Free Energy Of ATP Hydrolysis Research Articles

Elevated Na is a dynamic and reversible modulator of mitochondrial metabolism in the heart

Elevated intracellular sodium Nai adversely affects mitochondrial metabolism and is a common feature of heart failure. The reversibility of acute Na induced metabolic changes is evaluated in Langendorff perfused rat hearts using the Na/K ATPase inhibitor ouabain and the myosin-uncoupler para-aminoblebbistatin to maintain constant energetic demand. Elevated Nai decreases Gibb’s free energy of ATP hydrolysis, increases the TCA cycle intermediates succinate and fumarate, decreases ETC activity at Complexes I, II and III, and causes a redox shift of CoQ to CoQH2, which are all reversed on lowering Nai to baseline levels. Pseudo hypoxia and stabilization of HIF-1α is observed despite normal tissue oxygenation. Inhibition of mitochondrial Na/Ca-exchange with CGP-37517 or treatment with the mitochondrial ROS scavenger MitoQ prevents the metabolic alterations during Nai elevation. Elevated Nai plays a reversible role in the metabolic and functional changes and is a novel therapeutic target to correct metabolic dysfunction in heart failure.

Abstract 15515: SGLT2 Inhibitor Empagliflozin Increases Fatty Acid Oxidation, Coupling Between Glycolysis and Glucose Oxidation, and Decreases Left Ventricular Hypertrophy in Mice With Hypertrophic Cardiomyopathy Due to Myosin R403Q Mutation

Background: A metabolic switch from fatty acid oxidation (FAO) to glycolysis associates with LV hypertrophy (LVH). Glucagon signaling increases FAO in the heart and sodium-glucose co-transporter 2 inhibitors (SGLT2i) raise glucagon/insulin ratio (GIR) in patients. We have shown that SGLT2i reprogram cardiac metabolic genes favoring FAO, yet the mechanism is unknown. Hypothesis: SGLT2i increases GIR, thereby increasing FAO and glycolysis/glucose oxidation coupling (GGC), which in turn attenuates LVH and fibrosis in a murine model of HCM (R403Q myosin mutation). Methods: Mice 9 weeks of age were treated ± SGLT2i empagliflozin (EMPA, 0.15 mg/g chow). After 2 weeks, prior to LVH onset, myocardial transcriptomic analysis was performed. After 16 weeks, echocardiography, proteomics, fasted GIR, and histology were obtained. Glucose fluxes, energetics and 13 C substrate oxidation were measured in isolated beating hearts by 31 P and 13 C NMR spectroscopy. Results: R403Q mice had ↓GIR which was normalized by EMPA. Transcriptomics (2 weeks) and proteomics (16 weeks) confirmed downregulation of electron transport and FAO pathways, and upregulation of LVH and fibrosis pathways. At 16 weeks, R403Q hearts exhibited LVH, fibrosis, ↓diastolic function and ↓contractile reserve (rate pressure product increase between low and high workload). Metabolically, R403Q had ↑glucose uptake and ↓GGC with ↑lactate production; ↓FAO and impaired energetics (↓free energy of ATP hydrolysis, ΔG ~ATP , at both workloads). The HCM phenotype and all measures of metabolic dysfunction were partially or completely prevented by EMPA. Conclusion: R403Q hearts display marked metabolic reprogramming that appears early in the disease process and leads to energetic dysfunction. SGLT2i corrects GIR, attenuates metabolic reprogramming and the energetic, structural and functional features of HCM. SGLT2i and possibly other measures to modulate glucagon signaling hold therapeutic potential in HCM.

Autoencoders for dimensionality reduction in molecular dynamics: Collective variable dimension, biasing, and transition states.

