Energy transfer from adenosine triphosphate

Simulation toolkits at the molecular scale for trans-scale thermal signaling

Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in global changes in cell morphology and signaling. Therefore, we hypothesize an inevitable contribution of thermogenesis in modulating biological system functions throughout the spatial scales from molecules to individual organisms. One key issue examining the hypothesis, namely, the "trans-scale thermal signaling," resides at the molecular scale on the amount of heat released via individual reactions and by which mechanism the heat is employed for cellular function operations. This review introduces atomistic simulation tool kits for studying the mechanisms of thermal signaling processes at the molecular scale that even state-of-the-art experimental methodologies of today are hardly accessible. We consider biological processes and biomolecules as potential heat sources in cells, such as ATP/GTP hydrolysis and multiple biopolymer complex formation and disassembly. Microscopic heat release could be related to mesoscopic processes via thermal conductivity and thermal conductance. Additionally, theoretical simulations to estimate these thermal properties in biological membranes and proteins are introduced. Finally, we envisage the future direction of this research field.

The Rationale for Using Neridronate in Musculoskeletal Disorders: From Metabolic Bone Diseases to Musculoskeletal Pain

Neridronate or ((6-amino-1-hydroxy-1-phosphonohexyl) phosphonic acid) is an amino-bisphosphonate (BP) synthetized in Italy in 1986. Bisphosphonates are molecules with a P-C-P bond in their structure that allows strong and selectively binding to hydroxyapatite (HAP) as well as osteoclasts inhibition through different mechanisms of action. Neridronate was initially used to treat Paget disease of the bone, demonstrating effectiveness in reducing bone turnover markers as well as pain. The interesting molecular properties of neridronate foster its wide use in several other conditions, such as osteogenesis imperfecta, and osteoporosis. Thanks to the unique safety and efficacy profile, neridronate has been used in secondary osteoporosis due to genetic, rheumatic, and oncological diseases, including in pediatric patients. In the last decade, this drug has also been studied in chronic musculoskeletal pain conditions, such as algodystrophy, demonstrating effectiveness in improving extraskeletal outcomes. This review highlights historical and clinical insights about the use of neridronate for metabolic bone disorders and musculoskeletal pain conditions.

Single gold nanowire-based nanosensor for adenosine triphosphate sensing by using in-situ surface-enhanced Raman scattering technique

Development of new hot spots for surface enhanced Raman scattering (SERS) technique is of great significance recently. Herein, we developed a single Au nanowire (NW)-based nanosensor for adenosine triphosphate (ATP) sensing by using in-situ SERS technique. Single Au NWs, fabricated by laser-assisted pulling method and hydrofluoric acid (HF) etching process, were linked with single-stranded HS-terminated DNA. After that, gold-silver bimetallic nanoparticles (Au/Ag NPs), attached with thiol-containing Raman dyes and ATP aptamer, were immobilized on DNA-modified single AuNW due to the designed affinity between ATP aptamer and single-stranded DNA. This single AuNW-based device exhibited strong SERS signals. In the presence of adenosine triphosphate (ATP), due to the strong specific affinity between the aptamer and the target, the Au/Ag NPs will be separated from the AuNW, resulting in the obvious decrease of the Raman signals, which can be used for ATP sensing with high sensitivity, selectivity and stability. This nanosensor can be used as an ideal platform for real applications, especially at some confined-space samples, such as trace detection, single cell and in vivo analysis.

