Methyl transfer in glycine N-methyltransferase. A theoretical study

Density functional theory calculations using the hybrid functional B3LYP have been performed to study the methyl transfer step in glycine N-methyltransferase (GNMT). This enzyme catalyzes the S-adenosyl-L-methionine (SAM)-dependent methylation of glycine to form sarcosine. The starting point for the calculations is the recent X-ray crystal structure of GNMT complexed with SAM and acetate. Several quantum chemical models with different sizes, employing up to 98 atoms, were used. The calculations demonstrate that the suggested mechanism, where the methyl group is transferred in a single S(N)2 step, is thermodynamically plausible. By adding or eliminating various groups at the active site, it was furthermore demonstrated that hydrogen bonds to the amino group of the glycine substrate lower the reaction barrier, while hydrogen bonds to the carboxylate group raise the barrier.     

Determination of the antioxidant alurofen in synthetic rubbers by pyrolysis-gas chromatography

A pyrolysis—gas chromatographic (Py—GC) method for the determination of the antioxidant Alurofen in synthetic rubbers was developed. The Alurofen was extracted from the rubber, then pyrolysed as 873 K in continuous-mode furnace pyrolyser in 20 s. Chromatographic conditions for the separation of the pyrolysis products were established. The pyrolysis of the Alurofen at several temperatures was investigated by measuring the yields of the pyrolysis products. It was observed that 2-phenyl-2-(4-hydroxyphenyl)propane was produced in the greatest, amounts, and the effect of the pyrolysis temperature on the yield of this compound was studied. The overall Py—GC method for the determination of the Alurofen content of rubbers had a mean relative error of 2.7% and a relative standard deviation of 2.94%.     

Titania-supported mixed HPMoV polyoxometallates as precursors of hydrodesulfurization catalysts

HDS catalysts were prepared by loading H₃PMo₁₂O₄₀ or H₄PMo₁₁V₁O₄₀ polyoxometallates on TiO₂ (0.5 and 1.0 mmol (Mo+V)). Activity of the catalysts was tested in the HDS of thiophene. The activity of catalysts of low concentration was 2–3 times higher than the activity of those of high concentration. Temperature programmed reduction (TPR) and IR spectroscopy were used to determine the properties of the catalyst. TPR measurements proved that vanadium promotes and stabilizes HDS activity due to an increase in the Mo⁵⁺/Mo⁴⁺ ratio.     

Reversible pH-Responsive Coacervate Formation in Lipid Vesicles Activates Dormant Enzymatic Reactions

In situ, reversible coacervate formation within lipid vesicles represents a key step in the development of responsive synthetic cellular models. Herein, we exploit the pH responsiveness of a polycation above and below its pK_a, to drive liquid–liquid phase separation, to form single coacervate droplets within lipid vesicles. The process is completely reversible as coacervate droplets can be disassembled by increasing the pH above the pK_a. We further show that pH-triggered coacervation in the presence of low concentrations of enzymes activates dormant enzyme reactions by increasing the local concentration within the coacervate droplets and changing the local environment around the enzyme. In conclusion, this work establishes a tunable, pH responsive, enzymatically active multi-compartment synthetic cell. The system is readily transferred into microfluidics, making it a robust model for addressing general questions in biology, such as the role of phase separation and its effect on enzymatic reactions using a bottom-up synthetic biology approach.     

Polymerization of cyclic acetals. I. Polymerization of 1,3,6-trioxacyclooctane and copolymerization with p-methoxystyrene

The polymerization of 1,3,6-trioxacyclooctane initiated by trityl salts with various counterions in CH₂Cl₂ was investigated. The reaction mixtures and the isolated polymers were analyzed by GPC (double detection—IR and UV at 254 nm),¹H-, and¹³C-NMR spectroscopy. In the early stage of polymerization only oligomers (mainly cyclic) were formed. With longer reaction times, linear polymers (yield 86–94%, M = 70,000–80,000) were obtained. The concentration of each individual oligomer passed through a maximum and decreased, reaching its equilibrium concentration. The time interval necessary to reach the maximum concentration increased with n. The total concentration of the oligomers was 0.2 mol L^?1 regardless of the initiator used. Conditions for polymerization with virtually no termination were found. Addition of p-methoxystyrene to the “living” polyacetals resulted in block copolymers. GPC,¹H- and ¹³C-NMR and acidolytic degradation were used to prove the formation of AB block copolymers. The reactive alkoxycarbenium growing species are responsible for the formation of block polyacetal-polymethoxystyrene copolymer.     

