Academic literature on the topic 'Isotope kinetic effect'

There is currently experimental evidence of hydrogen tunnelling in over 20 different enzymes include yeast alcohol dehydrogenase (YADH), morphinone reductase (MR) and methylamine dehydrogenase (MADH). Various models have been used to describe hydrogen tunnelling in enzymes including the static barrier model, the vibrationally enhanced ground state tunnelling model (VEGST) and the environmentally coupled tunnelling model (ECT). Despite some differences in these models, there is a general consensus that a temperature dependent kinetic isotope effect (KIE) is indicative of tunnelling dominated by a ratepromoting motion. Stopped flow studies of MADH with ethanolamine as substrate (mm-MADH/EA) show that the KIE of the proton transfer decreases with temperature - within the framework of the ECT model, the kinetics of this proton transfer are consistent with ground state tunnelling dominated by active dynamics (a promoting vibration). However, an alternative hypothesis is that this temperature dependence can be attributed to the population of multiple reactive configurations within the active site. If distinct substrate configurations are associated with distinct kinetic behaviour, the temperature dependence of the KIE could be due to temperature dependent fluctuations in the relative populations of these configurations. Long and short time molecular dynamics simulations of mm-MADH/EA were carried out to explore both of these scenarios. Theethanoliminoquinone intermediate was found to adopt a number of different hydrogen bonding configurations in the active site of MADH. Adiabatic scans of the proton transfer event in conjunction with WKB calculations of the KIE showed that these hydrogen bonding patterns are associated with different barrier heights and KIEs. However, simple modelling with the Boltzmann distribution showed that fluctuations in the relative population of these configurations of the magnitude expected in the temperature range 278K-308K leads to negligible changes in the magnitude of the KIE. This suggested thatmultiple reactive configurations are unlikely to account for the temperature dependence of the KIE. Spectral density analysis of the short-time MD simulations was then carried out try to identify any promoting motions in mm-MADH/EA. Since no evidence of promoting motions was found, the origin of the temperature dependence on the KIE remains an open question: the analysis in this study was restricted to one of four possible proton transfers in this substrate (HI3-OD1). Further work might look at the possibility of a promoting motion pertinent to the other transfers.

Thesis (Ph.D.)--Boston University PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.<br>The hydroxyl radical is widely used as a high-resolution footprinting agent for DNA and RNA. The hydroxyl radical abstracts a hydrogen atom from the sugar- phosphate backbone of a nucleic acid molecule, creating a sugar-based radical that eventually results in a strand break. It was shown previously that replacement of deoxyribose hydrogen atoms with deuterium results in a kinetic isotope effect (KIE) on hydroxyl radical cleavage of DNA. The KIE correlates well with the solvent accessible surface area of a deoxyribose hydrogen atom in DNA. We chose the structurally well-defmed sarcin-ricin loop (SRL) RNA molecule as a model system to extend the deuterium KIE/hydroxyl radical cleavage experiment to RNA. We observed a substantial KIE upon deuteration of the 5'-carbon of the ribose. Values ranged from 1.20 to 1.96, and depended on the position of the residue within the SRL. We found a smaller KIE upon 4'-deuteration. Values ranged from 1.05 to 1.23. Values of 5' and 4' KIEs correlate with the extent of cleavage and with the solvent accessible surface areas of ribose hydrogen atoms ofthe SRL. Gel electrophoresis of cleavage products reveals that the strand break is terminated at the 5' end by multiple chemical species. Upon 3'-radiolabeling a specifically 5'-deuterated SRL RNA molecule, we observed a KIE on the production of a cleavage product having a gel mobility different from that of a phosphate-terminated RNA strand. Reduction with sodium borohydride gave rise to an RNA fragment terminated by a 5'-hydroxyl group. These experiments are consistent with 5' hydrogen abstraction by the hydroxyl radical producing a 5'-aldehyde-terminated RNA strand that retains the nucleotide from which the hydrogen atom was abstracted. This is the first report of such a species. This chemistry has important implications for the interpretation of structural analysis experiments on RNA that rely on primer extension to synthesize eDNA copies of hydroxyl radical cleavage products. The different 5'-terminated products resulting from hydroxyl radical cleavage at a given nucleotide would yield cDNAs of two different lengths, thereby distributing the cleavage intensity over two nucleotides instead ofone and lowering the resolution ofthe experiment.