Elucidating microscopic events driven by GTP hydrolysis reaction in the Ras-GAP system with semi-reactive molecular dynamics simulations: the alternative role of a phosphate binding loop for mechanical energy storage

ATPase and GTPase have been widely found as chemical energy-mechanical work transducers, whereas the physicochemical mechanisms are not satisfactorily understood. We addressed the problem by examining John Ross' conjecture that repulsive Coulomb interaction between ADP/GDP and inorganic phosphate (P_i) does the mechanical work upon the system. We effectively simulated the consequence of a GTP hydrolysis reaction in a complex system of Rat sarcoma (Ras) and GTPase activation protein (GAP) in the framework of classical molecular dynamics by switching force field parameters between the reactant and product systems. We then observed a ca. 5 kcal mol^-1 increase of potential energy about the phosphate-binding loop (P-loop) in the Ras protein, indicating that the mechanical work generated via the GTP hydrolysis is converted into the local interaction energy and stored in the P-loop. Interestingly, this local energy storage in the P-loop depends on neither impulsive nor consecutive collisions of GDP and P_i with the P-loop. Instead, GTP-GDP conversion itself does work on the Ras system, elevating the potential energy. These observations encourage us to challenge a conjecture previously given by Ross. We assert that triphosphate nucleotide hydrolyses do mechanical work by producing emergent steric interaction accompanied by relaxation, namely, a shift of the biomolecular system to the non-equilibrium state on the reshaped potential energy landscape. Recalling the universality of the P-loop motif among GTPases and ATPases, the observations that we obtained through this study would progress the physicochemical understanding of the operating principles of GTP/ATP hydrolysis-driven biological nano-machines.

Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method

HlyB functions as an adenosine triphosphate (ATP)-binding cassette (ABC) transporter that enables bacteria to secrete toxins at the expense of ATP hydrolysis. Our previous work, based on potential energy profiles from combined quantum mechanical and molecular mechanical (QM/MM) calculations, has suggested that the highly conserved H-loop His residue H662 in the nucleotide binding domain (NBD) of E. coli HlyB may catalyze the hydrolysis of ATP through proton relay. To further test this hypothesis when entropic contributions are taken into account, we obtained QM/MM minimum free energy paths (MFEPs) for the HlyB reaction, making use of the string method in collective variables. The free energy profiles along the MFEPs confirm the direct participation of H662 in catalysis. The MFEP simulations of HlyB also reveal an intimate coupling between the chemical steps and a local protein conformational change involving the signature-loop residue S607, which may serve a catalytic role similar to an Arg-finger motif in many ATPases and GTPases in stabilizing the phosphoryl-transfer transition state.

Biochemical bases of growth variation during development: a study of protein turnover in pedigreed families of bivalve larvae (Crassostrea gigas)

Animal size is a highly variable trait regulated by complex interactions between biological and environmental processes. Despite the importance of understanding the mechanistic bases of growth, predicting size variation in early stages of development remains challenging. Pedigreed lines of the Pacific oyster (Crassostrea gigas) were crossed to produce contrasting growth phenotypes to analyze the metabolic bases of growth variation in larval stages. Under controlled environmental conditions, substantial growth variation of up to 430% in shell length occurred among 12 larval families. Protein was the major biochemical constituent in larvae, with an average protein-to-lipid content ratio of 2.8. On average, 86% of protein synthesized was turned over (i.e. only 14% retained as protein accreted), with a regulatory shift in depositional efficiency resulting in increased protein accretion during later larval growth. Variation in protein depositional efficiency among families did not explain the range in larval growth rates. Instead, changes in protein synthesis rates predicted 72% of growth variation. High rates of protein synthesis to support faster growth, in turn, necessitated greater allocation of the total ATP pool to protein synthesis. An ATP allocation model is presented for larvae of C. gigas that includes the major components (82%) of energy demand: protein synthesis (45%), ion pump activity (20%), shell formation (14%) and protein degradation (3%). The metabolic trade-offs between faster growth and the need for higher ATP allocation to protein synthesis could be a major determinant of fitness for larvae of different genotypes responding to the stress of environmental change.

