Insights Into the Known 13C Depletion of Methane—Contribution of the Kinetic Isotope Effects on the Serine Hydroxymethyltransferase Reaction

We determined the kinetic isotope effect on the serine hydroxymethyltransferase reaction (SHMT), which provides important C1 metabolites that are essential for the biosynthesis of DNA bases, O-methyl groups of lignin and methane. An isotope effect on the SHMT reaction was suggested being responsible for the well-known isotopic depletion of methane. Using the cytosolic SHMT from pig liver, we measured the natural carbon isotope ratios of both atoms involved in the bond splitting by chemical degradation of the remaining serine before and after partial turnover. The kinetic isotope effect 13(VMax/Km) was 0.994 0.006 and 0.995 0.007 on position C-3 and C-2, respectively. The results indicated that the SHMT reaction does not contribute to the 13C depletion observed for methyl groups in natural products and methane. However, from the isotopic pattern of caffeine, isotope effects on the methionine synthetase reaction and on reactions forming Grignard compounds, the involved formation and fission of metal organic bonds are likely responsible for the observed general depletion of “activated” methyl groups. As metal organic bond formations in methyl transferases are also rate limiting in the formation of methane, they may likely be the origin of the known 13C depletion in methane.

Oxygen and magnesium mass-independent isotopic fractionation induced by chemical reactions in plasma

Enrichment or depletion ranging from −40 to +100% in the major isotopes 16O and 24Mg were observed experimentally in solids condensed from carbonaceous plasma composed of CO2/MgCl2/Pentanol or N2O/Pentanol for O and MgCl2/Pentanol for Mg. In NanoSims imaging, isotope effects appear as micrometer-size hotspots embedded in a carbonaceous matrix showing no isotope fractionation. For Mg, these hotspots are localized in carbonaceous grains, which show positive and negative isotopic effects so that the whole grain has a standard isotope composition. For O, no specific structure was observed at hotspot locations. These results suggest that MIF (mass-independent fractionation) effects can be induced by chemical reactions taking place in plasma. The close agreement between the slopes of the linear correlations observed between δ25Mg versus δ26Mg and between δ17O versus δ18O and the slopes calculated using the empirical MIF factor η discovered in ozone [M. H. Thiemens, J. E. Heidenreich, III. Science 219, 1073–1075; C. Janssen, J. Guenther, K. Mauersberger, D. Krankowsky. Phys. Chem. Chem. Phys. 3, 4718–4721] attests to the ubiquity of this process. Although the chemical reactants used in the present experiments cannot be directly transposed to the protosolar nebula, a similar MIF mechanism is proposed for oxygen isotopes: at high temperature, at the surface of grains, a mass-independent isotope exchange could have taken place between condensing oxides and oxygen atoms originated form the dissociation of CO or H2O gas.

Deuterium Isotope Effects on Acid-Base Equilibrium of Organic Compounds

Deuterium isotope effects on acid–base equilibrium have been investigated using a combined path integral and free-energy perturbation simulation method. To understand the origin of the linear free-energy relationship of ΔpKa=pKaD2O−pKaH2O versus pKaH2O, we examined two theoretical models for computing the deuterium isotope effects. In Model 1, only the intrinsic isotope exchange effect of the acid itself in water was included by replacing the titratable protons with deuterons. Here, the dominant contribution is due to the difference in zero-point energy between the two isotopologues. In Model 2, the medium isotope effects are considered, in which the free energy change as a result of replacing H2O by D2O in solute–solvent hydrogen-bonding complexes is determined. Although the average ΔpKa change from Model 1 was found to be in reasonable agreement with the experimental average result, the pKaH2O dependence of the solvent isotope effects is absent. A linear free-energy relationship is obtained by including the medium effect in Model 2, and the main factor is due to solvent isotope effects in the anion–water complexes. The present study highlights the significant roles of both the intrinsic isotope exchange effect and the medium solvent isotope effect.

Nitrogen Kinetic Isotope Effects of Nitrification by the Complete Ammonia Oxidizer Nitrospira inopinata

Nitrification is an important nitrogen cycle process in terrestrial and aquatic environments. The discovery of comammox has changed the view that canonical AOA, AOB, and NOB are the only chemolithoautotrophic organisms catalyzing nitrification.

RESEARCH ON THE PROPERTIES OF SORBENTS AND DECONTAMINANTS IN THE PROCESSES WITH SMALL ISOTOPE EFFECTS

The low values of isotope effects in the sorption/decontamination processes make it possible to investigate the properties of the sorbing and decontaminating agents with the use of stable isotope simulators. In the work present-ed here the element content was determined from the characteristic X-ray emission induced by the proton beam (PIXE), by gamma-ray emission from the radioactive source, and by emission from the X-ray tube. Based on the results of efficiency determination for different kinds of sorbents and decontaminants, recommendations have been given for the choice of materials having the wanted performance characteristics.

A Substrate-triggered µ-Peroxodiiron(III) Intermediate in the 4-Choro-L-Lysine-Fragmenting Heme-Oxygenase-like Diiron Oxidase (HDO) BesC: Substrate Dissociation from, and C4 Targeting by, the Intermediate

ABSTRACTThe enzyme BesC from the β-ethynyl-L-serine biosynthetic pathway in Streptomyces cattleya fragments 4-chloro-L-lysine (produced from L-Lysine by BesD) to ammonia, formaldehyde, and 4-chloro-L-allylglycine and can analogously fragment L-Lys itself. BesC belongs to the emerging family of O2-activating non-heme-diiron enzymes with the "heme-oxygenase-like" protein fold (HDOs). Here we show that binding of L-Lys or an analog triggers capture of O2 by the protein’s diiron(II) cofactor to form a blue µ-peroxodiiron(III) intermediate analogous to those previously characterized in two other HDOs, the olefin-installing fatty acid decarboxylase, UndA, and the guanidino-N-oxygenase domain of SznF. The ∼ 5- and ∼ 30-fold faster decay of the intermediate in reactions with 4-thia-L-Lys and (4RS)-chloro-DL-lysine than in the reaction with L-Lys itself, and the primary deuterium kinetic isotope effects (D-KIEs) on decay of the intermediate and production of L-allylglycine in the reaction with 4,4,5,5-[2H]-L-Lys, imply that the peroxide intermediate or a successor complex with which it reversibly interconverts initiates the oxidative fragmentation by abstracting hydrogen from C4. Surprisingly, the sluggish substrate L-Lys can dissociate after triggering the intermediate to form, thereby allowing one of the better substrates to bind and react. Observed linkage between Fe(II) and substrate binding suggests that the triggering event involves a previously documented (in SznF) ordering of the dynamic HDO architecture that contributes one of the iron sites, a hypothesis consistent with the observation that the diiron(III) product cluster produced upon decay of the intermediate spontaneously degrades, as it has been shown to do in all other HDOs studied to date.