Myosin-catalyzed ATP hydrolysis elucidated by 31P NMR kinetic studies and 1H PFG-diffusion measurements

We conducted ³¹P NMR kinetic studies and ¹H-diffusion measurements on myosin-catalyzed hydrolysis of adenosine triphosphate (ATP) under varied conditions. The data elucidate well the overall hydrolysis rate and various factors that significantly impact the reaction. We found that the enzymatic hydrolysis of ATP to adenosine diphosphate (ADP) was followed by ADP hydrolysis, and different nucleotides such as ADP and guanosine triphosphate acted as competitors of ATP. Increasing ATP or Mg²⁺ concentration resulted in decreased hydrolysis rate, and such effect can be related to the decrease of ATP diffusion constants. Below 50 °C, the hydrolysis was accelerated by increasing temperature following the Arrhenius’ law, but the hydrolysis rate was significantly lowered at higher temperature (~60 °C), due to the thermal–denaturation of myosin. The optimal pH range was around pH 6–8. These results are important for characterization of myosin-catalyzed ATP hydrolysis, and the method is also applicable to other enzymatic nucleotide reactions.     

Kinetic energy release in ionic fragmentations: Use as an ion structure probe

The kinetic energy released in unimolecular reactions, as measured from the width of the corresponding metastable peak, shows only a small dependence on such parameters as source temperature, ion-source residence time and ion acceleration voltage. Similarly, fragmenting ions generated from different members of an homologous series of molecular ions have been found to release the same kinetic energy and hence do not exhibit a degrees-of-freedom effect analogous to that for metastable abundances. In general, molecular ions formed by electron-impact have been found to release slightly less kinetic energy on fragmentation than the corresponding ions formed via a fragmentation sequence. These observations suggest that kinetic energy release is a useful method of structural characterization of metastable ions; while increase in the average internal energies of the ions sample lead to larger energy releases, this effect is usually small. The use of a very narrow energy resolving (β) slit and a procedure in which the metastable peak width is extrapolated to zero slit width has been found to improve the accuracy of measurement of the kinetic energy release, particularly when the metastable and main beam peak widths are of comparable magnitude.     

Microwave-Assisted Hydrothermal Rapid Synthesis of Ultralong Hydroxyapatite Nanowires Using Adenosine 5′-Triphosphate

Ultralong hydroxyapatite (HAP) nanowires are promising for various biomedical applications owing to their chemical similarity to the inorganic constituent of bone, high biocompatibility, good flexibility, excellent mechanical properties, etc. However, it is still challenging to control the formation of ultralong HAP nanowires because of the presence of free PO₄³⁻ ions in the reaction system containing the inorganic phosphate source. In addition, it takes a long period of time (usually tens of hours) for the synthetic process of ultralong HAP nanowires. Herein, for the first time, we have developed an eco-friendly calcium oleate precursor microwave hydrothermal method using biocompatible adenosine 5′-triphosphate (ATP) as a bio-phosphorus source and water as the only solvent for the rapid synthesis of ultralong HAP nanowires. The controllable hydrolysis of ATP can avoid the premature formation of calcium phosphate nuclei and uncontrollable crystal growth. Microwave heating can significantly shorten the synthetic time from tens of hours required by the traditional heating to 1 h, thus achieving high efficiency, energy saving and low cost. The as-prepared ultralong HAP nanowires with high flexibility have lengths of several hundred micrometers and diameters of 10~20 nm, and they usually self-assemble into nanowire bundles along their longitudinal direction. The as-prepared ultralong HAP nanowire/chitosan porous scaffold has excellent bioactivity, good biodegradation and cytocompatibility owing to the bioactive adenosine adsorbed on the surface of ultralong HAP nanowires. It is expected that ultralong HAP nanowires will be promising for various applications in the biomedical fields, such as bone defect repair, skin wound healing, and as a drug nanocarrier.     

ATP Drives the Formation of a Catalytic Hydrazone through an Energy Ratchet Mechanism

An energy ratchet mechanism is exploited for the synthesis of a molecule. In the presence of adenosine triphosphate (ATP), hydrazone-bond formation between an aldehyde and hydrazide is accelerated and the composition at thermodynamic equilibrium is shifted towards the hydrazone. Enzymatic hydrolysis of ATP installs a kinetically stable state, at which hydrazone is present at a higher concentration compared to the composition at thermodynamic equilibrium in the presence of the degradation products of ATP. It is shown that the kinetic state has an enhanced catalytic activity in the hydrolysis of an RNA-model compound.     

