On-Line Raman Measurement of the Radiation-Enhanced Reaction of Cellobiose with Hydrogen Peroxide.
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ABSTRACT:
SUBMITTER: Lackey HE
PROVIDER: S-EPMC8717536 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe ability of fungal cellobiose dehydrogenase (CDH) to generate H2O2 in-situ is highly interesting for biotechnological applications like cotton bleaching, laundry detergents or antimicrobial functionalization of medical devices. CDH's ability to directly use polysaccharide derived mono- and oligosaccharides as substrates is a considerable advantage compared to other oxidases such as glucose oxidase which are limited to monosaccharides. However CDH's low activity with oxygen as electron acceptor hampers its industrial use for H2O2 production. A CDH variant with increased oxygen reactivity is therefore of high importance for biotechnological application. Uniform expression levels and an easy to use screening assay is a necessity to facilitate screening for CDH variants with increased oxygen turnover.ResultsA uniform production and secretion of active Myriococcum thermophilum CDH was obtained by using Saccharomyces cerevisiae as expression host. It was found that the native secretory leader sequence of the cdh gene gives a 3 times higher expression than the prepro leader of the yeast α-mating factor. The homogeneity of the expression in 96-well deep-well plates was good (variation coefficient <15%). A high-throughput screening assay was developed to explore saturation mutagenesis libraries of cdh for improved H2O2 production. A 4.5-fold increase for variant N700S over the parent enzyme was found. For production, N700S was expressed in P. pastoris and purified to homogeneity. Characterization revealed that not only the kcat for oxygen turnover was increased in N700S (4.5-fold), but also substrate turnover. A 3-fold increase of the kcat for cellobiose with alternative electron acceptors indicates that mutation N700S influences the oxidative- and reductive FAD half-reaction.ConclusionsSite-directed mutagenesis and directed evolution of CDH is simplified by the use of S. cerevisiae instead of the high-yield-host P. pastoris due to easier handling and higher transformation efficiencies with autonomous plasmids. Twelve clones which exhibited an increased H2O2 production in the subsequent screening were all found to carry the same amino acid exchange in the cdh gene (N700S). The sensitive location of the five targeted amino acid positions in the active site of CDH explains the high rate of variants with decreased or entirely abolished activity. The discovery of only one beneficial exchange indicates that a dehydrogenase's oxygen turnover is a complex phenomenon and the increase therefore not an easy target for protein engineering.
| S-EPMC3654988 | biostudies-literature
Project description:Genomics provides a comprehensive view of the complete genetic makeup of an organism. Individual sequence variations, as manifested by single nucleotide polymorphisms (SNPs), can provide insight into the basis for a large number of phenotypes and diseases including cancer. The ability rapidly screen for SNPs will have a profound impact on a number of applications, most notably personalized medicine. Here we demonstrate a new approach to SNP detection through the application of surface-enhanced Raman scattering (SERS) to the ligase detection reaction (LDR). The reaction uses two LDR primers, one of which contains a Raman enhancer and the other a reporter dye. In LDR, one of the primers is designed to interrogate the SNP. When the SNP being interrogated matches the discriminating primer sequence, the primers are ligated and the enhancer and dye are brought into close proximity enabling the dye's Raman signature to be detected. By detecting the Raman signature of the dye rather than its fluorescence emission, our technique avoids the problem of spectral overlap which limits number of reactions which can be carried out in parallel by existing systems. We demonstrate the LDR-SERS reaction for the detection of point mutations in the human K-ras oncogene. The reaction is implemented in an electrokinetically active microfluidic device that enables physical concentration of the reaction products for enhanced detection sensitivity and quantization. We report a limit of detection of 20 pM of target DNA with the anticipated specificity engendered by the LDR platform.
| S-EPMC2716065 | biostudies-literature
Project description:Chronic oxidative stress has been associated with genomic instability following exposure to ionizing radiation. However, results showing direct causal linkages between specific ROS (reactive oxygen species) and the ionizing radiation-induced mutator phenotype are lacking. The present study demonstrates that ionizing radiation-induced genomically unstable cells (characterized by chromosomal instability and an increase in mutation and gene amplification frequencies) show a 3-fold increase in steady-state levels of hydrogen peroxide, but not superoxide. Furthermore, stable clones isolated from parallel studies showed significant increases in catalase and GPx (glutathione peroxidase) activity. Treatment of unstable cells with PEG-CAT (polyethylene glycol-conjugated catalase) reduced the mutation frequency and mutation rate in a dose-dependent fashion. In addition, inhibiting catalase activity in the stable clones using AT (3-aminotriazole) increased mutation frequency and rate. These results clearly demonstrate the causal relationship between chronic oxidative stress mediated by hydrogen peroxide and the mutator phenotype that persists for many generations following exposure of mammalian cells to ionizing radiation.