The heat shock protein 90 (Hsp90) is a molecular chaperone that controls the folding and activation of client proteins using the free energy of ATP hydrolysis. The Hsp90 active site is in its N-terminal domain (NTD). Our goal is to characterize the dynamics of NTD using an autoencoder-learned collective variable (CV) in conjunction with adaptive biasing force Langevin dynamics. Using dihedral analysis, we cluster all available experimental Hsp90 NTD structures into distinct native states. We then perform unbiased molecular dynamics (MD) simulations to construct a dataset that represents each state and use this dataset to train an autoencoder. Two autoencoder architectures are considered, with one and two hidden layers, respectively, and bottlenecks of dimension k ranging from 1 to 10. We demonstrate that the addition of an extra hidden layer does not significantly improve the performance, while it leads to complicated CVs that increase the computational cost of biased MD calculations. In addition, a two-dimensional (2D) bottleneck can provide enough information of the different states, while the optimal bottleneck dimension is five. For the 2D bottleneck, the 2D CV is directly used in biased MD simulations. For the five-dimensional (5D) bottleneck, we perform an analysis of the latent CV space and identify the pair of CV coordinates that best separates the states of Hsp90. Interestingly, selecting a 2D CV out of the 5D CV space leads to better results than directly learning a 2D CV and allows observation of transitions between native states when running free energy biased dynamics.

Microcalorimetry reveals multi-state thermal denaturation of G. stearothermophilus tryptophanyl-tRNA synthetase.

Mechanistic studies of Geobacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford an unusually detailed description-the escapement mechanism-for the distinct steps coupling catalysis to domain motion, efficiently converting the free energy of ATP hydrolysis into biologically useful alternative forms of information and work. Further elucidation of the escapement mechanism requires understanding thermodynamic linkages between domain configuration and conformational stability. To that end, we compare experimental thermal melting of fully liganded and apo TrpRS with a computational simulation of the melting of its fully liganded form. The simulation also provides important structural cameos at successively higher temperatures, enabling more confident interpretation. Experimental and simulated melting both proceed through a succession of three transitions at successively higher temperature. The low-temperature transition occurs at approximately the growth temperature of the organism and so may be functionally relevant but remains too subtle to characterize structurally. Structural metrics from the simulation imply that the two higher-temperature transitions entail forming a molten globular state followed by unfolding of secondary structures. Ligands that stabilize the enzyme in a pre-transition (PreTS) state compress the temperature range over which these transitions occur and sharpen the transitions to the molten globule and fully denatured states, while broadening the low-temperature transition. The experimental enthalpy changes provide a key parameter necessary to convert changes in melting temperature of combinatorial mutants into mutationally induced conformational free energy changes. The TrpRS urzyme, an excerpted model representing an early ancestral form, containing virtually the entire catalytic apparatus, remains largely intact at the highest simulated temperatures.

Two-component molecular motor driven by a GTPase cycle

AbstractATPases are a group of enzymes that can cyclically convert the free energy of ATP hydrolysis into mechanical work. GTPases are another class of enzymes that are predominantly associated with signal transduction processes, but their role in mechanotransduction is less established. It was previously shown that the binding of the GTPase Rab5 to the tethering protein EEA1 induces a large conformational change in EEA1 from a rigid, extended to a flexible, collapsed state. This entropic collapse of EEA1 gives rise to an effective force that can pull tethered membranes closer. It currently remains unclear if EEA1 can return from the collapsed to the extended conformation without the aid of chaperone proteins. Here we show that EEA1 in a bulk solution can undergo multiple flexibility transition cycles driven by the energetics of Rab5 binding and unbinding as well as GTP hydrolysis. Each cycle can perform up to 20kBT of mechanical work. Hence, Rab5 and EEA1 constitute a two-component molecular motor driven by the chemical energy derived from the Rab5 GTPase cycle. We conclude that tethering proteins and their small GTPase partners can have active mechanical roles in membrane trafficking.

On the interdependence of ketone body oxidation, glycogen content, glycolysis and energy metabolism in the heart.