Structure and function of the energy-converting system of mitochondria

The main energy source for all endergonic processes occurring in living organisms is the phosphate bond energy of nucleoside triphosphates, especially adenosine triphosphate (ATP). In aerobic organisms, as for instance in mammals, more than 90% of ATP is formed during the process called oxidative phosphorylation. In this process, similar to that of muscle contraction and nerve excitation, nature works with vectorial processes taking place at a membrane separating distinct spaces from each other. The present article deals with the operation of a set of water-insoluble membrane proteins and enzymes vectorially transporting electrons, protons and other ions, which finally leads to the formation of ATP. This machinery transforming substrate oxidation energy into chemical energy in the form of the phosphoric anhydride bond of ATP operates with a very high efficiency. The structure and function of the machinery of mitochondrial oxidative phosphorylation are described. It consists of the electron transfer chain, the ATP-synthetase, the adenine nucleotide translocase and the phosphate carrier. The electron transfer chain can be resolved into multiprotein complexes—at three of them energy conversion takes place—and into the electron carriers ubiquinone and cytochrome c. The substrate oxidation energy is converted into the chemical energy of ATP with an electrochemical proton gradient as intermediary form. The energetic aspects of the processes are analyzed by linear irreversible thermodynamics. Great success has been gained during the past few years on the structural characterization of the participating proteins. The function of the various systems is partially elucidated on the molecular level; this concerns especially the mechanism of proton and adenine nucleotide translocation, as well as ATP formation.     

A study of the decomposition of field ionized doubly charged molecular ions

The dissociation of field ionized doubly charged organic molecular ions into doubly charged fragment ions and neutral fragments is discussed. The kinetic energy released during the dissociation of the singly and doubly charged molecular ions rules out the possibility of a direct correlation between their mechanisms of formation. Further, the pressure as well as the temperature dependence revealed that the singly charged molecular ions are formed by direct ionization of the neutral molecules, while the doubly charged molecular ions are formed through a second ionization process of the adsorbed molecular ions on the field anode surface.     

Towards Artificial Cells: Engineering Encapsulated Molecular Signaling with Intelligent DNA Nanomachines

The building and engineering of an artificial molecular signaling system in encapsulated vesicles is a key step towards artificial cells. Recently, Tan et al. reached a new milestone by integrating an intelligent DNA nano- gatekeeper with an artificial vesicle system. The DNA nanogatekeeper driven by adenosine triphosphate(ATP) is able to receive outside stimulus, which in turn switches the diffusion of environmental ions into the integrated vesicle. Most importantly, this system enables triggering downstream signaling cascaded reactions confined in the artificial vesicle, as well as returning feedback to the DNA nanogatekeeper, mimicking real cellular behaviors of reception, transduction and response. This work has been published online in Nature Communications aon February 20, 2020.     

Hsc70 ATPase: an insight into water dissociation and joint catalytic role of K+ and Mg2+ metal cations in the hydrolysis reaction

Hybrid quantum mechanics/molecular mechanics simulations, coupled to the recently introduced metadynamics method, performed on the adenosine triphosphate (ATP) of the bovine Hsc70 ATPase protein, show which specific water molecule of the solvation shell of the Mg2+ metal cation acts as a trigger in the initial phase of the ATP hydrolysis reaction in ATP synthase. Furthermore, we provide a detailed picture of the reaction mechanism, not accessible to experimental probes, that allows us to address two important issues not yet unraveled: (i) the pathway followed by a proton and a hydroxyl anion, produced upon dissociation of a putative catalytic H2O molecule, that is crucial in the selection of the reaction channel leading to the hydrolysis; (ii) the unique and cooperative role of K+ and Mg2+ metal ions in the reaction, acting as co-catalysts and promoting the release of the inorganic phosphate via an exchange of the OH- hydroxyl anion between their respective solvation shells. This is deeply different from the proton wire mechanism evidenced, for instance, in actin and lowers significantly the free energy barrier of the reaction.     

Hybrid molecular dynamics simulations of living filaments

We propose a hybrid molecular dynamics/multi-particle collision dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte Carlo scheme to deal with single monomer addition (polymerization) or removal (depolymerization), satisfying the detailed balance condition within a proper statistical mechanical framework. This model of filaments, based on the wormlike chain, aims to represent equilibrium polymers with distinct reaction rates at both ends, such as self-assembled adenosine diphosphate-actin filaments in the absence of adenosine triphosphate (ATP) hydrolysis and other proteins. We report the distribution of filament lengths and the corresponding dynamical fluctuations on an equilibrium trajectory. Potential generalizations of this method to include irreversible steps like ATP-actin hydrolysis are discussed.     