| S-EPMC2677991 | biostudies-literature
Project description:Adaptation to hydrogen peroxide in Saccharomyces cerevisiae is profiled with expression arrays. Adaptation describes the process in which a mild dose of toxin (in this case, hydrogen peroxide) is able to protect against a later acute dose. Here, we study two adaptive protocols (0.1 mM H2O2 and 0.1 + 0.4 mM H2O2) and one acute protocol (0.4 mM H2O2) to identify processes uniquely involved in adaptation. Predictions from these studies are validated in expression profiling of deletion mutants of the transcription factors Yap1, Mga2, and Rox1.
2009-04-23 | GSE12602 | GEO
Project description:It was proposed that the reaction of sodium pyruvate and H2O2 generates the intermediate 2-hydroperoxy-2-hydroxypropanoate, which converts into acetate, CO2, and H2O ( Aleksankin et al. Kernenergie 1962 , 5 , 362 - 365 ). These conclusions were based on the products generated in (18)O-enriched water and H2O2 reacting with pyruvic acid at room temperature; however, the lifetime of 2-hydroperoxy-2-hydroxypropanoate at room temperature is too short for direct spectroscopic observation. Therefore, we applied the combination of low-temperature and (13)C NMR techniques to verify, for the first time, the formation of 2-deuteroperoxy-2-deuteroxypropanoate in mixtures of D2O and methanol-d4 and to monitor directly each species involved in the reaction between D2O2 and (13)C-enriched pyruvate. Our NMR results confirm the formation of 2-deuteroperoxy-2-deuteroxypropanoate, where the respective chemical shifts are supported by density functional theory (DFT) calculations. At near-neutral apparent pD (pD*) and -35 °C, the formation of 2-deuteroperoxy-2-deuteroxypropanoate occurred with k = 2.43 × 10(-3) dm(3)·mol(-1)·s(-1). The subsequent decomposition of 2-deuteroperoxy-2-deuteroxypropanoate into acetate, CO2, and D2O occurred with k = 2.58 × 10(-4) s(-1) at -35 °C. In order to provide a full kinetic analysis, we also monitored the equilibrium of pyruvate and methanol with the hemiacetal (2-deuteroxy-2-methoxypropanoate). The kinetics for the reaction of sodium pyruvate and D2O2 were fitted by taking into account all these equilibria and species.
| S-EPMC4782753 | biostudies-literature
Project description:Hydrogen peroxide (H2O2) is known as a key molecule in a variety of biological processes, as well as a crucial byproduct in many enzymatic reactions. Therefore, being able to selectively and sensitively detect H2O2 is not only important in monitoring, estimating, and decoding H2O2 relevant physiological pathways but also very helpful in developing enzymatic-based biosensors for other analytes of interest. Herein, we report a plasmonic probe for H2O2 based on 3-mercaptophenylboronic acid (3-MPBA) modified gold nanoparticles (AuNPs) which is coupled with surface-enhanced Raman scattering (SERS) to yield a limit of detection (LOD) of 70 nM. Our probe quantifies both exogenous and endogenous H2O2 levels in living cells and can further be coupled with glucose oxidase (GOx) to achieve quantitative and selective detection of glucose in artificial urine and human serum.