Formaldehyde emissions from non-structural wood composites are regulated and the regulation target is urea-formaldehyde (UF) resin. UF resins are hydrolytically unstable and constantly emit formaldehyde as a function of temperature and relative humidity. When heated, wood also generates formaldehyde, but this was of little concern until 2010 when formaldehyde regulations became much more demanding. This regulation motivated the industry to account for all formaldehyde sources, synthetic as from resin, and biogenic as from wood. This effort represents first steps towards quantifying biogenic and synthetic contributions to formaldehyde emissions in non-structural wood composites. It is possible to distinguish the 13C/12C isotope ratio of UF resins from the isotope ratio of plant biomass. Conditions during and after composite hot-pressing promote reactions that generate formaldehyde from wood and UF resin, and the kinetic isotope effect continuously lowers the product isotope ratios as a function of yield. If such isotope fractionation did not occur, it would be a simple matter to quantify contributions of wood and UF resin to formaldehyde emissions using static isotope ratios. Isotope fractionation, therefore, complicates the requirements for distinguishing biogenic and synthetic formaldehyde in wood composite emissions. Those requirements are 1) establish the reference carbon isotope ratios in wood and in UF resin (just the formaldehyde portion of UF), and 2) estimate the kinetic isotope effects in formaldehyde generation by wood and cured UF resin. The latter requirement fixes a range for the respective isotope ratios; the numerical ranges enable a simple model of the average isotope ratio for a mixture of biogenic and synthetic formaldehyde in wood composite emissions. Finally, the measured isotope ratio of captured emissions would be compared to the model. This work did not achieve all aspects of the requirements mentioned, but a solid foundation was established for future completion of the ultimate goals. In reference to requirement 1, the carbon isotope ratio of experimental Pinus taeda wood was accurately measured (including some isolated fractions) using isotope ratio mass spectroscopy (IRMS). IRMS of UF resin first requires removal of urea carbons- UF resin was subjected to acid hydrolysis and capture of the resin formaldehyde into aqueous ammonium hydroxide. This provided a nearly quantitative conversion (negligible isotope fractionation) of resin formaldehyde into hexamine for IRMS. Using this hexamine method, the formaldehyde carbon isotope ratios of two industrial UF resins were accurately measured, demonstrating basic feasibility for the project goal. Estimating the kinetic isotope effect (Requirement 2) required creation of a thermochemical reactor, where wood or cured UF resin was heated under N2 flow such that the emitted formaldehyde was easily captured. In this case, conversion of captured formaldehyde into hexamine was abandoned in favor of silica gel cartridges loaded with sodium bisulfite. Isolation and IRMS of the formaldehyde-bisulfite adduct were effective and considered easily transferable to industrial settings. This system was employed to measure fractionation in cured resin as a function of relative humidity, and in Pinus taeda wood as a function of relative humidity, temperature, and time. More information about isotope fractionation is required; but most notable was the fractionation behavior in wood where evidence was found for multiple formaldehyde generating reactions. Overall, this work established feasibility for the goals and laid the foundation for future efforts.<br>Master of Science<br>Home-interior products like cabinetry are often produced with wood composites adhesively bonded with urea-formaldehyde (UF) resin. UF resins are low cost and highly effective, but their chemical nature results in formaldehyde emission from the composite. High emissions are avoided, and the federal government has regulated and steadily reduced allowable emissions since 1985. The industry continuously improved UF technologies to meet regulations, as in 2010 when the most demanding regulations were implemented. At that time, many people were unaware that wood also generates formaldehyde; this occurs at very low levels but heating during composite manufacture causes a temporary burst of natural formaldehyde. Some wood types produce unusually high formaldehyde levels, making regulation compliance more difficult. This situation, and the desire to raise public awareness, created a major industrial goal: determine how much formaldehyde emission originates from the resin and