Mitochondrial glycerol 3-phosphate facilitates bumblebee pre-flight thermogenesis

Bumblebees (Bombus terrestris) fly at low ambient temperatures where other insects cannot, and to do so they must pre-warm their flight muscles. While some have proposed mechanisms, none fully explain how pre-flight thermogenesis occurs. Here, we present a novel hypothesis based on the less studied mitochondrial glycerol 3-phosphate dehydrogenase pathway (mGPDH). Using calorimetry, and high resolution respirometry coupled with fluorimetry, we report substrate oxidation by mGPDH in permeabilised flight muscles operates, in vitro, at a high flux, even in the absence of ADP. This may be facilitated by an endogenous, mGPDH-mediated uncoupling of mitochondria. This uncoupling increases ETS activity, which results in increased heat release. Furthermore, passive regulation of this mechanism is achieved via dampened temperature sensitivity of mGPDH relative to other respiratory pathways, and subsequent consumption of its substrate, glycerol 3-phosphate (G3P), at low temperatures. Mitochondrial GPDH may therefore facilitate pre-flight thermogenesis through poor mitochondrial coupling. We calculate this can occur at a sufficient rate to warm flight muscles until shivering commences, and until flight muscle function is adequate for bumblebees to fly in the cold.

Effect of protonation on the mechanism of phosphate monoester hydrolysis and comparison with the hydrolysis of nucleoside triphosphate in biomolecular motors

Hydrolysis of phosphate groups is a crucial reaction in living cells. It involves the breaking of two strong bonds, i.e. the O_aH bond of the attacking water molecule, and the PO_l bond of the substrate (O_a and O_l stand for attacking and leaving oxygen atoms). Mechanism of the hydrolysis reaction can proceed either by a concurrent or a sequential mechanism. In the concurrent mechanism, the breaking of O_aH and PO_l bonds occurs simultaneously, whereas in the sequential mechanism, the O_aH and PO_l bonds break at different stages of the reaction. To understand how protonation affects the mechanism of hydrolysis of phosphate monoester, we have studied the mechanism of hydrolysis of protonated and deprotonated phosphate monoester at M06-2X/6-311+G**//M06-2X/6-31+G*+ZPE level of theory (where ZPE stands for zero point energy). Our calculations show that in both protonated and deprotonated cases, the breaking of the water O_aH bond occurs before the breaking of the PO_l bond. Because the two events are not separated by a stable intermediate, the mechanism can be categorized as semi-concurrent. The overall energy barrier is 41kcalmol^-1 in the unprotonated case. Most (5/6th) of this is due to the initial breaking of the water O_aH bond. This component is lowered from 34 to 25kcalmol^-1 by adding one proton to the phosphate. The rest of the overall energy barrier comes from the subsequent breaking of the PO_l bond and is not sensitive to protonation. This is consistent with previous findings about the effect of triphosphate protonation on the hydrolysis, where the equivalent protonation (on the γ-phosphate) was seen to lower the barrier of breaking the water O_aH bond and to have little effect on the PO_l bond breaking. Hydrolysis pathways of phosphate monoester with initial breaking of the PO_l bond could not be found here. This is because the leaving group in phosphate monoester cannot be protonated, unlike in triphosphate hydrolysis, where protonation of the β- and γ-phosphates had been shown to promote a mechanism where the PO_l bond breaks before the O_aH bond does. We also point out that the charge shift due to PO_l bond breaking during sequential ATP hydrolysis in bio-molecular motors onsets the week unbinding of hydrolysis product that finally leads to the product release during power stroke.

Drastic Compensation of Electronic and Solvation Effects on ATP Hydrolysis Revealed through Large-Scale QM/MM Simulations Combined with a Theory of Solutions

