Radiation- and Photo-Induced Oxidation Pathways of Methionine in Model Peptide Backbone under Anoxic Conditions.
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ABSTRACT:
SUBMITTER: Pedzinski T
PROVIDER: S-EPMC8125225 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:A toluene-degrading sulfate-reducing bacterium, strain Tol2, was isolated from marine sediment under strictly anoxic conditions. Toluene was toxic if applied directly to the medium at concentrations higher than 0.5 mM. To provide toluene continuously at a nontoxic concentration, it was supplied in an inert hydrophobic carrier phase. The isolate had oval, sometimes motile cells (1.2 to 1.4 by 1.2 to 2.0 microns). The doubling time was 27 h. Toluene was completely oxidized to CO2, as demonstrated by measurement of the degradation balance. The presence of carbon monoxide dehydrogenase and formate dehydrogenase indicated a terminal oxidation of acetyl coenzyme A via the CO dehydrogenase pathway. The use of hypothetical intermediates of toluene degradation was tested in growth experiments and adaptation studies with dense cell suspensions. Results do not support a degradation of toluene via one of the cresols or methylbenzoates, benzyl alcohol, or phenylacetate as free intermediate. Benzyl alcohol did not serve as growth substrate; moreover, it was a strong, specific inhibitor of toluene degradation, whereas benzoate utilization was not affected by benzyl alcohol. Sequencing of 16S rRNA revealed a relationship to the metabolically dissimilar genus Desulfobacter and on a deeper level to the genus Desulfobacterium. The new genus and species Desulfobacula toluolica is proposed.
| S-EPMC182102 | biostudies-other
Project description:The iron phosphate mineral vivianite Fe(II)3(PO4)2·8H2O has emerged as a potential renewable P source. Although the importance of vivianite as a potential P sink in the global P cycle had previously been recognized, a mechanistic understanding of vivianite dissolution at the molecular level, critical to its potential application, is still elusive. The potential of vivianite as a P sink or source in natural or engineered systems is directly dependent on its dissolution kinetics under environmentally relevant conditions. To understand the thermodynamic and kinetic controls on bioavailability, the oxidation and dissolution processes of vivianite must be disentangled. In this study, we conducted controlled batch and flow-through experiments to quantitatively determine the dissolution rates and mechanisms of vivianite under anoxic conditions as a function of pH and temperature. Our results demonstrate that vivianite solubility and dissolution rates strongly decreased with increasing solution pH. Dissolution was nonstoichiometric at alkaline pH (>7). The rapid initial dissolution rate of vivianite is related to the solution saturation state, indicating a thermodynamic rather than a kinetic control. A defect-driven dissolution mechanism is proposed. Dissolution kinetics over pH 5-9 could be described with a rate law with a single rate constant and a reaction order of 0.61 with respect to {H+}: Rexp=36.0·e-1.41·pH·[1-e(0.2·ΔG/RT)]4.7 The activation energy of vivianite dissolution proved low (Ea = 20.3 kJ mol-1), suggesting hydrogen bridge dissociation as the rate-determining step.
| S-EPMC10653223 | biostudies-literature
Project description:ObjectiveThe objectives of the present work were to optimize and validate the synthesis and stability of 14(R,S)-[18F]fluoro-6-thia-heptadecanoic acid ([18F]FTHA) and 16-[18F]fluoro-4-thia-palmitic acid ([18F]FTP) under cGMP conditions for clinical applications.MethodsBenzyl-14-(R,S)-tosyloxy-6-thiaheptadecanoate and methyl 16-bromo-4-thia-palmitate were used as precursors for the synthesis of [18F]FTHA and [18F]FTP, respectively. For comparison, a fatty acid analog lacking a thia-substitution, 16-[18F]fluoro-palmitic acid ([18F]FP), was synthesized from the precursor methyl 16-bromo-palmitate. A standard nucleophilic reaction using cryptand (Kryptofix/K222, 8.1?mg), potassium carbonate (K2CO3, 4.0?mg) and 18F-fluoride were employed for the 18F-labeling and