In heart, glucose and glycolysis are important for anaplerosis and potentially therefore for d-β-hydroxybutyrate (βHB) oxidation. As a glucose store, glycogen may also furnish anaplerosis. We determined the effects of glycogen content on βHB oxidation and glycolytic rates, and their downstream effects on energetics, in the isolated rat heart. High glycogen (HG) and low glycogen (LG) containing hearts were perfused with 11mM [5-3 H]glucose and/or 4mM [14 C]βHB to measure glycolytic rates or βHB oxidation, respectively, then freeze-clamped for glycogen and metabolomic analyses. Free cytosolic [NAD+ ]/[NADH] and mitochondrial [Q+ ]/[QH2 ] ratios were estimated using the lactate dehydrogenase and succinate dehydrogenase reaction, respectively. Phosphocreatine (PCr) and inorganic phosphate (Pi ) concentrations were measured using 31 P-nuclear magnetic resonance spectroscopy. Rates of βHB oxidation in LG hearts were half that in HG hearts, with βHB oxidation directly proportional to glycogen content. βHB oxidation decreased glycolysis in all hearts. Glycogenolysis in glycogen-replete hearts perfused with βHB alone was twice that of hearts perfused with βHB and glucose, which had significantly higher levels of the glycolytic intermediates fructose 1,6-bisphosphate and 3-phosphoglycerate, and higher free cytosolic [NAD+ ]/[NADH]. βHB oxidation increased the Krebs cycle intermediates citrate, 2-oxoglutarate and succinate, the total NADP/H pool, reduced mitochondrial [Q+ ]/[QH2 ], and increased the calculated free energy of ATP hydrolysis (∆GATP ). Although βHB oxidation inhibited glycolysis, glycolytic intermediates were not depleted, and cytosolic free NAD remained oxidised. βHB oxidation alone increased Krebs cycle intermediates, reduced mitochondrial Q and increased ∆GATP . We conclude that glycogen facilitates cardiac βHB oxidation by anaplerosis. KEY POINTS: Ketone bodies (d-β-hydroxybutyrate, acetoacetate) are increasingly recognised as important cardiac energetic substrates, in both healthy and diseased hearts. As 2-carbon equivalents they are cataplerotic, causing depletion of Krebs cycle intermediates; therefore their utilisation requires anaplerotic supplementation, and intra-myocardial glycogen has been suggested as a potential anaplerotic source during ketone oxidation. It is demonstrated here that cardiac glycogen does indeed provide anaplerotic substrate to facilitate β-hydroxybutyrate oxidation in isolated perfused rat heart, and this contribution was quantified using a novel pulse-chase metabolic approach. Further, using metabolomics and 31 P-MR, it was shown that glycolytic flux from myocardial glycogen increased the heart's ability to oxidise βHB, and βHB oxidation increased the mitochondrial redox potential, ultimately increasing the free energy of ATP hydrolysis.

ATP hydrolysis kinetics and thermodynamics as determinants of calcium oscillation in pancreatic β cells

Cellular ATP plays an important role in the calcium oscillation signal transduction pathway of pancreatic $\ensuremath{\beta}$ cells. It triggers oscillation by binding the ATP-sensitive ${\text{K}}^{+}$ channels $({\text{K}}_{\mathrm{ATP}})$, and maintains the oscillation by providing ATP hydrolysis free energy for the normal function of ion pumps on the plasma membrane. To reveal how cellular ATP level and ATP hydrolysis free energy affect calcium oscillation, we first constructed a simplified kinetic model of ${\text{K}}_{\mathrm{ATP}}$ and calcium pumps, then analyzed their thermodynamic characteristics. Bifurcation of calcium oscillation is determined by both cellular ATP concentration and ATP hydrolysis free energy such that an insufficient ATP energy supply would result in dysfunctional calcium oscillation. Second, to investigate the glucose sensing in $\ensuremath{\beta}$ cells, we developed a glycolysis-calcium model that considers the dynamics of ATP and free energy levels. The model simulated three calcium patterns in wild type cells and impaired calcium response of ${\text{K}}_{\mathrm{ATP}}$ mutant cells, allowing the use of the ATP-free energy phase plane to explore the underlying mechanism. Our results reveal the thermodynamics of calcium oscillation and provide a framework for understanding the thermodynamics of other ion transport systems.

How Does F1-ATPase Generate Torque?: Analysis From Cryo-Electron Microscopy and Rotational Catalysis of Thermophilic F1.

The F1-ATPase is a rotary motor fueled by ATP hydrolysis. Its rotational dynamics have been well characterized using single-molecule rotation assays. While F1-ATPases from various species have been studied using rotation assays, the standard model for single-molecule studies has been the F1-ATPase from thermophilic Bacillus sp. PS3, named TF1. Single-molecule studies of TF1 have revealed fundamental features of the F1-ATPase, such as the principal stoichiometry of chemo-mechanical coupling (hydrolysis of 3 ATP per turn), torque (approximately 40 pN·nm), and work per hydrolysis reaction (80 pN·nm = 48 kJ/mol), which is nearly equivalent to the free energy of ATP hydrolysis. Rotation assays have also revealed that TF1 exhibits two stable conformational states during turn: a binding dwell state and a catalytic dwell state. Although many structures of F1 have been reported, most of them represent the catalytic dwell state or its related states, and the structure of the binding dwell state remained unknown. A recent cryo-EM study on TF1 revealed the structure of the binding dwell state, providing insights into how F1 generates torque coupled to ATP hydrolysis. In this review, we discuss the torque generation mechanism of F1 based on the structure of the binding dwell state and single-molecule studies.