Hydrolysis of adenosine triphosphate (ATP) is the "energy source" for a variety of biochemical processes. In the present work, we address key features of ATP hydrolysis: the relatively moderate value (about -10 kcal/mol) of the standard free energy, ΔG_hyd, of reaction and the insensitivity of ΔG_hyd to the number of excess electrons on ATP. We conducted quantum mechanical/molecular mechanical simulation combined with the energy-representation theory of solutions to analyze the electronic-state and solvation contributions to ΔG_hyd. It was revealed that the electronic-state contribution in ΔG_hyd is largely negative (favorable) upon hydrolysis, due to the reduction of electrostatic repulsion accompanying the breakage of the P-O bond. In contrast, the solvation effect was found to be strongly more favorable on the reactant side. Thus, we showed that a drastic compensation of the two opposite effects takes place, leading to the modest value of ΔG_hyd at each number of excess electrons examined. The computational analyses were also conducted for pyrophosphate ions (PPi), and the parallelism between the ATP and PPi hydrolyses was confirmed. Classical molecular dynamics simulation was further carried out to discuss the effect of the solvent environment; the insensitivity of ΔG_hyd to the number of excess electrons was seen to hold in solvent water and ethanol.

Facile synthesis of Au/Al2O3nanocomposites for improving the detection sensitivity of adenosine triphosphate

Alumina is widely recognized as chemically inert, and resistant to oxidation and high temperature.

Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism

The rotary motor enzyme FoF1-ATP synthase uses the proton-motive force across a membrane to synthesize ATP from ADP and Pi (H2PO4(-)) under cellular conditions that favor the hydrolysis reaction by a factor of 2 × 10(5). This remarkable ability to drive a reaction away from equilibrium by harnessing an external force differentiates it from an ordinary enzyme, which increases the rate of reaction without shifting the equilibrium. Hydrolysis takes place in the neighborhood of one conformation of the catalytic moiety F1-ATPase, whose structure is known from crystallography. By use of molecular dynamics simulations we trap a second structure, which is rotated by 40° from the catalytic dwell conformation and represents the state associated with ATP binding, in accord with single-molecule experiments. Using the two structures, we show why Pi is not released immediately after ATP hydrolysis, but only after a subsequent 120° rotation, in agreement with experiment. A concerted conformational change of the α3β3 crown is shown to induce the 40° rotation of the γ-subunit only when the βE subunit is empty, whereas with Pi bound, βE serves as a latch to prevent the rotation of γ. The present results provide a rationalization of how F1-ATPase achieves the coupling between the small changes in the active site of βDP and the 40° rotation of γ.

The interrelation between mechanical characteristics of contracting muscle, cross-bridge internal structure, and the mechanism of chemomechanical energy transduction

The cross-bridge working stroke is regarded as a continuous (without jumps) change of myosin head internal state under the action of a force exerted within the nucleotide-binding site. Involvement of a concept of continuous cross-bridge conformation enables discussion of the nature of the force propelling muscle, and the Coulomb repulsion of like-charged adenosine triphosphate (ATP) fragments ADP(2-) and P (i) (2-) can quite naturally be considered as the source of this force. Two entirely different types of working stroke termination are considered. Along with the fluctuation mechanism, which controls the working stroke duration t (w) at isometric contraction, another interrupt mechanism is initially taken into account. It is triggered when the lever arm shift amounts to the maximal value S ≈ 11 nm, the back door opens, and P(i) crashes out. As a result, t (w) becomes inversely proportional to the velocity v of sliding filaments t (w) ≈ S/v for a wide range of values of v. Principal features of the experimentally observed dependences of force, efficiency, and rate of heat production on velocity and ATP concentration can then be reproduced by fitting a single parameter: the velocity-independent time span t (r) between the termination of the last and beginning of the next working stroke. v becomes the principal variable of the model, and the muscle force changes under external load are determined by variations in v rather than in the tension of filaments. The Boltzmann equation for an ensemble of cross-bridges is obtained, and some collective effects are discussed.

