Elastic deformations of the rotary double motor of single FoF1-ATP synthases detected in real time by Förster resonance energy transfer

Time-Resolved Oxygen Exchange Measurements Offer Novel Mechanistic Insights into Enzyme-Catalyzed ATP Synthesis during Photophosphorylation

Techniques to probe molecular mechanistic events occurring at a single catalytic site of multi-subunit enzymes in real time are few and are still under development. Here time-resolved information is extracted from measurements of the extensive oxygen exchange that occurs at an intermediate stage of adenosine triphosphate (ATP) synthesis during photophosphorylation by chloroplast thylakoids. A stochastic process-based approach for modeling exchange reactions is formulated that provides a physical basis for the kinetic theory. Compatible with the assumptions made in such a model of randomness, the formulation is shown to lead to a Poisson-type theory that enables kinetic analysis of oxygen-exchange data and offers novel physical insights. Parameters such as the apparent rate constant of exchange and the average lifetime of the exchanging intermediates during the synthesis of ATP by the chloroplast F₁F_O-ATP synthase have been determined over a 5000-fold range of ADP concentration. Experimental isotopomer distributions of [¹⁸O]ATP at high (0.5 mM), intermediate (10 μM), and low (0.2 μM) ADP concentrations have been quantified and compared to expected distributions from the theory. The observed distributions are shown to closely match the predicted distributions. A wealth of novel mechanistic insights such as the number of sites/pathways of oxygen exchange, the order of substrate binding steps at the enzyme catalytic site, and regulation of the process of energy coupling have been deduced, and the results are interpreted with the help of available high-resolution X-ray structures. The various biological implications for models of energy coupling have been discussed. Permutation of oxygen ligands about the phosphorus center is proposed as a possible and general but not well-recognized mechanism for oxygen exchange that is consistent with the principal results of this work, and several suggestions for future research are offered.

Structure of a bacterial ATP synthase

ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest form of the enzyme and because of the relative ease of genetic manipulation of these complexes. We expressed the Bacillus PS3 ATP synthase in Eschericia coli, purified it, and imaged it by cryo-EM, allowing us to build atomic models of the complex in three rotational states. The position of subunit ε shows how it is able to inhibit ATP hydrolysis while allowing ATP synthesis. The architecture of the membrane region shows how the simple bacterial ATP synthase is able to perform the same core functions as the equivalent, but more complicated, mitochondrial complex. The structures reveal the path of transmembrane proton translocation and provide a model for understanding decades of biochemical analysis interrogating the roles of specific residues in the enzyme.

Structural Asymmetry and Kinetic Limping of Single Rotary F-ATP Synthases

F-ATP synthases use proton flow through the FO domain to synthesize ATP in the F₁ domain. In Escherichia coli, the enzyme consists of rotor subunits γεc10 and stator subunits (αβ)₃δab₂. Subunits c10 or (αβ)₃ alone are rotationally symmetric. However, symmetry is broken by the b₂ homodimer, which together with subunit δa, forms a single eccentric stalk connecting the membrane embedded FO domain with the soluble F₁ domain, and the central rotating and curved stalk composed of subunit γε. Although each of the three catalytic binding sites in (αβ)₃ catalyzes the same set of partial reactions in the time average, they might not be fully equivalent at any moment, because the structural symmetry is broken by contact with b₂δ in F₁ and with b₂a in FO. We monitored the enzyme's rotary progression during ATP hydrolysis by three single-molecule techniques: fluorescence video-microscopy with attached actin filaments, Förster resonance energy transfer between pairs of fluorescence probes, and a polarization assay using gold nanorods. We found that one dwell in the three-stepped rotary progression lasting longer than the other two by a factor of up to 1.6. This effect of the structural asymmetry is small due to the internal elastic coupling.