Classical kinetic theory of drift tube experiments involving molecular ion-neutral systems

A classical-mechanical kinetic theory is developed for drift tube experiments involving atomic ions in non-vibrating (rigid rotor) diatomic gases and for non-vibrating diatomic ions in atomic or non-vibrating diatomic gases. The relative ease with which classical transport cross sections can be computed makes this theory computationally feasible. First-approximation results of the present theory have the same general forms found previously with a semiclassical theory, and the present work indicates how higher approximations will modify these forms. Experimental implications are discussed, particularly as to how drift tube experiments can be used to quantitatively study the separate effects of internal and translational energy upon molecular ion-molecule reactions.     

ATP-Independent and Cell-Free Biosynthesis of β-Hydroxy Acids Using Vinyl Esters as Smart Substrates

In vitro biosynthetic pathways that condense and reduce molecules through coenzyme A (CoASH) activation demand energy and redox power in the form of ATP and NAD(P)H, respectively. These coenzymes must be orthogonally recycled by ancillary reactions that consume chemicals, electricity, or light, impacting the atom economy and/or the energy consumption of the biosystem. In this work, we have exploited vinyl esters as dual acyl and electron donor substrates to synthesize β-hydroxy acids through a non-decarboxylating Claisen condensation, reduction and hydrolysis stepwise cascade, including a NADH recycling step, catalyzed by a total of 4 enzymes. Herein, the chemical energy to activate the acyl group with CoASH and the redox power for the reduction are embedded into the vinyl esters. Upon optimization, this self-sustaining cascade reached a titer of (S)-3-hydroxy butyrate of 24 mM without requiring ATP and simultaneously recycling CoASH and NADH. This work illustrates the potential of in vitro biocatalysis to transform simple molecules into multi-functional ones.     

Destabilized carbenium ions: α-imidoyl carbenium ions and the electron impact mass spectra of α-haloaldimines and α-haloketimines

A series of α-chloro- and α-bromoketimines compounds (1-9) with different substituents at the α-position and at the imino group has been investigated by electron impact mass spectrometry as possible precursors of the correspondingly substituted α-imidoyl carbenium ion, an important class of destabilized carbenium ions. The main fragmentation of the molecular ions of compounds, 1-9 in the ion source corresponds to an α-cleavage at the imino group; however, fragment ions are also formed by loss of the α-halo substituent. These fragment ions correspond at least formally to α-imidoyl carbenium ions. Their further reactions in dependence on the type of substituents at the imino group and at the α-C atom, were studied by mass-analysed ion kinetic energy and collisional activation mass spectrometry. The results agree with the initial formation of destabilized α-imidoyl carbenium ions but indicate an easy rearrangement of these ions in the presence of suitable alkyl substituents by 1,2- and 1,4-hydrogen shifts to more stable isomers.     

气相中二氯苯的双电荷离子[C6H4CI2]^2+和[C6H3CI]^2+的动能谱研究

本文利用质量分析离子动能(MIKES)和碰撞诱导解离(CID)技术, 研究了邻、间、对二氯苯分子在电子轰击质谱(EIMS)中产生的[C6H4CI2]^2+和[C6H4CI]^2+双电荷离子的单分子电荷分离(CS)反应。根据测定和CS反应的动能释放值T和由此估算的反应过渡态的电荷间距的最小值R, 推测过渡态的结构。有趣的是, 可以利用双电荷离子[C6H4CI2]^2+的分解反应区分二氯苯的位置异构体。     

Experimental investigation of the molecular ions of the xylenes

A mass spectrometric method of distinguishing between molecular ions of the three isomeric xylenes (dimethylbenzenes) was sought, in light of recent findigs that photoexcited ions could be distinguished via measurements of kinetic energy release accompanying expulsion of a methyl radical. Provided the molecular ions are formed with low internal energies, reproducible differences were found between relative intensities of collision induced reactions of higher critical energies, than for methyl expulsion. These differences exist both for collision energies in the kilovolt range (double focusing mass spectrometers) and in the range of a few tens of volts (triple quadrupole instrument). Though statistically significant, these differences were small. The mechanism of isomerization and fragmentation was investigated via isotopic labelling studies and measurements of kinetic energy release. Most of the present findings can be rationalized in terms of the most recent version of established mechanisms for reactions of ionized methylbenzenes.     

Stacked-ring electrostatic ion guide

In 1969 Bahr, Gerlich, and Teloy introduced an rf device that consisted of a stack of ring electrodes, with charge sign alternation between neighboring rings, to store or transport ions. Here we propose to operate such a device with electrostatic potentials rather than rf potentials: ions that move axially along the center of the guide are thereby subjected to an oscillating electrical potential similar to the sinusoidal rf potential in familiar rf-only multipole ion guides. The oscillating potential of the stacked-ring static ion guide focuses ions by exerting a field gradient force on the ions so as to push ions toward the central axis where the field is weakest. The stacked-ring ion guide produces an effectively static “pseudopotential” that is much steeper at the edge (potential varies as e ^r) compared to a quadrupole or octupole guide (for which the potential varies as r ² or r ⁶, where r is radial position) and that is much flatter near the center of the guide (for potentially higher ion flux). Advantages of the new ion guide include static rather than rf potential, low electrical noise, a large field-free region near the central axis of the guide, and simple mechanical construction. A disadvantage of the stacked-ring ion guide is that high ion axial kinetic energy is required; ions with axial kinetic energy that is too low may be trapped in the shallow pseudopotential well between adjacent ring electrodes.     