Detection of adenosine triphosphate with an aptamer biosensor based on surface-enhanced Raman scattering

A simple, ultrasensitive, highly selective, and reagent-free aptamer-based biosensor has been developed for quantitative detection of adenosine triphosphate (ATP) using surface-enhanced Raman scattering (SERS). The sensor contains a SERS probe made of gold nanostar@Raman label@SiO(2) core-shell nanoparticles in which the Raman label (malachite green isothiocyanate, MGITC) molecules are sandwiched between a gold nanostar core and a thin silica shell. Such a SERS probe brings enhanced signal and low background fluorescence, shows good water-solubility and stability, and exhibits no sign of photobleaching. The aptamer labeled with the SERS probe is designed to hybridize with the cDNA on a gold film to form a rigid duplex DNA. In the presence of ATP, the interaction between ATP and the aptamer results in the dissociation of the duplex DNA structure and thereby removal of the SERS probe from the gold film, reducing the Raman signal. The response of the SERS biosensor varies linearly with the logarithmic ATP concentration up to 2.0 nM with a limit of detection of 12.4 pM. Our work has provided an effective method for detection of small molecules with SERS.

Interfacial viscoelasticity of myoglobin at air/water and air/solution interfaces: role of folding and clustering

This study describes the folding and organization of myoglobin (Mb) at the solution/air interface at different pH values of 2.5, 3.5, 5.5, 7.5, and 8.5. Dynamic surface tension and the associated dilational and shear viscoelasticity for Mb at these pH's have been studied using a sinusoidal surface compression and expansion for frequencies ranging from 0.01 to 0.4 Hz. The changes in dilational viscosity, elasticity, and fluorescence lifetime measurements have been related to the conformational changes of the protein films at the interface. It is observed that while acid-induced denaturation of the protein does not lead to large changes in dilational properties, the shear properties on the other hand are strongly influenced by it, and the protein behaves like a shear-thickening fluid. At higher pH, particularly at the isoelectric point, Mb is pseudoplastic indicating an increase in the shear viscosity. These results are strongly suggestive of formation of hydrophobic clusters at the protein-buffer interface because of the change in the overall charge distributions.

Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase

Understanding the nature of energy transduction in life processes requires a quantitative description of the energetics of the conversion of ATP to ADP by ATPases. Previous attempts to do so have provided an interesting insight but could not account for the rotary mechanism by a nonphenomenological structure/energy description. In particular it has been very challenging to account for the observations of the 80° and 40° rotational substates, without any prior information about such states in the simulation procedure. Here we use a coarse-grained model of F1-ATPase and generate, without the adjustment of phenomenological parameters, a structure-based free energy landscape that reproduces the energetics of the mechanochemical process. It is found that the landscape along the relevant rotary path is determined by the electrostatic free energy and not by steric effects. Furthermore, the generated surface and the corresponding Langevin dynamics simulations identify a hidden conformational barrier that provides a new fundamental interpretation of the catalytic dwell and illuminate the nature of the energy conversion process.

On the energetics of ATP hydrolysis in solution

ATP hydrolysis is the driving force of many life processes, yet the exact nature of and contributions to the energetics of this reaction are far from being clear. In particular, it is unclear how much of the driving force of this reaction is due to the separation of the already dissociated ADP + P(i) moieties rather than to the chemical event. This fundamental issue is explored here by ab initio calculations that use different solvation models, and it is found that, while the calculations are sensitive to the theoretical approach used, it is quite likely that the dissociation of the charged fragments makes a significant contribution to the energetics of ATP hydrolysis.

Heat transfer in protein-water interfaces

We investigate using transient non-equilibrum molecular dynamics simulation the temperature relaxation process of three structurally different proteins in water, namely; myoglobin, green fluorescence protein (GFP) and two conformations of the Ca(2+)-ATPase protein. By modeling the temperature relaxation process using the solution of the heat diffusion equation we compute the thermal conductivity and thermal diffusivity of the proteins, as well as the thermal conductance of the protein-water interface. Our results indicate that the temperature relaxation of the protein can be described using a macroscopic approach. The protein-water interface has a thermal conductance of the order of 100-270 MW K(-1) m(-2), characteristic of water-hydrophilic interfaces. The thermal conductivity of the proteins is of the order of 0.1-0.2 W K(-1) m(-1) as compared with approximately 0.6 W K(-1) m(-1) for water, suggesting that these proteins can develop temperature gradients within the biomolecular structures that are larger than those of aqueous solutions. We find that the thermal diffusivity of the transmembrane protein, Ca(2+)-ATPase is about three times larger than that of myoglobin or GFP. Our simulation shows that the Kapitza length of these structurally different proteins is of the order of 1 nm, showing that the protein-water interface should play a major role in defining the thermal relaxation of biomolecules.

