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BioRxiv : the Preprint Server For... Jun 2024The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires...
The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor Nub1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal system and revealed that Nub1 utilizes FAT10's intrinsic instability to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin- and p97-independent manner. Through hydrogen-deuterium exchange, structural modeling, and site-directed mutagenesis, we identified the formation of a peculiar complex with FAT10 that activates Nub1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic Nub1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These studies thus identified a novel mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.
PubMed: 38915702
DOI: 10.1101/2024.06.12.598715 -
Chemosphere Jun 2024The processes leading to high levels of arsenic (As), iron (Fe), and manganese (Mn) in groundwater, in a naturally reducing aquifer at a controlled municipal landfill...
The processes leading to high levels of arsenic (As), iron (Fe), and manganese (Mn) in groundwater, in a naturally reducing aquifer at a controlled municipal landfill site, are investigated. The challenge is to distinguish the natural water-rock interaction processes, that allow these substances to dissolve in groundwater, from direct pollution or enhanced dissolution of hydroxides as undesired consequences of the anthropic activities above. Ordinary groundwater monitoring of physical-chemical parameters and inorganic compounds (major and trace elements) was complemented by environmental isotopes of groundwater (tritium, deuterium, oxygen-18 and carbon-13) and dissolved gases (carbon-13 of methane and carbon dioxide and carbon-14 of methane). Pearson/Spearman correlation indices, as well as Principal Component Analysis (PCA), were used to determine the main correlations among variables. The concurrent presence of As, Fe and CH, as reported in similar anoxic environments, suggests that anaerobic oxidation of methane could drive the reductive dissolution of As-rich Fe(III)(hydro)oxides. Manganese is more sensitive to carbon dioxide, possibly due to a decrease in pH which accelerates the dissolution of Mn-oxides. Finally, we found that tritium and deuterium, which have been used for decades as leachate tracer in groundwater, may be subject to false positives due to the reuse of water recovered from leachate treatment (which has the same isotopic signature of leachate) within the plants, to comply with the requirements of the circular economy. The integration of the environmental isotope analysis into the traditional monitoring approach can effectively support the comprehension of processes. However, this strategy needs to be complemented by a good conceptual hydrogeological model and expert evaluation to avoid misinterpretations.
PubMed: 38901701
DOI: 10.1016/j.chemosphere.2024.142657 -
BioRxiv : the Preprint Server For... Jun 2024The synthesis and degradation rates of proteins form an essential component of gene expression control. Heavy water labeling has been used in conjunction with mass...
UNLABELLED
The synthesis and degradation rates of proteins form an essential component of gene expression control. Heavy water labeling has been used in conjunction with mass spectrometry to measure protein turnover rates, but the optimal analytical approaches to derive turnover rates from the isotopomer patterns of deuterium labeled peptides continue to be a subject of research. Here we describe a method, which comprises a reverse lookup of numerically approximated peptide isotope envelopes, coupled to the selection of optimal isotopomer pairs based on peptide sequence, to calculate the molar fraction of new peptide synthesis in heavy water labeling mass spectrometry experiments. We validated this approach using an experimental calibration curve comprising mixtures of fully unlabeled and fully labeled proteomes. We then re-analyzed 17 proteome-wide turnover experiments from four mouse organs, and showed that the method increases the coverage of well-fitted peptides in protein turnover experiments by 25-82%. The method is implemented in the Riana software tool for protein turnover analysis, and may avail ongoing efforts to study the synthesis and degradation kinetics of proteins in animals on a proteome-wide scale.
WHAT’S NEW
We describe a reverse lookup method to calculate the molar fraction of new synthesis from numerically approximated peptide isotopomer profiles in heavy water labeling mass spectrometry experiments. Using an experimental calibration curve comprising mixtures of fully unlabeled and fully labeled proteomes at various proportions, we show that this method provides a straightforward way to calculate the proportion of new proteins in a protein pool from arbitrarily chosen isotopomer ratios. We next analyzed which of the isotopomer pairs within the peptide isotope envelope yielded isotopomer time courses that fit most closely to kinetic models, and found that the identity of the isotopomer pair depends partially on the number of deuterium accessible labeling sites of the peptide. We next derived a strategy to automatically select the isotopomer pairs to calculate turnover rates based on peptide sequence, and showed that this increases the coverage of existing proteome-wide turnover experiments in multiple data sets of the mouse heart, liver, kidney, and skeletal muscle by up to 25-82%.
PubMed: 38895333
DOI: 10.1101/2024.06.04.597043 -
Materials (Basel, Switzerland) May 2024The WMoTaNbV alloy has shown promise for applications as a solid state hydrogen storage material. It absorbs significant quantities of H directly from the atmosphere,...
The WMoTaNbV alloy has shown promise for applications as a solid state hydrogen storage material. It absorbs significant quantities of H directly from the atmosphere, trapping it with high energy. In this work, the dynamics of the absorption of hydrogen isotopes are studied by determining the activation energy for the solubility and the solution enthalpy of H in the WMoTaNbV alloy. The activation energy was studied by heating samples in a H atmosphere at temperatures ranging from 20 °C to 400 °C and comparing the amounts of absorbed H. The solution activation energy EA of H was determined to be EA=0.22±0.02 eV (21.2 ± 1.9 kJ/mol). The performed density functional theory calculations revealed that the neighbouring host atoms strongly influenced the solution enthalpy, leading to a range of theoretical values from -0.40 eV to 0.29 eV (-38.6 kJ/mol to 28.0 kJ/mol).