Energy production in anaerobic organisms

Biological redox processes are required for the synthesis of “energy-rich” compounds which are in an enzyme-controlled equilibrium with the general energy carrier adenosine triphosphate (ATP). The basic mechanisms of biological energy transformation are substrate level (SLP) and electron transport phosphorylations (ETP). In anaerobic catabolism the numerous nutrients are channelled into only a few substrate level phosphorylations; the occurrence in chemotrophic anaerobes of energy conservation coupled to electron transport has not yet been demonstrated unequivocally. At present, the determination of the ATP turnover (Y_ATP) in growing cells appears to be a promising method of approaching this problem. The existing knowledge of oxygen dependent enzyme reactions and their molecular evolution provides the basis for a biochemical definition of aerobic and anaerobic organisms.     

Evidence for concerted pathways in ion-pairing coupled electron transfers

Ion-pairing with electro-inactive metal ions may change drastically the thermodynamic and kinetic reactivity of electron transfer in chemical and biochemical processes. Besides the classical stepwise pathways (electron-transfer first, followed by ion-pairing or vice versa), ion-pairing may also occur concertedly with electron transfer. The latter pathway avoids high-energy intermediates but a key issue is that of the kinetic price to pay to benefit from this thermodynamic advantage. A model is proposed leading to activation/driving force relationships characterizing such concerted associative electron transfers for intermolecular and intramolecular homogeneous reactions and for electrochemical reactions. Contrary to previous assertions, the driving force of the reaction (defined as the opposite of the reaction standard free energy), as well as the intrinsic barrier, does not depend on the concentration of the ion-pairing agent, which simply plays the role of one of the reactants. Besides solvent and intramolecular reorganization, the energy of the bond being formed is the main component of the intrinsic barrier. Application of these considerations to reactions reported in recent literature illustrates how concerted ion-pairing electron-transfer reactions can be diagnosed and how competition between stepwise and concerted pathways can be analyzed. It provided the first experimental evidence of the viability of concerted ion-pairing electron-transfer reactions.     

A label-free fluorescent molecular beacon based on DNA-templated silver nanoclusters for detection of adenosine and adenosine deaminase

A simple and reliable fluorescent molecular beacon is developed utilizing DNA-templated silver nanoclusters as a signal indicator and adenosine triphosphate (ATP) and adenosine deaminase as mechanical activators.     

Microscopic description of elementary growth processes and classification of structural defects in pentacene thin films

Elementary growth processes such as kink initiation, adding a molecule to a kink, and adding a molecule between two neighboring kinks and between two grains are theoretically studied in pentacene films by adding one molecule at a time to a predefined aggregate. For each molecule, the potential energy surface is calculated using the MM3 molecular mechanics force field, which allowed one to identify useful parameters like the energy barrier for diffusion and the energy to create kinks, as well as defect configurations. Depending on the properties of the potential energy surface and the resulting growth-condition-dependent probabilities of initiating defect configurations in the film, three types of pentacene defects are identified: a thermally activated defect, an intrinsic defect, and a kinetic defect. Upon film growth, most defects relax into the ideal crystal configuration. Bulk defects that resist relaxation have densities lower than 10(16) defects/cm3 at typical growth conditions. Grain boundary defects, on the other hand, are very stable. Moreover, interstitial molecules at grain boundaries are identified as a source of compressive stress.     

Consecutive reactions in the vitamin D series. A New insight into the mechanism of vitamin D and provitamin D isomerizations in the mass spectrometer

The individual steps of the consecutive reactions arising from metastable molecular ions, derived from vitamin D₃, vitamin D₂ and their respective provitamins (7-dehydrocholesterol, ergosterol), were examined in different field-free regions of a triple-sector mass spectrometer of B/E/E geometry. The comparison of the translational energy release (T) and the metastable peak shapes corresponding to these reactions, as well as unimolecular and collision-induced dissociation mass-analysed ion kinetic energy spectra, showed that there are probably two structures of the [M – H₂O]⁺˙ and [M – CH₃˙]⁺ ions depending upon whether the respective ions are formed in the ion source through high-energy reactions, or from the fragmentation of metastable molecular ions through slow, low-energy processes which occur in the first field-free region.