Interactions of alkali metal chlorides with phosphatidylcholine vesicles

We study the interaction of alkali metal chlorides with lipid vesicles made of palmitoyloleoylphosphatidylcholine (POPC). An elaborate set of techniques is used to investigate the binding process at physiological conditions. The alkali cation binding to POPC is characterized thermodynamically using isothermal titration calorimetry. The isotherms show that for all ions in the alkali group the binding process is endothermic, counterintuitively to what is expected for Coulomb interactions between the slightly negatively charged POPC liposomes and the cations. The process is entropy driven and presumably related to the liberation of water molecules from the hydration shells of the ions and the lipid headgroups. The measured molar enthalpies of the binding of the ions follows the Hofmeister series. The binding constants were also estimated, whereby lithium shows the strongest affinity to POPC membranes, followed by the rest of the ions according to the Hofmeister series. Cation adsorption increases the net surface potential of the vesicles as observed from electrophoretic mobility and zeta potential measurements. While lithium adsorption leads to slightly positive zeta potentials above a concentration of 100 mM, the adsorption of the rest of the ions mainly causes neutralization of the membrane. This is the first study characterizing the binding equilibrium of alkali metal chlorides to phosphatidylcholine membranes at physiological salt concentrations.     

Polymerization of styrene oxide by nitronium tetrafluoroborate

The polymerization of styrene oxide by nitronium tetrafluoroborate in nitromethane and methylene chloride at 5, 20, and 50°C is investigated. GPC analyses of the products combined with isocyanate method show that both cyclic and linear oligomers are formed. In CH₃NO₂ the cyclic dimer and trimer are 2-benzyl-4-phenyl-1,3-dioxolane and 1,3,5-tribenzyl-trioxane, respectively. In CH₂Cl₂ 2,5-diphenyldioxane is isolated. In nitromethane, mainly isomerized structures with acetal linkage are produced, while in methylene chloride isomerization does not proceed. By NMR and IR spectra the presence of C?O and OH end groups in the linear oligomers is shown. There are indications that oligomers are formed both directly from the monomer and by degradation of the polymer.     

Lamellar-non-lamellar phase transitions in synthetic glycoglycerolipids studied by time-resolved X-ray diffraction

The phase sequences of eight fully hydrated synthetic, stereochemically pure glycoglycerolipids with saturated alkyl chains 12-18 carbon atoms long and a glucose, galactose or mannose head group are followed in real time during heating and cooling scans using synchrotron X-ray diffraction. One of them, 1,2-di-O-hexadecyl-3-O-β-D-glucosyl-sn-glycerol, has been characterized by X-ray diffraction for the first time. A summary of the lamellar-non-lamellar transition sequences and reversibility for all eight glycoglycerolipids studied is provided. It includes also observations of intermediate phases, previously not detected. Lattice parameters of the various phases have been determined as functions of chain length in monoglucosides. While the repeat periods of the lamellar phases increase linearly with chain length, an anomalously high lattice spacing of the inverted hexagonal phase is observed at a chain length of 14 carbon atoms. This maximum coincides with the disappearance of the cubic phases from the phase sequence upon chain elongation from 12 to 14 carbon atoms. It thus appears that the expanded H_II phase in 14-Glc retains structural characteristics of the anticipated cubic phases. Upon heating to high temperatures, its high lattice spacing gradually approaches that of the 'normal' hexagonal phase. A direct transition from lamellar subgel to inverted hexagonal phase has been observed to proceed without intermediate structures, but with an extended phase coexistence region, in 1,2-di-O-tetradecyl-3-O-β-D-galactosyl-sn-glycerol and 1,2-di-O-octadecyl-3-O-β-D-galactosyl-sn-glycerol. This transition is not reversible on cooling when lamellar phases skipped in the heating scan intervene. By contrast, the direct lamellar gel-inverted hexagonal phase transitions are fully reversible with minor or absent temperature hysteresis.     

Theoretical study of the methyl transfer in guanidinoacetate methyltransferase

The reaction mechanism of the guanidinoacetate methyltransferase (GAMT) enzyme has been investigated by means of density functional theory using the B3LYP hybrid functional. GAMT catalyzes the S-adenosyl-L-methionine (SAM)-dependent methylation of guanidinoacetate (GAA) to form creatine. A quantum chemical model was built on the basis of the recent crystal structure of GAMT complexed with S-adenosylhomocysteine (SAH) and GAA. The methyl group transfer from SAM to N(E) of GAA is shown to occur concertedly with a proton transfer from NE to the neighboring OD1 of Asp134. Good agreement is found between the calculated barrier and the experimental rate.