Diffusion Measurements of Swimming Enzymes with Fluorescence Correlation Spectroscopy

Self-propelled chemical motors are chemically powered micro- or nanosized swimmers. The energy required for these motors' active motion derives from catalytic chemical reactions and the transformation of a fuel dissolved in the solution. While self-propulsion is now well established for larger particles, it is still unclear if enzymes, nature's nanometer-sized catalysts, are potentially also self-powered nanomotors. Because of its small size, any increase in an enzyme's diffusion due to active self-propulsion must be observed on top of the enzyme's passive Brownian motion, which dominates at this scale. Fluorescence correlation spectroscopy (FCS) is a sensitive method to quantify the diffusion properties of single fluorescently labeled molecules in solution. FCS experiments have shown a general increase in the diffusion constant of a number of enzymes when the enzyme is catalytically active. Diffusion enhancements after addition of the enzyme's substrate (and sometimes its inhibitor) of up to 80% have been reported, which is at least 1 order of magnitude higher than what theory would predict. However, many factors contribute to the FCS signal and in particular the shape of the autocorrelation function, which underlies diffusion measurements by fluorescence correlation spectroscopy. These effects need to be considered to establish if and by how much the catalytic activity changes an enzyme's diffusion. We carefully review phenomena that can play a role in FCS experiments and the determination of enzyme diffusion, including the dissociation of enzyme oligomers upon interaction with the substrate, surface binding of the enzyme to glass during the experiment, conformational changes upon binding, and quenching of the fluorophore. We show that these effects can cause changes in the FCS signal that behave similar to an increase in diffusion. However, in the case of the enzymes F₁-ATPase and alkaline phosphatase, we demonstrate that there is no measurable increase in enzyme diffusion. Rather, dissociation and conformational changes account for the changes in the FCS signal in the former and fluorophore quenching in the latter. Within the experimental accuracy of our FCS measurements, we do not observe any change in diffusion due to activity for the enzymes we have investigated. We suggest useful control experiments and additional tests for future FCS experiments that should help establish if the observed diffusion enhancement is real or if it is due to an experimental or data analysis artifact. We show that fluorescence lifetime and mean intensity measurements are essential in order to identify the nature of the observed changes in the autocorrelation function. While it is clear from theory that chemically active enzymes should also act as self-propelled nanomotors, our FCS measurements show that the associated increase in diffusion is much smaller than previously reported. Further experiments are needed to quantify the contribution of the enzymes' catalytic activity to their self-propulsion. We hope that our findings help to establish a useful protocol for future FCS studies in this field and help establish by how much the diffusion of an enzyme is enhanced through catalytic activity.

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.

Towards monitoring conformational changes of the GPCR neurotensin receptor 1 by single-molecule FRET

Neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that is important for signaling in the brain and the gut. Its agonist ligand neurotensin (NTS), a 13-amino-acid peptide, binds with nanomolar affinity from the extracellular side to NTSR1 and induces conformational changes that trigger intracellular signaling processes. Our goal is to monitor the conformational dynamics of single fluorescently labeled NTSR1. For this, we fused the fluorescent protein mNeonGreen to the C terminus of NTSR1, purified the receptor fusion protein from E. coli membranes, and reconstituted NTSR1 into liposomes with E. coli polar lipids. Using single-molecule anisotropy measurements, NTSR1 was found to be monomeric in liposomes, with a small fraction being dimeric and oligomeric, showing homoFRET. Similar results were obtained for NTSR1 in detergent solution. Furthermore, we demonstrated agonist binding to NTSR1 by time-resolved single-molecule Förster resonance energy transfer (smFRET), using neurotensin labeled with the fluorophore ATTO594.

Conformational dynamics of the rotary subunit F in the A3 B3 DF complex of Methanosarcina mazei Gö1 A-ATP synthase monitored by single-molecule FRET

In archaea the A₁ A_O ATP synthase uses a transmembrane electrochemical potential to generate ATP, while the soluble A₁ domain (subunits A₃ B₃ DF) alone can hydrolyse ATP. The three nucleotide-binding AB pairs form a barrel-like structure with a central orifice that hosts the rotating central stalk subunits DF. ATP binding, hydrolysis and product release cause a conformational change inside the A:B-interface, which enforces the rotation of subunits DF. Recently, we reported that subunit F is a stimulator of ATPase activity. Here, we investigated the nucleotide-dependent conformational changes of subunit F relative to subunit D during ATP hydrolysis in the A₃ B₃ DF complex of the Methanosarcina mazei Gö1 A-ATP synthase using single-molecule Förster resonance energy transfer. We found two conformations for subunit F during ATP hydrolysis.

Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase

F₁-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned energy conversion mechanism are not fully understood. Here, we use extensive molecular dynamics simulations to reconcile recent single-molecule experiments with structural data and provide a consistent thermodynamic, kinetic and mechanistic description of the main rotary substep in the synthetic cycle of mammalian ATP synthase. The calculated free energy profiles capture a discrete pattern in the rotation of the central γ-shaft, with a metastable intermediate located-consistently with recent experimental findings-at 70° relative to the X-ray position. We identify this rotary step as the ATP-dependent substep, and find that the associated free energy input supports the mechanism involving concurrent nucleotide binding and release. During the main substep, our simulations show no significant opening of the ATP-bound β subunit; instead, we observe that mechanical energy is transmitted to its nucleotide binding site, thus lowering the affinity for ATP. Simultaneously, the empty subunit assumes a conformation that enables the enzyme to harness the free energy of ADP binding to drive ATP release. Finally, we show that ligand exchange is regulated by a checkpoint mechanism, an apparent prerequisite for high efficiency in protein nanomotors.

A capillary zone electrophoresis method for adenine nucleotides analysis in Saccharomyces cerevisiae

Adenosine triphosphate and its metabolites are involved in the cellular metabolism process in Saccharomyces cerevisiae. It is very important to simultaneously determine the relative contents of ATP and its metabolites in yeast. In this study, an effective capillary zone electrophoresis method with high selectivity was established. The calibration curves were linear in the concentration range from 1 to 20mg/L (ATP and cAMP) and 2 to 40mg/L (ADP and AMP) with excellent correlation coefficients (r(2))>0.999. The recovery of ATP, ADP, AMP, and cAMP were 99.4%, 94.7%, 100.3% and 99.6%, respectively. Simple sample preparation and easy detection of ATP and its metabolites make this method suitable for the study of changes in the four adenine nucleotides levels caused by caloric restriction in yeast. It is expected that the current method may contribute to further energy metabolism and related investigations of yeast.

The Mitochondrial Permeability Transition Pore: Channel Formation by F-ATP Synthase, Integration in Signal Transduction, and Role in Pathophysiology

The mitochondrial permeability transition (PT) is a permeability increase of the inner mitochondrial membrane mediated by a channel, the permeability transition pore (PTP). After a brief historical introduction, we cover the key regulatory features of the PTP and provide a critical assessment of putative protein components that have been tested by genetic analysis. The discovery that under conditions of oxidative stress the F-ATP synthases of mammals, yeast, and Drosophila can be turned into Ca(2+)-dependent channels, whose electrophysiological properties match those of the corresponding PTPs, opens new perspectives to the field. We discuss structural and functional features of F-ATP synthases that may provide clues to its transition from an energy-conserving into an energy-dissipating device as well as recent advances on signal transduction to the PTP and on its role in cellular pathophysiology.

Lighting Up the Force: Investigating Mechanisms of Mechanotransduction Using Fluorescent Tension Probes

The ability of cells to sense the physical nature of their surroundings is critical to the survival of multicellular organisms. Cellular response to physical cues from adjacent cells and the extracellular matrix leads to a dynamic cycle in which cells respond by remodeling their local microenvironment, fine-tuning cell stiffness, polarity, and shape. Mechanical regulation is important in cellular development, normal morphogenesis, and wound healing. The mechanisms by which these finely balanced mechanotransduction events occur, however, are not well understood. In large part, this is due to the limited availability of tools to study molecular mechanotransduction events in live cells. Several classes of molecular tension probes have been recently developed which are rapidly transforming the study of mechanotransduction. Molecular tension probes are primarily based on fluorescence resonance energy transfer (FRET) and report on piconewton scale tension events in live cells. In this minireview, we describe the two main classes of tension probes, genetically encoded tension sensors and immobilized tension sensors, and discuss the advantages and limitations of each type. We discuss future opportunities to address major biological questions and outline the challenges facing the next generation of molecular tension probes.

Spotlighting motors and controls of single FoF1-ATP synthase

Subunit rotation is the mechanochemical intermediate for the catalytic activity of the membrane enzyme FoF1-ATP synthase. smFRET (single-molecule FRET) studies have provided insights into the step sizes of the F1 and Fo motors, internal transient elastic energy storage and controls of the motors. To develop and interpret smFRET experiments, atomic structural information is required. The recent F1 structure of the Escherichia coli enzyme with the ϵ-subunit in an inhibitory conformation initiated a study for real-time monitoring of the conformational changes of ϵ. The present mini-review summarizes smFRET rotation experiments and previews new smFRET data on the conformational changes of the CTD (C-terminal domain) of ϵ in the E. coli enzyme.