Does Inosine Monophosphate Formation Facilitate the Bioenergetic Response to Incremental Contractions in Human Skeletal Muscle In Vivo?

Traditionally, it has been accepted that working muscle will endeavor to maintain [ATP] near its resting level in order to maintain a favorable free energy of ATP hydrolysis (∆GATP). Recent reports of significant declines in [ATP] during maximal muscular contractions in vivo spark new interest in this concept. ATP is hydrolyzed to adenosine diphosphate (ADP) in the creatine kinase reaction to provide energy directly to working ATPases. As needed, additional energy can be provided by the breakdown of ADP to adenosine monophosphate (AMP), which is rapidly cleared by the formation of inosine monophosphate (IMP), with accompanying loss of total adenine nucleotides. IMP formation has been thought to occur only during very intense muscular work, wherein ATP production does not keep pace with ATP consumption. Here, we propose a role for IMP in managing both ∆GATP and flux through a key energetic pathway during contractions. To test our hypothesis that IMP formation mitigates the accumulation of ADP, 8 males (28.4 + 3.5 yr, mean + SD) performed 8 min of incremental, isotonic knee extension contractions (1 every 2 s, starting at 6% peak torque and incrementing by 3% every 2 min) on a magnetic resonance (MR)‐compatible ergometer in a 3‐Tesla MR system. 31Phosphorus MR spectra were obtained at rest (60‐s average) and throughout the contraction protocol (10‐s temporal resolution). Peaks corresponding to ATP, phosphocreatine (PCr), inorganic phosphate (Pi), and phosphomonoesters (PME) were fit in jMRUI, and concentrations for these metabolites were determined assuming resting [ATP] = 8.2 mM. [ADP], [AMP], [IMP], and the rate of ATP (mM∙s‐1) production by non‐oxidative glycolysis (i.e., wherein the fate of pyruvate is lactate; ATPgly) were also calculated. As expected, [PCr] decreased and [Pi] increased approximately linearly throughout the incremental contraction protocol. Surprisingly, [ATP] decreased and [IMP] increased (to 7.3 + 0.4 mM and 0.8 + 0.56 mM, respectively) steadily from the onset of contractions until the final stage, at which point no further changes were observed. In contrast, both [ADP] and [AMP] increased linearly from the start of contractions until the final stage, when they accumulated more rapidly; ultimately to 109.9 + 52.1 uM and 1.0 + 0.91 uM, respectively. The glycolytic contribution to ATP production was consistent for the first 3 stages, after which ATPgly increased rapidly to 0.102 + 0.14 mM·s‐1 at 480 s. Collectively, the timing and magnitude of these metabolic changes in working muscle suggest a sequence of responses designed to maintain cytosolic [ADP] sufficiently low as to mitigate changes in ∆GATP, but at a level sufficient to stimulate ATPgly as contraction intensity increases. A novel observation in this study was the decrease in [ATP] (and thus increase in [IMP]) from the onset of the contraction protocol, which then leveled off at the highest contraction intensity. The utility and consequences of these responses remain to be determined, but this study supports the concept that IMP formation is important in maintaining the cellular energy state as well as in directing the bioenergetic response to a series of incremental muscular contractions in vivo.

Abstract 9199: A Novel Small Molecule Troponin Activator Increases Cardiac Contractile Function Without Negative Impact on Energetics or Diastolic Function

