The Role of Arg228 in the phosphorylation of galactokinase: The mechanism of GHMP kinases by QM/MM studies

GHMP kinases are a group of structurally-related small molecule kinases. They have been found in all kingdoms of life and are mostly responsible for catalysing the ATP-dependent phosphorylation of intermediary metabolites. Although the GHMP kinases are of clinical, pharmaceutical and biotechnological importance, the mechanism of GHMP-kinases is controversial. A catalytic base mechanism was suggested for mevalonate kinase that has a structural feature of the ?-phosphate of ATP close to an aspartate residue; however, for one GHMP member, homoserine kinase, where the residue acting as general base is absent, a direct phosphorylation mechanism was suggested. Furthermore, it has been proposed by some authors that all the GHMP kinases function via the direct phosphorylation mechanism. This controversy in mechanism has limited our ability to exploit these enzymes as drug targets and in biotechnology. Here the phosphorylation reaction mechanism of the human galactokinase, a member of GHMP kinase was investigated using molecular dynamics simulations and density functional theory-based QM/MM calculations (B3LYP-D/AMBER99). The reaction coordinates were localized by potential energy scan using adiabatic mapping method. Our results indicate that a highly conserved Glu174 captures Arg105 to the proximity of the a-phosphate of ATP forming a H-bond network, therefore the mobility of ATP in the large oxyanion hole is restricted. Arg228 functions to stabilize the negative charge developed at the ß,?-bridging oxygen of the ATP during bond cleavage. The reaction occurs via direct phosphorylation mechanism and the Asp186 in proximity of ATP does not directly participate in the reaction pathway. Since Arg228 is not conserved among GHMP kinases, reagents which form interactions with Arg228, and therefore can interrupt its function in phosphorylation may be developed into potential selective inhibitors for galactokinase.

Fructose Chemistry

Fructose is a six-carbon ketose monosaccharide. In aqueous solution and in the crystalline form, the majority of the molecules form ring structures. Of these, the six-membered pyranose form is the most abundant; however, about one-quarter of the molecules are in the five-membered, furanose form. While many of its reactions are similar to those of glucose, the presence of a ketone group in the chain, and the relative ease with which the molecule forms a five-membered furanose ring affects its chemistry and biochemistry. Specific pathways are required to enable organisms to exploit fructose in energy metabolism; these require the enzyme fructokinase and involve the conversion of fructose to glycolytic intermediates. Similarly, specific pathways for the biosynthesis of fructose and fructose-containing polymers, such as inulin, are required. Non-enzymatic glycation (fructation) by fructose has not been as extensively studied as the corresponding reactions with glucose. Nevertheless, especially in diabetic patients and fructose-rich foodstuffs, this reaction is likely to be important.

Photodissociation and chemistry of N2 in the circumstellar envelope of carbon-rich AGB stars

The envelopes of AGB stars are irradiated externally by ultraviolet photons; hence, the chemistry is sensitive to the photodissociation of N$_2$ and CO, which are major reservoirs of nitrogen and carbon, respectively. The photodissociation of N$_2$ has recently been quantified by laboratory and theoretical studies. Improvements have also been made for CO photodissociation. For the first time, we use accurate N$_2$ and CO photodissociation rates and shielding functions in a model of the circumstellar envelope of the carbon-rich AGB star, IRC +10216. We use a state-of-the-art chemical model of an AGB envelope, the latest CO and N$_2$ photodissociation data, and a new method for implementing molecular shielding functions in full spherical geometry with isotropic incident radiation. We compare computed column densities and radial distributions of molecules with observations. The transition of N$_2$ $\to$ N (also, CO $\to$ C $\to$ C$^+$) is shifted towards the outer envelope relative to previous models. This leads to different column densities and radial distributions of N-bearing species, especially those species whose formation/destruction processes largely depend on the availability of atomic or molecular nitrogen, for example, C$_n$N ($n$=1, 3, 5), C$_n$N$^-$ ($n$=1, 3, 5), HC$_n$N ($n$=1, 3, 5, 7, 9), H$_2$CN and CH$_2$CN. The chemistry of many species is directly or indirectly affected by the photodissociation of N$_2$ and CO, especially in the outer shell of AGB stars where photodissociation is important. Thus, it is important to include N$_2$ and CO shielding in astrochemical models of AGB envelopes and other irradiated environments. In general, while differences remain between our model of IRC +10216 and the observed molecular column densities, better agreement is found between the calculated and observed radii of peak abundance.