potassium hydroxide (0.8?M) was used for the post-labeling ester hydrolysis. The final products were purified via reverse phase semi-preparative HPLC and concentrated via trap and release on a C-18 plus solid phase extraction cartridge. The radiochemical purities of the [18F]fluorothia fatty acids and [18F]FP were examined over a period of 4?h post-synthesis using an analytical HPLC. All the syntheses were optimized in an automated TRACERlab FX-N Pro synthesizer. Liquid chromatography mass spectrometry (LCMS) and high resolution mass spectrometry (HRMS) was employed to study the identity and nature of side products formed during radiosynthesis and as a consequence of post-synthesis radiation induced oxidation.ResultsRadiosyntheses of [18F]FTHA, [18F]FTP and [18F]FP were achieved in moderate (8-20% uncorrected) yields. However, it was observed that the HPLC-purified [18F]fluorothia fatty acids, [18F]FTHA and [18F]FTP at higher radioactivity concentrations (>1.11?GBq/mL, 30?mCi/mL) underwent formation of 18F-labeled side products over time but [18F]FP (lacking a sulfur heteroatom) remained stable up to 4?h post-synthesis. Various radiation protectors like ethanol and ascorbic acid were examined to minimize the formation of side products formed during [18F]FTHA and [18F]FTP synthesis but showed only limited to no effect. Analysis of the side products by LCMS showed formation of sulfoxides of both [18F]FTHA and [18F]FTP. The identity of the sulfoxide side product was further confirmed by synthesizing a non-radioactive reference standard of the sulfoxide analog of FTP and matching retention times on HPLC and molecular ion peaks on LC/HRMS. Radiation-induced oxidation of the sulfur heteroatom was mitigated by dilution of product with isotonic saline to reduce the radioactivity concentration to <0.518?GBq/mL (14?mCi/mL).ConclusionsSuccessful automated synthesis of [18F]fluorothia fatty acids were carried out in cGMP facility for their routine production and clinical applications. Instability of [18F]fluorothia fatty acids were observed at radioactivity concentrations exceeding 1.11?GBq/mL (30?mCi/mL) but mitigated through dilution of the product to <0.518?GBq/mL (14?mCi/mL). The identities of the side products formed were established as the sulfoxides of the respective thia fatty acids caused by radiation-induced oxidation of the sulfur heteroatom.
| S-EPMC7056516 | biostudies-literature
Project description:Selective photosensitized oxidation of amyloid protein aggregates is being investigated as a possible therapeutic strategy for treating Alzheimer's disease (AD). Photo-oxidation has been shown to degrade amyloid-β (Aβ) aggregates and ameliorate aggregate toxicity in vitro and reduce aggregate levels in the brains of AD animal models. To shed light on the mechanism by which photo-oxidation induces fibril destabilization, we carried out an all-atom molecular dynamics (MD) simulation to examine the effect of methionine (Met35) oxidation on the conformation and stability of a β-sheet-rich Aβ9-40 protofibril. Analyses of up to 1 μs simulations showed that the oxidation of the Met35 residues, which resulted in the addition of hydrophilic oxygens in the fibril core, reduced the overall conformational stability of the protofibril. Specifically, Met35 disrupted the hydrophobic interface that stabilizes the stacking of the two hexamers that comprise the protofibril. The oxidized protofibril is more solvent exposed and exhibits more backbone flexibility. However, the protofibril retained the underlying U-shaped architecture of each peptide upon oxidation, and although some loss of β-sheets occurred, a significant portion remained. Our simulation results are thus consistent with our experimental observation that photo-oxidation of Aβ40 fibril resulted in the dis-agglomeration and fragmentation of Aβ fibrils but did not cause complete disruption of the fibrillar morphology or β-sheet structures. The partial destabilization of Aβ aggregates supports the further development of photosensitized platforms for the targeting and clearing of Aβ aggregates as a therapeutic strategy for treating AD.