Background: Current heart failure (HF) therapies improve cardiac energy balance and prolong survival by unloading the failing heart without targeting the underlying problem of reduced cardiac contractility. Traditional inotropic medications, also termed calcitropes, stimulate contractility via energetically costly augmentation of calcium cycling and worsen patient survival. Myotropes are a new class of agents that activate the sarcomere directly, independent of cAMP and calcium. We hypothesize that a novel myotrope, troponin activator (TA1), increases contractility without the deleterious myocardial energetic impact of calcitrope dobutamine (DOB). Methods: We determined the pharmacodynamics of TA1 ex vivo and in vivo in anesthetized normal rats. Isolated rat hearts were perfused with incremental concentrations of TA1 or DOB to compare their effect on cardiac contractility and high-energy phosphate concentrations using 31 P NMR spectroscopy. Results: A dose dependent increase in contractility was observed in vivo by echocardiography after acute administration of TA1. In isolated hearts, increasing concentrations of TA1 and DOB similarly increased rate pressure product (RPP), which is a product of developed pressure (DevP) and heart rate (HR). At equivalent doses (DOB 120 nM, TA1 60 nM), TA1 increased DevP more and HR less compared to DOB. DOB decreased phosphocreatine (PCr) to ATP ratio and free energy of ATP hydrolysis (ΔG ~ATP ) and elevated left ventricular end-diastolic pressure (LVEDP). In contrast, the TA1 increased RPP without any effect on HR, LVEDP, PCr/ATP ratio or ΔG ~ATP . Conclusions: Here we describe a novel myotrope, TA1, that increased myocardial contractility by sensitizing the sarcomere to calcium without impairing diastolic function or depleting the cardiac energy reserve. Since energetic depletion negatively correlates with long term survival, TA1 may represent a superior alternative to traditional inotropes in HF management.

Abstract 10678: Butyrate Improves Energetics, Diastolic Function and Contractile Reserve in Hearts from Mice with Hypertrophic Cardiomyopathy Due to Myosin R403Q Mutation

Background: It is well established that hearts with hypertrophic cardiomyopathy (HCM) are energy starved as reflected by a decreased phosphocreatine to ATP ratio that corresponds to increased ADP and decreased free energy of ATP hydrolysis (ΔG ~ATP ). Notably, worsened energetics precedes hypertrophy in development of HCM and mitochondrial mutations impeding ATP synthesis frequently lead to a hypertrophic phenotype similar to HCM. It remains unclear whether targeted strategies to boost mitochondrial ATP synthesis may improve chronically depressed diastolic function and contractile reserve. Here we hypothesize that saturating mitochondria with an accessible substrate, butyrate, acutely improves energetics and function in HCM. Methods and Results: Isolated hearts from 6 months old mice with HCM due to R403Q myosin mutation (R403Q) vs. the wild type littermates (WT) were studied using 31 P NMR spectroscopy to measure ATP synthesis, ADP and ΔG ~ATP at low (LW) and high workload (HW) and HW plus 4 mM butyrate (HWB). As expected, compared to WT, R403Q hearts showed: ↑ATP synthesis associated with a trend for ↑rate pressure product (RPP, p=0.08) at LW but were unable to increase these parameters further at HW. Energetics (↑ADP and ↓ΔG ~ATP ) were depressed at LW and worsened further at HW. Diastolic dysfunction (↑EDP) developed at HW. Butyrate perfusion (HWB) significantly improved all energetic and contractile parameters in R403Q hearts. Conclusion: Here we show that mouse hearts with HCM due to myosin R403Q mutation have worsened energetics despite a higher ATP synthesis rate at baseline. With higher work demand R403Q hearts are unable to dynamically increase ATP synthesis or work. Acute saturation with butyrate enables a further increase in ATP synthesis, normalizing energetics and improving diastolic function and contractile reserve. Thus, our results suggest that targeting mitochondrial function may be a promising strategy in management of HCM.

Novel Small-Molecule Troponin Activator Increases Cardiac Contractile Function Without Negative Impact on Energetics.