On the Performances of Ionic Liquid-Based Electrolytes for Li-NMC Batteries

Herein, the N-butyl-N-methylpyrrolidinium bis(fluorosulfonyl)amide and the N-propyl-N-methylpyrrolidinium bis(fluorosulfonyl)amide room temperature ionic liquids, combined with the lithium bis(trifluoromethanesulfonyl)amide salt, are investigated as electrolytes for Li/LiNi1/3Mn1/3Co1/3O2 (Li/NMC) batteries. To conduct this study, volumetric properties, ionic conductivity and viscosity of the pure ionic liquids and selected electrolytes were firstly determined as a function of temperature and composition in solution. These data were then compared with those measured in the case of the standard alkyl carbonate-based electrolyte: e.g. the EC/PC/3DMC + 1 mol·L−1 LiPF6. The compatibility of the selected electrolytes with the lithium electrode was then investigated by following the evolution of Li/electrolyte interfaces through impedance measurements. Interestingly, the impedances of the investigated Li/electrolyte interfaces were found to be more than three times lower than that measured using the standard electrolyte. Finally, electrochemical performances of the ionic liquid-based electrolytes were investigated using galvanostatic charge and discharge and cyclic voltammetry of each Li/NMC cell. Using these electrolytes, each tested Li cell reaches up to 145 mA·h·g−1 at C/10 and 110 mA·h·g−1 at C with a coulombic efficiency close to 100 %.

Origin of extraordinarily high catalytic activity of Co3O4 and its morphological chemistry for CO oxidation at low temperature

Understanding and then designing efficient catalysts for CO oxidation at low temperature is one of the hottest topics in heterogeneous catalysis. Among the existing catalysts. Co3O4 is one of the most interesting systems: Morphology-controlled Co3O4 exhibits exceedingly high activity. In this study, by virtue of extensive density functional theory (OFT) calculations, the favored reaction mechanism in the system is identified. Through careful analyses on the energetics of elementary reactions on Co3O4(1 1 0)-A, Co3O4(1 1 0)-B, Co3O4(1 1 1) and Co3O4(1 0 0), which are the commonly exposed surfaces of Co3O4, we find the following regarding the relation between the activity and structure: (i) Co3+ is the active site rather than Co2+: and (ii) the three-coordinated surface oxygen bonded with three Co3+ may be slightly more reactive than the other two kinds of lattice oxygen, that is, the two-coordinated 0 bonded with one Co2+ and one Co3+ and the three-coordinated 0 bonded with one Co2+ and two Co3+. Following the results from Co3O4, we also extend the investigation to MnO2(1 1 0), Fe3O4(1 1 0), CuO(1 1 0) and CuO(1 1 1), which are the common metal oxide surfaces, aiming to understand the oxides in general. Three properties, such as the CO adsorption strength, the barrier of CO reacting with lattice 0 and the redox capacity, are identified to be the determining factors that can significantly affect the activity of oxides. Among these oxides, Co3O4 is found to be the most active one, stratifying all the three requirements. A new scheme to decompose barriers is introduced to understand the activity difference between lattice O-3c and O-2c on (1 1 0)-B surface. By utilizing the scheme, we demonstrate that the origin of activity variance lies in the geometric structures. (C) 2012 Elsevier Inc. All rights reserved.