| S-EPMC4955533 | biostudies-literature
Project description:The levels of hydrogen peroxide ([Formula: see text]) in human blood is of great relevance as it has emerged as an important signalling molecule in a variety of disease states. Fast and reliable measurement of [Formula: see text] levels in the blood, however, continues to remain a challenge. Herein we report an automated method employing a microfluidic device for direct and rapid measurement of [Formula: see text] in human blood based on laser-induced fluorescence measurement. Our study delineates the critical factors that affect measurement accuracy-we found blood cells and soluble proteins significantly alter the native [Formula: see text] levels in the time interval between sample withdrawal and detection. We show that separation of blood cells and subsequent dilution of the plasma with a buffer at a ratio of 1:6 inhibits the above effect, leading to reliable measurements. We demonstrate rapid measurement of [Formula: see text] in plasma in the concentration range of 0-49 µM, offering a limit of detection of 0.05 µM, a sensitivity of 0.60 µM-1, and detection time of 15 min; the device is amenable to the real-time measurement of [Formula: see text] in the patient's blood. Using the linear correlation obtained with known quantities of [Formula: see text], the endogenous [Formula: see text] concentration in the blood of healthy individuals is found to be in the range of 0.8-6 µM. The availability of this device at the point of care will have relevance in understanding the role of [Formula: see text] in health and disease.
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Project description: Not available
| S-EPMC2754069 | biostudies-literature
Project description:Current research on catalysts for proton exchange membrane fuel cells (PEMFC) is based on obtaining higher catalytic activity than platinum particle catalysts on porous carbon. In search of a more sustainable catalyst other than platinum for the catalytic conversion of water to hydrogen gas, a series of nanoparticles of transition metals viz., Rh, Co, Fe, Pt and their composites with functionalized graphene such as RhNPs@f-graphene, CoNPs@f-graphene, PtNPs@f-graphene were synthesized and characterized by SEM and TEM techniques. The SEM analysis indicates that the texture of RhNPs@f-graphene resemble the dispersion of water droplets on lotus leaf. TEM analysis indicates that RhNPs of <10 nm diameter are dispersed on the surface of f-graphene. The air-stable NPs and nanocomposites were used as electrocatalyts for conversion of acidic water to hydrogen gas. The composite RhNPs@f-graphene catalyses hydrogen gas evolution from water containing p-toluene sulphonic acid (p-TsOH) at an onset reduction potential, Ep, -0.117 V which is less than that of PtNPs@f-graphene (Ep, -0.380 V) under identical experimental conditions whereas the onset potential of CoNPs@f-graphene was at Ep, -0.97 V and the FeNPs@f-graphene displayed onset potential at Ep, -1.58 V. The pure rhodium nanoparticles, RhNPs also electrocatalyse at Ep, -0.186 V compared with that of PtNPs at Ep, -0.36 V and that of CoNPs at Ep, -0.98 V. The electrocatalytic experiments also indicate that the RhNPs and RhNPs@f-graphene are stable, durable and they can be recycled in several catalytic experiments after washing with water and drying. The results indicate that RhNPs and RhNPs@f-graphene are better nanoelectrocatalysts than PtNPs and the reduction potentials were much higher in other transition metal nanoparticles. The mechanism could involve a hydridic species, Rh-H- followed by interaction with protons to form hydrogen gas.
| S-EPMC6863816 | biostudies-literature
Project description:This paper presents our vision of how to use in silico approaches to extract the reaction mechanisms and kinetic parameters for complex condensed-phase chemical processes that underlie important technologies ranging from combustion to chemical vapor deposition. The goal is to provide an analytic description of the detailed evolution of a complex chemical system from reactants through various intermediates to products, so that one could optimize the efficiency of the reactive processes to produce the desired products and avoid unwanted side products. We could start with quantum mechanics (QM) to ensure an accurate description; however, to obtain useful kinetics we need to average over ∼10-nm spatial scales for ∼1 ns, which is prohibitively impractical with QM. Instead, we use the reactive force field (ReaxFF) trained to fit QM to carry out the reactive molecular dynamics (RMD). We focus here on showing that it is practical to extract from such RMD the reaction mechanisms and kinetics information needed to describe the reactions analytically. This analytic description can then be used to incorporate the correct reaction chemistry from the QM/ReaxFF atomistic description into larger-scale simulations of ∼10 nm to micrometers to millimeters to meters using analytic approaches of computational fluid dynamics and/or continuum chemical dynamics. In the paper we lay out the strategy to extract the mechanisms and rate parameters automatically without the necessity of knowing any details of the chemistry. We consider this to be a proof of concept. We refer to the process as RMD2Kin (reactive molecular dynamics to kinetics) for the general approach and as ReaxMD2Kin (ReaxFF molecular dynamics to kinetics) for QM-ReaxFF-based reaction kinetics.
| S-EPMC6744889 | biostudies-literature