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Faraday Discussions Jun 2024The prenylated-flavin mononucleotide-dependent decarboxylases (also known as UbiD-like enzymes) are the most recently discovered family of decarboxylases. The modified...
The prenylated-flavin mononucleotide-dependent decarboxylases (also known as UbiD-like enzymes) are the most recently discovered family of decarboxylases. The modified flavin facilitates the decarboxylation of unsaturated carboxylic acids through a novel mechanism involving 1,3-dipolar cyclo-addition chemistry. UbiD-like enzymes have attracted considerable interest for biocatalysis applications due to their ability to catalyse (de)carboxylation reactions on a broad range of aromatic substrates at otherwise unreactive carbon centres. There are now ∼35 000 protein sequences annotated as hypothetical UbiD-like enzymes. Sequence similarity network analyses of the UbiD protein family suggests that there are likely dozens of distinct decarboxylase enzymes represented within this family. Furthermore, many of the enzymes so far characterized can decarboxylate a broad range of substrates. Here we describe a strategy to identify potential substrates of UbiD-like enzymes based on detecting enzyme-catalysed solvent deuterium exchange into potential substrates. Using ferulic acid decarboxylase (FDC) as a model system, we tested a diverse range of aromatic and heterocyclic molecules for their ability to undergo enzyme-catalysed H/D exchange in deuterated buffer. We found that FDC catalyses H/D exchange, albeit at generally very low levels, into a wide range of small, aromatic molecules that have little resemblance to its physiological substrate. In contrast, the sub-set of aromatic carboxylic acids that are substrates for FDC-catalysed decarboxylation is much smaller. We discuss the implications of these findings for screening uncharacterized UbiD-like enzymes for novel (de)carboxylase activity.
PubMed: 38837123
DOI: 10.1039/d4fd00006d -
Journal of the American Society For... Jul 2024In a hydrogen exchange-mass spectrometry (HX-MS) experiment, the enzymatic proteolysis of the deuterated protein is an essential step. Often the differences in the...
In a hydrogen exchange-mass spectrometry (HX-MS) experiment, the enzymatic proteolysis of the deuterated protein is an essential step. Often the differences in the performance between different digestion protocols or between immobilized protease columns can be challenging to evaluate. To compare differences in the performance of immobilized protease columns, a new digestion efficiency metric known as digestible peptide scoring (DPS) was developed and is presented in this work. The measured response fraction of substance P peptide is used to assign a value between 0% and 100% based on the fraction of substance P digested by the enzyme, using angiotensin II as an undigested internal standard. In this work, the DPS approach was tested using multiple immobilized pepsin batches prepared using different protocols. The results demonstrate the repeatability of DPS values for batches prepared using the same conditions and the ability of the DPS evaluations to provide unique values when the immobilization conditions were altered. Protein digestions obtained with a higher scoring column were better than digestions obtained using a lower scoring column. The DPS evaluation is simple and quickly provides an unambiguous assessment which can be used to evaluate an immobilized enzyme column's suitability prior to performing an experiment, to track performance over a column's lifetime, to optimize protease immobilization protocols specifically for the quench conditions of a particular experiment, and to optimize the digestion conditions.
Topics: Proteolysis; Pepsin A; Peptides; Hydrogen Deuterium Exchange-Mass Spectrometry; Substance P; Enzymes, Immobilized
PubMed: 38835173
DOI: 10.1021/jasms.4c00056 -
Langmuir : the ACS Journal of Surfaces... Jun 2024Due to their distinct and tailorable internal cavity structures, zeolites serve as promising materials for efficient and specific gas separations such as the separation...
Due to their distinct and tailorable internal cavity structures, zeolites serve as promising materials for efficient and specific gas separations such as the separation of /CO from N. A subset of zeolite materials exhibits trapdoor behavior which can be exploited for particularly challenging separations, such as the separation of hydrogen, deuterium, and tritium for the nuclear industry. This study systematically delves into the influence of the chabazite (CHA) and merlinoite (MER) zeolite frameworks combined with different door-keeping cations (K, Rb, and Cs) on the trapdoor separation behavior under a variety of thermal and gas conditions. Both CHA and MER frameworks were synthesized from the same parent Y-zeolite and studied using in situ X-ray diffraction as a function of increasing temperatures under 1 bar H exposures. This resulted in distinct thermal responses, with merlinoite zeolites exhibiting expansion and chabazite zeolites showing contraction of the crystal structure. Simultaneous thermal analysis (STA) and gas sorption techniques further demonstrated how the size of trapdoor cations restricts access to the internal porosities of the zeolite frameworks. These findings highlight that both the zeolite frameworks and the associated trapdoor cations dictate the thermal response and gas sorption behavior. Frameworks determine the crystalline geometry, the maximum porosities, and displacement of the cation in gas sorption, while associated cations directly affect the blockage of the functional sites and the thermal behavior of the frameworks. This work contributes new insights into the efficient design of zeolites for gas separation applications and highlights the significant role of the trapdoor mechanism.
PubMed: 38832461
DOI: 10.1021/acs.langmuir.4c00498 -
Oecologia Jun 2024Spatial and temporal zooplankton feeding dynamics across the water column of lakes are key for understanding site-specific acquisition of diet sources. During this...