| S-EPMC10035002 | biostudies-literature
Project description:Methane (CH4) emissions from Arctic lakes are a large and growing source of greenhouse gas to the atmosphere with critical implications for global climate. Because Arctic lakes are ice covered for much of the year, understanding the metabolic flexibility of methanotrophs under anoxic conditions would aid in characterizing the mechanisms responsible for limiting CH4 emissions from high-latitude regions. Using sediments from an active CH4 seep in Lake Qalluuraq, Alaska, we conducted DNA-based stable isotope probing (SIP) in anoxic mesocosms and found that aerobic Gammaproteobacterial methanotrophs dominated in assimilating CH4. Aerobic methanotrophs were also detected down to 70 cm deep in sediments at the seep site, where anoxic conditions persist. Metagenomic analyses of the heavy DNA from 13CH4-SIP incubations showed that these aerobic methanotrophs had the capacity to generate intermediates such as methanol, formaldehyde, and formate from CH4 oxidation and to oxidize formaldehyde in the tetrahydromethanopterin (H4MPT)-dependent pathway under anoxic conditions. The high levels of Fe present in sediments, combined with Fe and CH4 profiles in the persistent CH4 seep site, suggested that oxidation of CH4, or, more specifically, its intermediates such as methanol and formaldehyde might be coupled to iron reduction. Aerobic methanotrophs also possessed genes associated with nitrogen and hydrogen metabolism, which might provide potentially alternative energy conservation options under anoxic conditions. These results expand the known metabolic spectrum of aerobic methanotrophs under anoxic conditions and necessitate the re-assessment of the mechanisms underlying CH4 oxidation in the Arctic, especially under lakes that experience extended O2 limitations during ice cover.
| S-EPMC8692461 | biostudies-literature
Project description:In the bone marrow (BM) hematopoietic niche, the oxygen tension is usually very low. Such condition affects stem and progenitor cell proliferation and differentiation and, at cellular level regulates hematopoietic growth factors, chemokines and adhesion molecules expression. In turn, these molecules affect the proliferation and maturation of other cellular components of the niche. Due to the complexity of the system we started the in vitro investigations of the IL-6, IL-8, TNFα cytokines expression and the vascular endothelial growth factor (VEGF), considered key mediators of the hematopoietic niche, in human macrophages and macrophage cell line. Since in the niche the oxygen availability is mediated by red blood cells (RBCs), we have influenced the anoxic cell cultures by the administration of oxygenated or deoxygenated RBCs (deoxy RBCs). The results reported in this brief paper show that the presence of RBCs up-regulates IL-8 mRNA while IL-6 and VEGF mRNA expression appears down-regulated. This does not occur when deoxy RBCs are used. Moreover, it appears that the administration of RBCs leads to an increase of TNFα expression levels in MonoMac 6 (MM6). Interestingly, the modulation of these factors likely occurs in a hypoxia-inducible factor-1α (HIF-1α) independent manner. Considering the role of oxygen in the hematopoietic niche further studies should explore these preliminary observations in more details.
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Project description:The effects of soil minerals on chromate (CrVIO42-, noted as Cr(VI)) reduction by sulfide were investigated in the pH range of 7.67 to 9.07 under the anoxic condition. The examined minerals included montmorillonite (Swy-2), illite (IMt-2), kaolinite (KGa-2), aluminum oxide (gamma-Al2O3), titanium oxide (TiO2, P-25, primarily anatase), and silica (SiO2). Based on their effects on Cr(VI) reduction, these minerals were categorized into three groups: (i) minerals catalyzing Cr(VI) reduction - illite; (ii) minerals with no effect - Al2O3; and (iii) minerals inhibiting Cr(VI) reduction- kaolinite, montmorillonite, SiO2 and TiO2 . The catalysis of illite was attributed primarily to the low concentration of iron solubilized from the mineral, which could accelerate Cr(VI) reduction by shuttling electrons from sulfide to Cr(VI). Additionally, elemental sulfur produced as the primary product of sulfide oxidation could further catalyze Cr(VI) reduction in the heterogeneous system. Previous studies have shown that adsorption of sulfide onto elemental sulfur nanoparticles could greatly increase sulfide reactivity towards Cr(VI) reduction. Consequently, the observed rate constant, kobs, increased with increasing amounts of both iron solubilized from illite and elemental sulfur produced during the reaction. The catalysis of iron, however, was found to be blocked by phenanthroline, a strong complexing agent for ferrous iron. In this case, the overall reaction rate at the initial stage of reaction was pseudo first order with respect to Cr(VI), i.e., the reaction kinetics was similar to that in the homogeneous system, because elemental sulfur exerted no effect at the initial stage prior to accumulation of elemental sulfur nanoparticles. In the suspension of kaolinite, which belonged to group (iii), an inhibitive effect to Cr(VI) reduction was observed and subsequently examined in more details. The inhibition was due to the sorption of elemental sulfur onto kaolinite, which reduced or completely eliminated the catalytic effect of elemental sulfur, depending on kaolinite concentration. This was consistent with the observation that the catalysis of externally added elemental sulfur (50 muM) on Cr(VI) reduction would disappear with a kaolinite concentration of more than 5.0 g/L. In kaolinite suspension, the overall reaction rate law was:-d[Cr(VI)]/dt = kobs[H+]2[Cr(VI)][HS-]0.70.