The regulatory switch of F1-ATPase studied by single-molecule FRET in the ABEL Trap

F₁-ATPase is the soluble portion of the membrane-embedded enzyme F_oF₁-ATP synthase that catalyzes the production of adenosine triphosphate in eukaryotic and eubacterial cells. In reverse, the F₁ part can also hydrolyze ATP quickly at three catalytic binding sites. Therefore, catalysis of 'non-productive' ATP hydrolysis by F₁ (or F_oF₁) must be minimized in the cell. In bacteria, the ε subunit is thought to control and block ATP hydrolysis by mechanically inserting its C-terminus into the rotary motor region of F₁. We investigate this proposed mechanism by labeling F₁ specifically with two fluorophores to monitor the C-terminus of the ε subunit by Förster resonance energy transfer. Single F₁ molecules are trapped in solution by an Anti-Brownian electrokinetic trap which keeps the FRET-labeled F₁ in place for extended observation times of several hundreds of milliseconds, limited by photobleaching. FRET changes in single F₁ and FRET histograms for different biochemical conditions are compared to evaluate the proposed regulatory mechanism.

Regulatory conformational changes of the ε subunit in single FRET-labeled FoF1-ATP synthase

Subunit ε is an intrinsic regulator of the bacterial F_oF₁-ATP synthase, the ubiquitous membrane-embedded enzyme that utilizes a proton motive force in most organisms to synthesize adenosine triphosphate (ATP). The C-terminal domain of ε can extend into the central cavity formed by the α and β subunits, as revealed by the recent X-ray structure of the F₁ portion of the Escherichia coli enzyme. This insertion blocks the rotation of the central γ subunit and, thereby, prevents wasteful ATP hydrolysis. Here we aim to develop an experimental system that can reveal conditions under which ε inhibits the holoenzyme F_oF₁-ATP synthase in vitro. Labeling the C-terminal domain of ε and the γ subunit specifically with two different fluorophores for single-molecule Förster resonance energy transfer (smFRET) allowed monitoring of the conformation of ε in the reconstituted enzyme in real time. New mutants were made for future three-color smFRET experiments to unravel the details of regulatory conformational changes in ε.

Rotary ATPases--dynamic molecular machines

Recent work has provided the detailed overall architecture and subunit composition of three subtypes of rotary ATPases. Composite models of F-type, V-type and A-type ATPases have been constructed by fitting high-resolution X-ray structures of individual components into electron microscopy derived envelopes of the intact enzymes. Electron cryo-tomography has provided new insights into the supra-molecular arrangement of eukaryotic ATP synthases within mitochondria. An inherent flexibility in rotary ATPases observed by different techniques suggests greater dynamics during operation than previously envisioned. The concerted movement of subunits within the complex might provide means of regulation and information transfer between distant parts of rotary ATPases thereby fine tuning these molecular machines to their cellular environment, while optimizing their efficiency.

Microscopy of single F(o) F(1) -ATP synthases--the unraveling of motors, gears, and controls

Optical microscopy of single F(1) -ATPase and F(o) F(1) -ATP synthases started 15 years ago. Direct demonstration of ATP-driven subunit rotation by videomicroscopy became the new exciting tool to analyze the conformational changes of this enzyme during catalysis. Stimulated by these experiments, technical improvements for higher time resolution, better angular resolution, and reduced viscous drag were developed rapidly. Optics and single-molecule enzymology were entangled to benefit both biochemists and microscopists. Today, several single-molecule microscopy methods are established including controls for the precise nanomanipulation of individual enzymes in vitro. Förster resonance energy transfer, which has been used for simultaneous monitoring of conformational changes of different parts of this rotary motor, is one of them and may become the tool for the analysis of single F(o) F(1) -ATP synthases in membranes of living cells. Here, breakthrough experiments are critically reviewed and challenges are discussed for the future microscopy of single ATP synthesizing enzymes at work.

Twisting and subunit rotation in single F(O)(F1)-ATP synthase

F(O)F(1)-ATP synthases are ubiquitous proton- or ion-powered membrane enzymes providing ATP for all kinds of cellular processes. The mechanochemistry of catalysis is driven by two rotary nanomotors coupled within the enzyme. Their different step sizes have been observed by single-molecule microscopy including videomicroscopy of fluctuating nanobeads attached to single enzymes and single-molecule Förster resonance energy transfer. Here we review recent developments of approaches to monitor the step size of subunit rotation and the transient elastic energy storage mechanism in single F(O)F(1)-ATP synthases.