Spatial and temporal zooplankton feeding dynamics across the water column of lakes are key for understanding site-specific acquisition of diet sources. During this 6-week lake study, we examined stable carbon (δC) and nitrogen (δN) isotopes and conducted compound-specific fatty acid (FA) stable isotope analysis (CSIA) of edible seston in the epi-, meta-, and hypolimnion, and zooplankton of Lake Lunz, Austria. We predicted that CSIA of essential FA can discern the foraging grounds of zooplankton more accurately than the commonly used bulk stable isotopes. The δC and δN values of seston from different lake strata were similar, whereas a dual CSIA approach using stable carbon and hydrogen isotopes of FA (δC and δH) provided sufficient isotopic difference in essential FA to discern different lake strata-specific diet sources throughout the study period. We present a CSIA model that suggests strata-specific foraging grounds for different zooplankton groups, indicating higher preference of cladocerans for feeding on epilimnetic diet sources, while calanoid copepods retained more hypolimnetic resources. The CSIA approach thus yields strata-specific information on foraging strategies of different zooplankton taxa and provides more details on the spatial and temporal trophodynamics of planktonic food webs than commonly used bulk stable isotopes.
PubMed: 38829405
DOI: 10.1007/s00442-024-05574-3 -
Organic Letters Jun 2024A strategy for Co(III)-catalyzed C(sp)-H alkenylation of -protected isoquinolones with 1,4-naphthoquinones has been disclosed. The developed protocol was efficiently...
A strategy for Co(III)-catalyzed C(sp)-H alkenylation of -protected isoquinolones with 1,4-naphthoquinones has been disclosed. The developed protocol was efficiently applied for diversely substituted isoquinolones. Preliminary mechanistic experiments revealed the involvement of a five-membered cobaltacycle as an intermediate. Deuterium labeling experiments suggested the reversible nature of the C-H activation step. The scale-up reaction was also carried out, and the product was utilized as a chemosensor to detect Fe ions.
PubMed: 38829220
DOI: 10.1021/acs.orglett.4c01686 -
BioRxiv : the Preprint Server For... May 2024The oscillator of the cyanobacterial circadian clock relies on the ability of the KaiB protein to switch reversibly between a stable ground-state fold (gsKaiB) and an...
The oscillator of the cyanobacterial circadian clock relies on the ability of the KaiB protein to switch reversibly between a stable ground-state fold (gsKaiB) and an unstable fold-switched fold (fsKaiB). Rare fold-switching events by KaiB provide a critical delay in the negative feedback loop of this post-translational oscillator. In this study, we experimentally and computationally investigate the temperature dependence of fold switching and its mechanism. We demonstrate that the stability of gsKaiB increases with temperature compared to fsKaiB and that the Q10 value for the gsKaiB → fsKaiB transition is nearly three times smaller than that for the reverse transition. Simulations and native-state hydrogen-deuterium exchange NMR experiments suggest that fold switching can involve both subglobally and near-globally unfolded intermediates. The simulations predict that the transition state for fold switching coincides with isomerization of conserved prolines in the most rapidly exchanging region, and we confirm experimentally that proline isomerization is a rate-limiting step for fold switching. We explore the implications of our results for temperature compensation, a hallmark of circadian clocks, through a kinetic model.
PubMed: 38826295
DOI: 10.1101/2024.05.21.594594 -
Advances and prospects in deuterium metabolic imaging (DMI): a systematic review of in vivo studies.European Radiology Experimental Jun 2024Deuterium metabolic imaging (DMI) has emerged as a promising non-invasive technique for studying metabolism in vivo. This review aims to summarize the current... (Review)
Review
BACKGROUND
Deuterium metabolic imaging (DMI) has emerged as a promising non-invasive technique for studying metabolism in vivo. This review aims to summarize the current developments and discuss the futures in DMI technique in vivo.
METHODS
A systematic literature review was conducted based on the PRISMA 2020 statement by two authors. Specific technical details and potential applications of DMI in vivo were summarized, including strategies of deuterated metabolites detection, deuterium-labeled tracers and corresponding metabolic pathways in vivo, potential clinical applications, routes of tracer administration, quantitative evaluations of metabolisms, and spatial resolution.
RESULTS
Of the 2,248 articles initially retrieved, 34 were finally included, highlighting 2 strategies for detecting deuterated metabolites: direct and indirect DMI. Various deuterated tracers (e.g., [6,6'-H2]glucose, [2,2,2'-H3]acetate) were utilized in DMI to detect and quantify different metabolic pathways such as glycolysis, tricarboxylic acid cycle, and fatty acid oxidation. The quantifications (e.g., lactate level, lactate/glutamine and glutamate ratio) hold promise for diagnosing malignancies and assessing early anti-tumor treatment responses. Tracers can be administered orally, intravenously, or intraperitoneally, either through bolus administration or continuous infusion. For metabolic quantification, both serial time point methods (including kinetic analysis and calculation of area under the curves) and single time point quantifications are viable. However, insufficient spatial resolution remains a major challenge in DMI (e.g., 3.3-mL spatial resolution with 10-min acquisition at 3 T).