| S-EPMC1865374 | biostudies-literature
Project description:LA-PTH is a long-acting parathyroid hormone (PTH) peptide analogue in preclinical development for hypoparathyroidism (HP). Like native PTH, LA-PTH contains a methionine at position 8 (Met8) that is predicted to be critical for function. We assessed the impact of Met oxidation on the functional properties of LA-PTH and control PTH ligands. Oxidation of PTH(1-34) resulted in marked (~20-fold) reductions in binding affinity on the PTH receptor-1 (PTHR1) in cell membranes, similarly diminished potency for 3',5'-cyclic AMP signaling in osteoblastic cell lines (SaOS-2 and UMR106), and impaired efficacy for raising blood calcium in mice. Surprisingly, oxidation of LA-PTH resulted in little or no change in these functional responses. The signaling potency of oxidized-LA-PTH was, however, reduced approximately 40-fold compared to LA-PTH in cells expressing a PTHR1 construct that lacks the N-terminal extracellular domain (ECD). Molecular modeling revealed that while Met8 of both LA-PTH and PTH(1-34) is situated within the orthosteric ligand-binding pocket of the receptor's transmembrane domain bundle (TMD), the Met8 sidechain position is shifted for the 2 ligands so that on Met8 oxidation of PTH(1-34), steric clashes occur that are not seen with oxidized LA-PTH. The findings suggest that LA-PTH and PTH(1-34) engage the receptor differently in the Met8-interaction environment of the TMD bundle, and that this interaction environment can be allosterically influenced by the ECD component of the ligand-receptor complex. The findings should be useful for the future development of novel PTH-based peptide therapeutics for diseases of bone and mineral ion metabolism.
| S-EPMC7774776 | biostudies-literature
Project description:Aggregation of Aβ peptides into amyloid plaques is considered to trigger the Alzheimer's disease (AD), however the mechanism behind the AD onset has remained elusive. It is assumed that the insoluble Aβ aggregates enhance oxidative stress (OS) by generating free radicals with the assistance of bound copper ions. The aim of our study was to establish the role of Met35 residue in the oxidation and peptide aggregation processes. Met35 can be readily oxidized by H2O2. The fibrillization of Aβ with Met35 oxidized to sulfoxide was three times slower compared to that of the regular peptide. The fibrils of regular and oxidized peptides looked similar under transmission electron microscopy. The relatively small inhibitory effect of methionine oxidation on the fibrillization suggests that the possible variation in the Met oxidation state should not affect the in vivo plaque formation. The peptide oxidation pattern was more complex when copper ions were present: addition of one oxygen atom was still the fastest process, however, it was accompanied by multiple unspecific modifications of peptide residues. Addition of copper ions to the Aβ with oxidized Met35 in the presence of H2O2, resulted a similar pattern of nonspecific modifications, suggesting that the one-electron oxidation processes in the peptide molecule do not depend on the oxidation state of Met35 residue. Thus, it can be concluded that Met35 residue is not a part of the radical generating mechanism of Aβ-Cu(II) complex.
| S-EPMC5668694 | biostudies-literature
Project description:In irradiated DNA, by the base-to-base and backbone-to-base hole transfer processes, the hole (i.e., the unpaired spin) localizes on the most electropositive base, guanine. Phosphate radicals formed via ionization events in the DNA-backbone must play an important role in the backbone-to-base hole transfer process. However, earlier studies on irradiated hydrated DNA, on irradiated DNA-models in frozen aqueous solution and in neat dimethyl phosphate showed the formation of carbon-centered radicals and not phosphate radicals. Therefore, to model the backbone-to-base hole transfer process, we report picosecond pulse radiolysis studies of the reactions between H2PO4˙ with the DNA bases - G, A, T, and C in 6 M H3PO4 at 22 °C. The time-resolved observations show that in 6 M H3PO4, H2PO4˙ causes the one-electron oxidation of adenine, guanine and thymine, by forming the cation radicals via a single electron transfer (SET) process; however, the rate constant of the reaction of H2PO4˙ with cytosine is too low (<107 L mol-1 s-1) to be measured. The rates of these reactions are influenced by the protonation states and the reorganization energies of the base radicals and of the phosphate radical in 6 M H3PO4.
| S-EPMC5976554 | biostudies-literature