Energy transfer from adenosine triphosphate: quantitative analysis and mechanistic insights

The ATP-ADP thermodynamic cycle is the fundamental mode of energy exchange in oxidative phosphorylation, photophosphorylation, muscle contraction, and intracellular transport by various molecular motors and is therefore of vital importance in biological energy transduction and storage. Following a recent suggestion in the pages of this journal (Ross, J. J. Phys. Chem. B 2006, 110, 6987-6990), we have carried out a simple quantitative analysis of a direct molecular mechanism of energy transfer from adenosine triphosphate (ATP). The simulation provides new insights into the mechanistic events following terminal phosphorus-oxygen bond cleavage during ATP hydrolysis. This approach also allows for the division of the energy-transfer process into elementary steps and for the prediction of the distribution of the standard-state Gibbs free energy of the overall ATP hydrolysis process among the various steps of substrate binding, bond cleavage, and product release in the enzymatic cycle, which had proved very difficult to specify previously. These predictions are consistent with available experimental data on ATP hydrolysis by protein biomolecular machines. The fundamental biological implications arising from our results are also discussed in detail. The aspects considered in this work enable us to look at the entire process of ATP synthesis/hydrolysis and energy transduction and storage in various biological molecular machines in a logically consistent and unified way.

The new unified theory of ATP synthesis/hydrolysis and muscle contraction, its manifold fundamental consequences and mechanistic implications and its applications in health and disease

Complete details of the thermodynamics and molecular mechanisms of ATP synthesis/hydrolysis and muscle contraction are offered from the standpoint of the torsional mechanism of energy transduction and ATP synthesis and the rotation-uncoiling-tilt (RUT) energy storage mechanism of muscle contraction. The manifold fundamental consequences and mechanistic implications of the unified theory for oxidative phosphorylation and muscle contraction are explained. The consistency of current mechanisms of ATP synthesis and muscle contraction with experiment is assessed, and the novel insights of the unified theory are shown to take us beyond the binding change mechanism, the chemiosmotic theory and the lever arm model. It is shown from first principles how previous theories of ATP synthesis and muscle contraction violate both the first and second laws of thermodynamics, necessitating their revision. It is concluded that the new paradigm, ten years after making its first appearance, is now perfectly poised to replace the older theories. Finally, applications of the unified theory in cell life and cell death are outlined and prospects for future research are explored. While it is impossible to cover each and every specific aspect of the above, an attempt has been made here to address all the pertinent details and what is presented should be sufficient to convince the reader of the novelty, originality, breakthrough nature and power of the unified theory, its manifold fundamental consequences and mechanistic implications, and its applications in health and disease.

How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase

F(o)F(1)-ATP synthase manufactures the energy "currency," ATP, of living cells. The soluble F(1) portion, called F(1)-ATPase, can act as a rotary motor, with ATP binding, hydrolysis, and product release, inducing a torque on the gamma-subunit. A coarse-grained plastic network model is used to show at a residue level of detail how the conformational changes of the catalytic beta-subunits act on the gamma-subunit through repulsive van der Waals interactions to generate a torque that drives unidirectional rotation, as observed experimentally. The simulations suggest that the calculated 85 degrees substep rotation is driven primarily by ATP binding and that the subsequent 35 degrees substep rotation is produced by product release from one beta-subunit and a concomitant binding pocket expansion of another beta-subunit. The results of the simulation agree with single-molecule experiments [see, for example, Adachi K, et al. (2007) Cell 130:309-321] and support a tri-site rotary mechanism for F(1)-ATPase under physiological condition.