CONCLUSIONS
Enhancing spatial resolution can facilitate the clinical translation of DMI. Furthermore, optimizing tracer synthesis, administration protocols, and quantification methodologies will further enhance their clinical applicability.
RELEVANCE STATEMENT
Deuterium metabolic imaging, a promising non-invasive technique, is systematically discussed in this review for its current progression, limitations, and future directions in studying in vivo energetic metabolism, displaying a relevant clinical potential.
KEY POINTS
• Deuterium metabolic imaging (DMI) shows promise for studying in vivo energetic metabolism. • This review explores DMI's current state, limits, and future research directions comprehensively. • The clinical translation of DMI is mainly impeded by limitations in spatial resolution.
Topics: Humans; Deuterium; Animals
PubMed: 38825658
DOI: 10.1186/s41747-024-00464-y -
The Journal of Organic Chemistry Jun 2024Here, we present a straightforward α--selective hydroboration of alkynyl sulfones with NHC-boranes without the need for a catalyst. This reaction is compatible with a...
Here, we present a straightforward α--selective hydroboration of alkynyl sulfones with NHC-boranes without the need for a catalyst. This reaction is compatible with a wide range of substrates for efficiently producing structurally diverse α-borylated vinyl sulfones in satisfactory yields. The hydride transfer from NHC-borane to alkynyl triflone is studied by density functional theory (DFT) calculations for -hydroboration. Moreover, a regiodivergent deuterated semihydrogenation of alkynyl triflones has also been developed using DO as the deuterium source. A variety of diversity-oriented D-containing vinyl triflones were prepared in good to excellent yields with excellent deuterium incorporation ratios. Synthetic manipulations of the deuterated products are achieved for the conversion into valuable deuterated molecules, indicating the utility of this protocol.
PubMed: 38817078
DOI: 10.1021/acs.joc.3c02833 -
Environment International Jun 2024Fusion energy investigation has stepped to a new stage adopting deuterium and tritium as fuels from the previous stage concentrating hydrogen plasma physics. Special... (Review)
Review
Fusion energy investigation has stepped to a new stage adopting deuterium and tritium as fuels from the previous stage concentrating hydrogen plasma physics. Special radiation safety issues would be introduced during this stage. In addition to industrial and military uses, tungsten is also regarded as the most promising plasma facing material for fusion reactors. During the operation of fusion reactors, tungsten-based plasma facing materials can be activated via neutron nuclear reaction. Meanwhile, activated tungsten dust can be produced when high-energy plasma interacts with the tungsten-based plasma facing materials, namely plasma wall interaction. Activated tungsten dust would be an emerging environmental pollutant with radiation toxicity containing various radionuclides in addition to the chemical toxicity of tungsten itself. Nonetheless, the historical underestimation of its environmental availability has led to limited research on tungsten compared to other environmental contaminants. This paper presents the first systematic review on the safety issue of emerging activated tungsten dust, encompassing source terms, environmental behaviors, and health effects. The key contents are as follows: 1) to detail the source terms of activated tungsten dust from aspects of tungsten basic properties, generation mechanism, physical morphology and chemical component, radioactivity, as well as potential release pathways, 2) to illustrate the environmental behaviors from aspects of atmospheric dispersion and deposition, transformation and migration in soil, as well as plant absorption and distribution, 3) to identify the toxicity and health effects from aspects of toxicity to plants, distribution in human body, as well as health effects by radiation and chemical toxicity, 4) based on the research progress, research and development issues needed are also pointed out to better knowledge of safety issue of activated tungsten dust, which would be beneficial to the area of fusion energy and ecological impact caused by the routine tungsten related industrial and military applications.
Topics: Tungsten; Dust; Humans
PubMed: 38810497
DOI: 10.1016/j.envint.2024.108774 -
Biomacromolecules Jun 2024Lignin is an aromatic polymer that constitutes plant cell walls. The polymerization of lignin proceeds by radical coupling, and this process requires radicalization of...
Lignin is an aromatic polymer that constitutes plant cell walls. The polymerization of lignin proceeds by radical coupling, and this process requires radicalization of the phenolic end of lignin by enzymes. However, due to the steric hindrance between enzymes, lignin, and polysaccharides, the direct oxidation of the phenolic end of lignin by the enzyme would be difficult, and the details of the growth of lignin are still unknown. In this study, enzymatic dehydrogenative polymerization experiments were conducted using coniferyl alcohol (CA) and the deuterium-labeled lignin model compound (D-LM) under a noncontact condition in which horseradish peroxidase cannot directly oxidize D-LM due to separation by a dialysis membrane. Analysis of deuterium-labeled degraded compounds obtained by a combination of methylation and thioacidolysis revealed the formation of the bond between the phenolic end of D-LM and CA, suggesting that membrane-permeable, low-molecular-weight lignols functioned as a redox shuttle mediator.
Topics: Lignin; Oxidation-Reduction; Polymerization; Phenols; Horseradish Peroxidase; Molecular Weight; Phenylpropionates
PubMed: 38806062
DOI: 10.1021/acs.biomac.4c00230