Current heart failure therapies unload the failing heart without targeting the underlying problem of reduced cardiac contractility. Traditional inotropes (ie, calcitropes) stimulate contractility via energetically costly augmentation of calcium cycling and worsen patient survival. A new class of agents-myotropes-activates the sarcomere directly, independent of calcium. We hypothesize that a novel myotrope TA1 increases contractility without the deleterious myocardial energetic impact of a calcitrope dobutamine. We determined the effect of TA1 in bovine cardiac myofibrils and human cardiac microtissues, ex vivo in mouse cardiac fibers and in vivo in anesthetized normal rats. Effects of increasing concentrations of TA1 or dobutamine on contractile function, phosphocreatine and ATP concentrations, and ATP production were assessed by 31P nuclear magnetic resonance spectroscopy on isolated perfused rat hearts. TA1 increased the rate of myosin ATPase activity in isolated bovine myofibrils and calcium sensitivity in intact mouse papillary fibers. Contractility increased dose dependently in human cardiac microtissues and in vivo in rats as assessed by echocardiography. In isolated rat hearts, TA1 and dobutamine similarly increased the rate-pressure product. Dobutamine increased both developed pressure and heart rate accompanied by decreased phosphocreatine-to-ATP ratio and decreased free energy of ATP hydrolysis (ΔG~ATP) and elevated left ventricular end diastolic pressure. In contrast, the TA1 increased developed pressure without any effect on heart rate, left ventricular end diastolic pressure, phosphocreatine/ATP ratio, or ΔG~ATP. Novel myotrope TA1 increased myocardial contractility by sensitizing the sarcomere to calcium without impairing diastolic function or depleting the cardiac energy reserve. Since energetic depletion negatively correlates with long-term survival, myotropes may represent a superior alternative to traditional inotropes in heart failure management.

DNA-Topology Simplification by Topoisomerases.

The topological properties of DNA molecules, supercoiling, knotting, and catenation, are intimately connected with essential biological processes, such as gene expression, replication, recombination, and chromosome segregation. Non-trivial DNA topologies present challenges to the molecular machines that process and maintain genomic information, for example, by creating unwanted DNA entanglements. At the same time, topological distortion can facilitate DNA-sequence recognition through localized duplex unwinding and longer-range loop-mediated interactions between the DNA sequences. Topoisomerases are a special class of essential enzymes that homeostatically manage DNA topology through the passage of DNA strands. The activities of these enzymes are generally investigated using circular DNA as a model system, in which case it is possible to directly assay the formation and relaxation of DNA supercoils and the formation/resolution of knots and catenanes. Some topoisomerases use ATP as an energy cofactor, whereas others act in an ATP-independent manner. The free energy of ATP hydrolysis can be used to drive negative and positive supercoiling or to specifically relax DNA topologies to levels below those that are expected at thermodynamic equilibrium. The latter activity, which is known as topology simplification, is thus far exclusively associated with type-II topoisomerases and it can be understood through insight into the detailed non-equilibrium behavior of type-II enzymes. We use a non-equilibrium topological-network approach, which stands in contrast to the equilibrium models that are conventionally used in the DNA-topology field, to gain insights into the rates that govern individual transitions between topological states. We anticipate that our quantitative approach will stimulate experimental work and the theoretical/computational modeling of topoisomerases and similar enzyme systems.

Switch-1 instability at the active site decouples ATP hydrolysis from force generation in myosin II.

Myosin active site elements (i.e., switch‐1) bind both ATP and a divalent metal to coordinate ATP hydrolysis. ATP hydrolysis at the active site is linked via allosteric communication to the actin polymer binding site and lever arm movement, thus coupling the free energy of ATP hydrolysis to force generation. How active site motifs are functionally linked to actin binding and the power stroke is still poorly understood. We hypothesize that destabilizing switch‐1 movement at the active site will negatively affect the tight coupling of the ATPase catalytic cycle to force production. Using a metal‐switch system, we tested the effect of interfering with switch‐1 coordination of the divalent metal cofactor on force generation. We found that while ATPase activity increased, motility was inhibited. Our results demonstrate that a single atom change that affects the switch‐1 interaction with the divalent metal directly affects actin binding and productive force generation. Even slight modification of the switch‐1 divalent metal coordination can decouple ATP hydrolysis from motility. Switch‐1 movement is therefore critical for both structural communication with the actin binding site, as well as coupling the energy of ATP hydrolysis to force generation.

On the functioning mechanism of an ATP-driven molecular motor.

