Essential Role of the ε Subunit for Reversible Chemo-Mechanical Coupling in F1-ATPase

Rotary properties of hybrid F1-ATPases consisting of subunits from different species

F₁-ATPase (F₁) is an ATP-driven rotary motor protein ubiquitously found in many species as the catalytic portion of F_oF₁-ATP synthase. Despite the highly conserved amino acid sequence of the catalytic core subunits: α and β, F₁ shows diversity in the maximum catalytic turnover rate V_max and the number of rotary steps per turn. To study the design principle of F₁, we prepared eight hybrid F₁s composed of subunits from two of three genuine F₁s: thermophilic Bacillus PS3 (TF₁), bovine mitochondria (bMF₁), and Paracoccus denitrificans (PdF₁), differing in the V_max and the number of rotary steps. The V_max of the hybrids can be well fitted by a quadratic model highlighting the dominant roles of β and the couplings between α-β. Although there exist no simple rules on which subunit dominantly determines the number of steps, our findings show that the stepping behavior is characterized by the combination of all subunits.

F1-ATPase Rotary Mechanism: Interpreting Results of Diverse Experimental Modes With an Elastic Coupling Theory

In this chapter, we review single-molecule observations of rotary motors, focusing on the general theme that their mechanical motion proceeds in substeps with each substep described by an angle-dependent rate constant. In the molecular machine F1-ATPase, the stepping rotation is described for individual steps by forward and back reaction rate constants, some of which depend strongly on the rotation angle. The rotation of a central shaft is typically monitored by an optical probe. We review our recent work on the theory for the angle-dependent rate constants built to treat a variety of single-molecule and ensemble experiments on the F1-ATPase, and relating the free energy of activation of a step to the standard free energy of reaction for that step. This theory, an elastic molecular transfer theory, provides a framework for a multistate model and includes the probe used in single-molecule imaging and magnetic manipulation experiments. Several examples of its application are the following: (a) treatment of the angle-dependent rate constants in stalling experiments, (b) use of the model to enhance the time resolution of the single-molecule imaging apparatus and to detect short-lived states with a microsecond lifetime, states hidden by the fluctuations of the imaging probe, (c) treatment of out-of-equilibrium "controlled rotation" experiments, (d) use of the model to predict, without adjustable parameters, the angle-dependent rate constants of nucleotide binding and release, using data from other experiments, and (e) insights obtained from correlation of kinetic and cryo-EM structural data. It is also noted that in the case where the release of ADP would be a bottleneck process, the binding of ATP to another site acts to accelerate the release by 5-6 orders of magnitude. The relation of the present set of studies to previous and current theoretical work in the field is described. An overall goal is to gain mechanistic insight into the biological function in relation to structure.

The Molecular Basis for Purine Binding Selectivity in the Bacterial ATP Synthase ϵ Subunit

The ϵ subunit of ATP synthases has been proposed to regulate ATP hydrolysis in bacteria. Prevailing evidence supports the notion that when the ATP concentration falls below a certain threshold, the ϵ subunit changes its conformation from a non-inhibitory down-state to an extended up-state that then inhibits enzymatic ATP hydrolysis by binding to the catalytic domain. It has been demonstrated that the ϵ subunit from Bacillus PS3 is selective for ATP over other nucleotides, including GTP. In this study, the purine triphosphate selectivity is rationalized by using results from MD simulations and free energy calculations for the R103A/R115A mutant of the ϵ subunit from Bacillus PS3, which binds ATP more strongly than the wild-type protein. Our results are in good agreement with experimental data, and the elucidated molecular basis for selectivity could help to guide the design of novel GTP sensors.

F-ATP-ase of Escherichia coli membranes: The ubiquitous MgADP-inhibited state and the inhibited state induced by the ε-subunit's C-terminal domain are mutually exclusive

ATP synthases are important energy-coupling, rotary motor enzymes in all kingdoms of life. In all F-type ATP synthases, the central rotor of the catalytic F₁ complex is composed of the γ subunit and the N-terminal domain (NTD) of the ε subunit. In the enzymes of diverse bacteria, the C-terminal domain of ε (εCTD) can undergo a dramatic conformational change to trap the enzyme in a transiently inactive state. This inhibitory mechanism is absent in the mitochondrial enzyme, so the εCTD could provide a means to selectively target ATP synthases of pathogenic bacteria for antibiotic development. For Escherichia coli and other bacterial model systems, it has been difficult to dissect the relationship between ε inhibition and a MgADP-inhibited state that is ubiquitous for F_OF₁ from bacteria and eukaryotes. A prior study with the isolated catalytic complex from E. coli, EcF₁, showed that these two modes of inhibition are mutually exclusive, but it has long been known that interactions of F₁ with the membrane-embedded F_O complex modulate inhibition by the εCTD. Here, we study membranes containing EcF_OF₁ with wild-type ε, ε lacking the full εCTD, or ε with a small deletion at the C-terminus. By using compounds with distinct activating effects on F-ATP-ase activity, we confirm that εCTD inhibition and ubiquitous MgADP inhibition are mutually exclusive for membrane-bound E. coli F-ATP-ase. We determine that most of the enzyme complexes in wild-type membranes are in the ε-inhibited state (>50%) or in the MgADP-inhibited state (30%).

The regulatory subunit ε in Escherichia coli FOF1-ATP synthase

F-type ATP synthases are extraordinary multisubunit proteins that operate as nanomotors. The Escherichia coli (E. coli) enzyme uses the proton motive force (pmf) across the bacterial plasma membrane to drive rotation of the central rotor subunits within a stator subunit complex. Through this mechanical rotation, the rotor coordinates three nucleotide binding sites that sequentially catalyze the synthesis of ATP. Moreover, the enzyme can hydrolyze ATP to turn the rotor in the opposite direction and generate pmf. The direction of net catalysis, i.e. synthesis or hydrolysis of ATP, depends on the cell's bioenergetic conditions. Different control mechanisms have been found for ATP synthases in mitochondria, chloroplasts and bacteria. This review discusses the auto-inhibitory behavior of subunit ε found in F_OF₁-ATP synthases of many bacteria. We focus on E. coli F_OF₁-ATP synthase, with insights into the regulatory mechanism of subunit ε arising from structural and biochemical studies complemented by single-molecule microscopy experiments.