Elucidating the Molecular Origin of Hydrolysis Energy of Pyrophosphate in Water

A computational scheme of pKa values based on the three-dimensional reference interaction site model self-consistent field theory coupled with the linear fitting correction scheme

A scheme for quantitatively computing the acid dissociation constant, pKa, of hydrated molecules is proposed. It is based on the three-dimensional reference interaction site model self-consistent field (3D-RISM-SCF) theory coupled with the linear fitting correction (LFC) scheme. In LFC/3D-RISM-SCF, pKa values of target molecules are evaluated using the Gibbs energy difference between the protonated and unprotonated states calculated by 3D-RISM-SCF and the parameters fitted by the LFC scheme to the experimental values of training set systems. The pKa values computed by LFC/3D-RISM-SCF show quantitative agreement with the experimental data.

Biochemical and thermodynamic analyses of energy conversion in extremophiles

A variety of extreme environments, characterized by extreme values of various physicochemical parameters (temperature, pressure, salinity, pH, and so on), are found on Earth. Organisms that favorably live in such extreme environments are called extremophiles. All living organisms, including extremophiles, must acquire energy to maintain cellular homeostasis, including extremophiles. For energy conversion in harsh environments, thermodynamically useful reactions and stable biomolecules are essential. In this review, I briefly summarize recent studies of extreme environments and extremophiles living in these environments and describe energy conversion processes in various extremophiles based on my previous research. Furthermore, I discuss the correlation between the biological system of electrotrophy, a third biological energy acquisition system, and the mechanism underlying microbiologically influenced corrosion. These insights into energy conversion in extremophiles may improve our understanding of the "limits of life". Abbreviations: PPi: pyrophosphate; PPase: pyrophosphatase; ITC: isothermal titration microcalorimetry; SVNTase: Shewanella violacea 5'-nucleotidase; SANTase: Shewanella amazonensis 5'-nucleotidase.

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.

Pyrolysis temperature-dependent changes in dissolved phosphorus speciation of plant and manure biochars

Pyrolysis of plant and animal wastes produces a complex mixture of phosphorus species in amorphous, semicrystalline, and crystalline inorganic phases, organic (char) components, and within organo-mineral complexes. To understand the solubility of different phosphorus species, plant (cottonseed hull) and manure (broiler litter) wastes were pyrolyzed at 350, 500, 650, and 800 °C and exposed to increasingly more rigorous extraction procedures: water (16 h), Mehlich 3 (1 mM EDTA at pH 2.5 for 5 min), oxalate (200 mM oxalate at pH 3.5 for 4 h), NaOH-EDTA (250 mM NaOH + 5 mM EDTA for 16 h), and total by microwave digestion (concentrated HNO3/HCl + 30% H2O2). Relative to the total (microwave digestible) P, the percentage of extractable P increased in the following order: M3 < oxalate ≈ water < NaOH-EDTA for plant biochars and water < M3 < NaOH-EDTA < oxalate for manure biochars. Solution phase (31)P NMR analysis of NaOH-EDTA extracts showed the conversion of phytate to inorganic P by pyrolysis of manure and plant wastes at 350 °C. Inorganic orthophosphate (PO4(3-)) became the sole species of ≥ 500 °C manure biochars, whereas pyrophosphate (P2O7(4-)) persisted in plant biochars up to 650 °C. These observations suggested the predominance of (i) amorphous (rather than crystalline) calcium phosphate in manure biochars, especially at ≥ 650 °C, and (ii) strongly complexed pyrophosphate in plant biochars (especially at 350-500 °C). Correlation (Pearson's) was observed (i) between electric conductivity and ash content of biochars with the amount of inorganic P species and (ii) between total organic carbon and volatile matter contents with the organic P species.

Constant enthalpy change value during pyrophosphate hydrolysis within the physiological limits of NaCl

A decrease in water activity was thought to result in smaller enthalpy change values during PPi hydrolysis, indicating the importance of solvation for the reaction. However, the physiological significance of this phenomenon is unknown. Here, we combined biochemistry and calorimetry to solve this problem using NaCl, a physiologically occurring water activity-reducing reagent. The pyrophosphatase activities of extremely halophilic Haloarcula japonica, which can grow at ∼4 M NaCl, and non-halophilic Escherichia coli and Saccharomyces cerevisiae were maximal at 2.0 and 0.1 M NaCl, respectively. Thus, halophilic and non-halophilic pyrophosphatases exhibit distinct maximal activities at different NaCl concentration ranges. Upon calorimetry, the same exothermic enthalpy change of -35 kJ/mol was obtained for the halophile and non-halophiles at 1.5-4.0 and 0.1-2.0 M NaCl, respectively. These results show that solvation changes caused by up to 4.0 M NaCl (water activity of ∼0.84) do not affect the enthalpy change in PPi hydrolysis. It has been postulated that PPi is an ATP analog, having a so-called high energy phosphate bond, and that the hydrolysis of both compounds is enthalpically driven. Therefore, our results indicate that the hydrolysis of high energy phosphate compounds, which are responsible for biological energy conversion, is enthalpically driven within the physiological limits of NaCl.