A molecular motor, an ATP-driven protein or protein complex, fulfills its function by utilizing the ATP hydrolysis cycle comprising the following elementary processes: (1) the binding of ATP to the motor, (2) ATP hydrolysis (ATP+H2O→ADP+Pi), and (3) dissociation of ADP and Pi from the motor. Paradigmatic examples which have received extensive investigations are myosin achieving unidirectional movement along filamentous actin (F-actin) and F1-ATPase whose γ subunit accomplishes unidirectional rotation within the α3β3 complex (see Fig. 1). Though they are simpler than the sarcomere and the FoF1-ATP synthase, the investigations provide physical insights into and much useful information on the functioning mechanism of the motor. In the prevailing view, the motor converts the free energy of ATP hydrolysis to mechanical work that must be performed against the viscous resistance force by water during the unidirectional movement or rotation. The motor is highlighted as the system of interest and the aqueous solution surrounding it is regarded as the external system. In this article, the author suggests a new view by pointing out that the prevailing view is problematic and inconsistent with some of experi­mental observations. Detailed discussions are given in recent books written by the author [1,2] and references therein, and only the physical essence is recapitulated here. Open in a separate window Figure 1 Functional expression of a molecular motor utilizing ATP hydrolysis cycle. (a) Unidirectional movement of myosin, an ATP-driven protein, along F-actin. The ATP hydrolysis cycle occurs for myosin. In the real system, F-actin possesses a double helical structure. (b) Unidirectional rotation of γ subunit within α3β3 complex of F1-ATPase, an ATP-driven protein complex. The ATP hydrolysis cycle occurs for the α3β3 complex. The γ subunit rotates in the counterclockwise direction when F1-ATPase is viewed from the Fo side (θ denotes the rotation angle arbitrarily defined for the γ subunit).

Magnetic resonance spectroscopy reveals mitochondrial dysfunction in amyotrophic lateral sclerosis.

Mitochondrial dysfunction is postulated to be central to amyotrophic lateral sclerosis (ALS) pathophysiology. Evidence comes primarily from disease models and conclusive data to support bioenergetic dysfunction in vivo in patients is currently lacking. This study is the first to assess mitochondrial dysfunction in brain and muscle in individuals living with ALS using 31P-magnetic resonance spectroscopy (MRS), the modality of choice to assess energy metabolism in vivo. We recruited 20 patients and 10 healthy age and gender-matched control subjects in this cross-sectional clinico-radiological study. 31P-MRS was acquired from cerebral motor regions and from tibialis anterior during rest and exercise. Bioenergetic parameter estimates were derived including: ATP, phosphocreatine, inorganic phosphate, adenosine diphosphate, Gibbs free energy of ATP hydrolysis (ΔGATP), phosphomonoesters, phosphodiesters, pH, free magnesium concentration, and muscle dynamic recovery constants. Linear regression was used to test for associations between brain data and clinical parameters (revised amyotrophic functional rating scale, slow vital capacity, and upper motor neuron score) and between muscle data and clinico-neurophysiological measures (motor unit number and size indices, force of contraction, and speed of walking). Evidence for primary dysfunction of mitochondrial oxidative phosphorylation was detected in the brainstem where ΔGATPand phosphocreatine were reduced. Alterations were also detected in skeletal muscle in patients where resting inorganic phosphate, pH, and phosphomonoesters were increased, whereas resting ΔGATP, magnesium, and dynamic phosphocreatine to inorganic phosphate recovery were decreased. Phosphocreatine in brainstem correlated with respiratory dysfunction and disability; in muscle, energy metabolites correlated with motor unit number index, muscle power, and speed of walking. This study provides in vivo evidence for bioenergetic dysfunction in ALS in brain and skeletal muscle, which appears clinically and electrophysiologically relevant. 31P-MRS represents a promising technique to assess the pathophysiology of mitochondrial function in vivo in ALS and a potential tool for future clinical trials targeting bioenergetic dysfunction.

An Equivocal Final Link - Quantitative Determination of the Thermodynamic Efficiency of ATP Hydrolysis - Sullies the Chain of Electric, Ionic, Mechanical and Metabolic Steps Underlying Cardiac Contraction.

Each beat of the heart completes the final step in a sequence of events commencing with electrical excitation-triggered release of Ca2+ from the sarcoplasmic reticulum which, in turn, triggers ATP-hydrolysis-dependent mechanical contraction. Given that Thermodynamics is inherently detail-independent, the heart can be thus be viewed as a mechanical pump – the generator of pressure that drives blood through the systemic and pulmonary circulations. The beat-to-beat pressure-volume work (W) of the heart is relatively straightforward to measure experimentally. Given an ability to measure, simultaneously, the accompanying heat production or oxygen consumption, it is trivial to calculate the mechanical efficiency: ε = W/ΔH where ΔH is the change of enthalpy: (W + Q), Q representing the accompanying production of heat. But it is much less straightforward to measure the thermodynamic efficiency: η = W/ΔGATP, where ΔGATP signifies the Gibbs Free Energy of ATP hydrolysis. The difficulty arises because of uncertain quantification of the substrate-dependent yield of ATP - conveniently expressed as the P/O2 ratio. P/O2 ratios, originally (“classically”) inferred from thermal studies, have been considerably reduced over the past several decades by re-analysis of the stoichiometric coefficients separating sequential steps in the electron transport system – in particular, dropping the requirement that the coefficients have integer values. Since the early classical values are incompatible with the more recent estimates, we aim to probe this discrepancy with a view to its reconciliation. Our probe consists of a simple, thermodynamically constrained, algebraic model of cardiac mechano-energetics. Our analysis fails to reconcile recent and classical estimates of PO2 ratios; hence, we are left with a conundrum.