how much originates from the wood. These formaldehyde sources can be distinguished by measuring the carbon isotope ratio, 13C/12C. This ratio changes and varies due to the kinetic isotope effect. Slight differences in 13C and 12C reactivity reveal the source as either petrochemical (synthetic formaldehyde) or plant-based (biogenic formaldehyde). This work demonstrates that achieving the industry goal is entirely feasible, and it provides the analytical foundation. The technical strategy is: 1) establish reference isotope ratios in wood and in UF resin, and 2) from the corresponding wood composite, capture formaldehyde emissions, measure the isotope ratio, and simply calculate the percentage contributions from the reference sources. However, a complication exists. When the reference sources generate formaldehyde, the respective isotope ratios change systematically in a process called isotope fractionation (another term for the kinetic isotope effect). Consequently, this effort developed methods to measure fractionation when cured UF resin and wood separately generate formaldehyde, with greater emphasis on wood. Isotope fractionation in wood revealed multiple fractionation mechanisms. This complexity presents intriguing possibilities for new perspectives on formaldehyde emission from wood and cured UF resin. In summary, this work demonstrated how source contributions to formaldehyde emissions can be determined; it established effective methods required to refine and perfect the approach, and it revealed that isotope fractionation could serve as an entirely novel tool in the materials science of wood composites.

Enzyme dynamics occur on a wide range of length and timescales. This work is focused on understanding enzyme dynamic at the fs-ps timescale as this is the dynamic range at which bonds are typically made and broken during chemical reactions. Our work focuses on enzymes that catalyze hydride transfer between two carbon atoms - a fundamental reaction in biology. Primary kinetic isotope effects and their temperature dependence have implied that fast dynamics of the enzyme are important in facilitating hydride transfer, however these experiments do not measure any such motions directly. We make use of two-dimensional infrared spectroscopy (2D IR), a technique that interrogates the vibrations of molecules to extract dynamic information from the surrounding environment with 100 fs resolution. A model system, formate dehydrogenase (FDH), is an excellent probe of dynamics at the fs-ps timescale. Azide bound to the ternary complex of FDH offers the ability to measure dynamics of an analog structure of the reactive complex using 2D IR, while also studying the reaction directly with and KIE’s and their temperature dependence. By altering various parts of the structure of FDH via mutagenesis and other techniques, we investigate the role of structure and dynamics to determine how fast dynamics of the active site influence the the kinetics of hydride transfer. These experiments are the first means of providing a dynamic interpretation of KIEs and their temperature dependence.

Thyroxine (T4) is the predominant form of thyroid hormone (TH). In target tissues, T4 is enzymatically deiodinated to 3,5,3′-triiodothyronine (T3), a high-affinity ligand for the nuclear TH receptors TRα and Trβ. T3 modulates genes transcription via activation of TRα and TRβ. Non-genomic effects have also been described. In 2004 the research groups of professors Scanlan Grandy and Zucchi discovered an endogenous thyroid hormone derivative called 3-iodothyronamine (T1AM). They proved that at nanomolar concentrations it can activate trace amine associated receptors 1 (TAARs)[1] and it may also interact with other targets, such as plasma membrane transporters, mitochondrial proteins and vesicular biogenic amine transporters [2]–[4]. Endogenous T1AM has been detected in human and rodent blood and tissues samples by liquid chromatography coupled mass spectrometry (LC/MS/MS) [5]. Its endogenous levels are a matter of argument due to the challenges that its accurate quantification poses. For this reason, so far a worldwide adopted extraction method has not been established. Circulating T1AM has so far been considered to be largely bound to apolipoprotein apoB100 [6]. The first T1AM functional effect to be discovered was severe hypothermia [7]. This effect is associated to a decrease in oxygen consumption and a reduction of the respiratory quotient (CO2/O2), which reflects the relationship between glucose and fatty acid oxidation, resulting in a shift from carbohydrate to lipid as energy source [8]. The molecular mechanisms underlying