energy for ATP synthesis not being needed for the synthesis reaction itself, but for the dissociation of bound ATP (5). On this basis the so called 'binding change mechanism' was proposed (6). This mechanism requires the contribution of two interacting sites to catalysis, each of them alternating between a conformation with a tightly bound nucleotide, responsible for the catalytic reaction, and a conformation with a low binding affinity. The affinity of the bound product at the tight site is decreased when a nucleotide is bound at the low-affinity site and this latter site then becomes the new tight site. In the process of ATP synthesis the energy for the conformational change of the binding sites is delivered by the proton gradient, in the process of ATP hydrolysis by the binding energy of ATP (cf. (7)).After the subunit stoichiometry of MF 1 had been established as 3 : 3 : 1 : 1 : 1 (8, 9) and the group of Penefsky in the early eighties had discovered the phenomenon of single-site catalysis and enhancement of the catalysis at one site by binding of substrate to more sites (10-12), Boyer and Cross and others combined the binding change mechanism with the proposal that not two sites, but all three b sites are involved in (sequential) catalysis, concomitant with rotation of part of the enzyme (13).In spite of our challenges of the rotary three-sites mechanism (14, 15) it attracted substantial support and this support strongly increased when Abrahams et al. in 1994 reported the crystal structure of the mitochondrial F 1 ATPase (16) and chose to interpret their data on the basis of this model, proposing ...