How Cytoplasmic Dynein Couples ATP Hydrolysis Cycle to Diverse Stepping Motions: Kinetic Modeling

Cytoplasmic dynein is a two-headed molecular motor that moves to the minus end of a microtubule by ATP hydrolysis free energy. By employing its two heads (motor domains), cytoplasmic dynein exhibits various bipedal stepping motions: inchworm and hand-over-hand motions, as well as nonalternating steps of one head. However, the molecular basis to achieve such diverse stepping manners remains unclear because of the lack of an experimental method to observe stepping and the ATPase reaction of dynein simultaneously. Here, we propose a kinetic model for bipedal motions of cytoplasmic dynein and perform Gillespie Monte Carlo simulations that qualitatively reproduce most experimental data obtained to date. The model represents the status of each motor domain as five states according to conformation and nucleotide- and microtubule-binding conditions of the domain. In addition, the relative positions of the two domains were approximated by three discrete states. Accompanied by ATP hydrolysis cycles, the model dynein stochastically and processively moved forward in multiple steps via diverse pathways, including inchworm and hand-over-hand motions, similarly to experimental data. The model reproduced key experimental motility-related properties, including velocity and run length, as functions of the ATP concentration and external force, therefore providing a plausible explanation of how dynein achieves various stepping manners with explicit characterization of nucleotide states. Our model highlights the uniqueness of dynein in the coupling of ATPase with its movement during both inchworm and hand-over-hand stepping.

Conformational dynamics modulate the catalytic activity of the molecular chaperone Hsp90

The heat shock protein 90 (Hsp90) is a molecular chaperone that employs the free energy of ATP hydrolysis to control the folding and activation of several client proteins in the eukaryotic cell. To elucidate how the local ATPase reaction in the active site couples to the global conformational dynamics of Hsp90, we integrate here large-scale molecular simulations with biophysical experiments. We show that the conformational switching of conserved ion pairs between the N-terminal domain, harbouring the active site, and the middle domain strongly modulates the catalytic barrier of the ATP-hydrolysis reaction by electrostatic forces. Our combined findings provide a mechanistic model for the coupling between catalysis and protein dynamics in Hsp90, and show how long-range coupling effects can modulate enzymatic activity.

Increasing mitochondrial ATP synthesis with butyrate normalizes ADP and contractile function in metabolic heart disease.

Metabolic heart disease (MHD), which is strongly associated with heart failure with preserved ejection fraction, is characterized by reduced mitochondrial energy production and contractile performance. In this study, we tested the hypothesis that an acute increase in ATP synthesis, via short chain fatty acid (butyrate) perfusion, restores contractile function in MHD. Isolated hearts of mice with MHD due to consumption of a high fat high sucrose (HFHS) diet or on a control diet (CD) for 4 months were studied using 31 P NMR spectroscopy to measure high energy phosphates and ATP synthesis rates during increased work demand. At baseline, HFHS hearts had increased ADP and decreased free energy of ATP hydrolysis (ΔG~ATP ), although contractile function was similar between the two groups. At high work demand, the ATP synthesis rate in HFHS hearts was reduced by over 50%. Unlike CD hearts, HFHS hearts did not increase contractile function at high work demand, indicating a lack of contractile reserve. However, acutely supplementing HFHS hearts with 4mM butyrate normalized ATP synthesis, ADP, ΔG~ATP and contractile reserve. Thus, acute reversal of depressed mitochondrial ATP production improves contractile dysfunction in MHD. These findings suggest that energy starvation may be a reversible cause of myocardial dysfunction in MHD, and opens new therapeutic opportunities.