T1AM effects are still unknown, however Mariotti and colleagues [9] analyzed gene expression profiles in adipose tissue and liver of T1AM chronically treated rats and found significant transcriptional effects involving sirtuin genes, which regulate important metabolic pathways. Therefore, the first aim of this work was to compare the effect of T1AM and T3 chronic treatment on mammalian sirtuin expression in hepatoma cells (HepG2) and isolated hepatocytes. Isolated rat hepatocytes were obtained by liver in-situ collagenase perfusion. Sirtuin expression was determined by Western Blot analysis in cells treated for 24 h with 1-20 µM T1AM or T3. In addition, cell viability was evaluated by MTT test upon 24 h treatment with 100 nM to 20 µM T1AM or T3. In HepG2, T1AM significantly reduced SIRT1 and SIRT4 protein expression at 20 µM while T3 strongly decreased the expression of SIRT1 (20 µM) and SIRT2 (any tested concentration). In primary rat hepatocytes T1AM, did not affect protein expression whereas T3 decreased SIRT2 at 10 µM. The extent of MTT-staining was moderately but significantly reduced by T1AM, particularly in HepG2 cells, in which the effect occurred at concentration starting from 100 nM. T3 reduced MTT staining in HepG2 but not in isolated hepatocytes. T1AM and T3 differently affected sirtuin expression in hepatocytes. Since SIRT4 is an important regulator of lipid and glucose metabolism, whereas SIRT1 and SIRT2 have a key role in regulating cell cycle and tumorigenesis, our observations are consistent with the shift from carbohydrates to lipids induced by T1AM and indicate a potential new role of T1AM in modulating tumor proliferation. The second part of this project was aimed at clarifying the issue that, so far, every research group working on this molecule has encountered when trying to accurately quantifying T1AM endogenous levels. These difficulties were usually attributed to problems in extraction or other pre‐analytical steps. Most researchers have developed various workaround for this issue. For example, on cell culture experiments, to avoid the presence of serum proteins in the culturing media, experiments have often be performed with unphysiological protein‐free media. The second goal of this project was therefore to evaluate the effect of serum protein on the recovery of exogenous T1AM. Cell culture media (Krebs buffer, DMEM, FBS, DMEM+FBS, used either in the absence or in the presence of NG108‐15 cells) and other biological matrices (rat brain and liver homogenates, human plasma and blood) were spiked with T1AM and/or deuterated T1AM (d4‐T1AM) and incubated for times ranging from 0 to 240 min. Samples were extracted using a liquid/liquid method and analysed using liquid chromatography coupled to mass spectrometry (LC-MS/MS), to assay T1AM and some of its metabolites. For the first time in the history of this molecule, in FBS‐containing buffers, an exponential decrease in T1AM levels was observed over time. T1AM metabolites were not detected, except for minimum amounts of TA1. Notably, d4‐T1AM decreased over time at a much lower rate, reaching 50‐70% of the baseline at 60 min. These effects were completely abolished by protein denaturation and partly reduced by semicarbazide, however, the process could not be reverted. In the presence of cells, T1AM concentration decreased virtually to 0 within 60 min, but TA1 accumulated in the incubation medium, with quantitative recovery. Spontaneous decrease in T1AM concentration with isotopic difference was confirmed in rat organ homogenates and human whole blood. Conclusions. On the whole, these results suggest binding and sequestration of T1AM by blood and tissue proteins, with significant isotope effects. These issues might account for the technical problems complicating the analytical assays of endogenousT1AM.

Protein-tyrosine phosphatases (PTPs) catalyze the hydrolysis of phosphorylated tyrosines by a 2-step mechanism involving nucleophilic attack by cysteine and general acid catalysis by aspartic acid. In most PTPs the aspartic acid resides on a flexible protein loop, consisting of about a dozen residues, called the WPD loop. PTP catalysis rates span several orders of magnitude, and differences in WPD loop dynamics have recently been show to correlate with the rate of enzymatic catalysis. The rate of WPD loop motion could possibly be related to a widely conserved tryptophan residue on the WPD loop. Therefore, point mutants were made in PTP1B (a human PTP) to the conserved tryptophan residue and their effects on catalytic rate and chemical reaction were studied. The results of these studies are presented in this thesis.