PubMed: 38893838
DOI: 10.3390/ma17112574 -
Molecules (Basel, Switzerland) Jun 2024The origin of nuclear magnetic shielding in diamagnetic molecules is discussed, pointing out various contributions to the shielding from electrons and the effects of... (Review)
Review
The origin of nuclear magnetic shielding in diamagnetic molecules is discussed, pointing out various contributions to the shielding from electrons and the effects of intra- and intermolecular interactions. In NMR practice, chemical shifts are determined first as the measure of shielding in observed samples. The descriptions of shielding and chemical shifts are not fully consistent. Gas phase studies permit the withdrawal of intermolecular contributions from shielding and obtaining the magnetic shielding data in isolated molecules. The shielding determination in molecules is possible using at least three methods delivering the reference shielding standards for selected nuclei. The known shielding of one magnetic nucleus can be transferred to other nuclei if the appropriate nuclear magnetic moments are available with satisfactory accuracy. It is possible to determine the nuclear magnetic dipole moments using the most advanced ab initio shielding calculations jointly with the NMR frequencies measurements for small-sized isolated molecules. Helium-3 gas is postulated as all the molecules' primary and universal reference standard of shielding. It can be easily applied using common deuterium lock solvents as the secondary reference standards. The measurements of absolute shielding are available for everyone with the use of standard NMR spectrometers.
PubMed: 38893492
DOI: 10.3390/molecules29112617 -
Frontiers in Plant Science 2024The commonly used analytical tools for metabolomics cannot directly probe metabolic activities or distinguish metabolite differences between cells and suborgans in...
The commonly used analytical tools for metabolomics cannot directly probe metabolic activities or distinguish metabolite differences between cells and suborgans in multicellular organisms. These issues can be addressed by isotope labeling and mass spectrometry imaging (MSI), respectively, but the combination of the two, a newly emerging technology we call MSI, has been rarely applied to plant systems. In this study, we explored MSI of with DO labeling to study and visualize D-labeling in three classes of lipids: arabidopsides, chloroplast lipids, and epicuticular wax. Similar to other stress responses, DO-induced stress increased arabidopsides in an hour, but it was relatively minor for matured plants and reverted to the normal level in a few hours. The D-labeling isotopologue patterns of arabidopsides matched with those of galactolipid precursors, supporting the currently accepted biosynthesis mechanism. Matrix-assisted laser desorption/ionization (MALDI)-MSI was used to visualize the spatiotemporal distribution of deuterated chloroplast lipids, pheophytin , MGDGs, and DGDGs, after growing day-after-sowing (DAS) 28 plants in DO condition for 3-12 days. There was a gradual change of deuteration amount along the leaf tissues and with a longer labeling time, which was attributed to slow respiration leading to low DO concentration in the tissues. Finally, deuterium incorporation in epicuticular wax was visualized on the surfaces of the stem and flower. The conversion efficiency of newly synthesized C30 aldehyde to C29 ketone was very low in the lower stem but very high at the top of the stem near the flower or on the flower carpel. This study successfully demonstrated that MSI can unveil spatiotemporal metabolic activities in various tissues of .
PubMed: 38882571
DOI: 10.3389/fpls.2024.1379299 -
Science Advances Jun 2024Knowledge of the nucleosynthetic isotope composition of the outermost protoplanetary disk is critical to understand the formation and early dynamical evolution of the...
Knowledge of the nucleosynthetic isotope composition of the outermost protoplanetary disk is critical to understand the formation and early dynamical evolution of the Solar System. We report the discovery of outer disk material preserved in a pristine meteorite based on its chemical composition, organic-rich petrology, and N-rich, deuterium-rich, and O-poor isotope signatures. We infer that this outer disk material originated in the comet-forming region. The nucleosynthetic Fe, Mg, Si, and Cr compositions of this material reveal that, contrary to current belief, the isotope signature of the comet-forming region is ubiquitous among outer Solar System bodies, possibly reflecting an important planetary building block in the outer Solar System. This nucleosynthetic component represents fresh material added to the outer disk by late accretion streamers connected to the ambient molecular cloud. Our results show that most Solar System carbonaceous asteroids accreted material from the comet-forming region, a signature lacking in the terrestrial planet region.
PubMed: 38875339
DOI: 10.1126/sciadv.adp1613 -
Nature Communications Jun 2024Deuterium labeling compounds play a crucial role in organic and pharmaceutical chemistry. The synthesis of such compounds typically involves deuterated building blocks,...
Deuterium labeling compounds play a crucial role in organic and pharmaceutical chemistry. The synthesis of such compounds typically involves deuterated building blocks, allowing for the incorporation of deuterium atoms and functional groups into a target molecule in a single step. Unfortunately, the limited availability of synthetic approaches to deuterated synthons has impeded progress in this field. Here, we present an approach utilizing alkyl-substituted thianthrenium salts that efficiently and selectively introduce deuterium at the α position of alkyl chains through a pH-dependent HIE process, using DO as the deuterium source. The resulting α-deuterated alkyl thianthrenium salts, which bear two deuterium atoms, exhibit excellent selectivity and deuterium incorporation in electrophilic substitution reactions. Through in situ formation of isotopically labelled alkyl halides, these thianthrenium salts demonstrate excellent compatibility in a series of metallaphotoredox cross-electrophile coupling with (hetero)aryl, alkenyl, alkyl bromides, and other alkyl thianthrenium salts. Our technique allows for a wide range of substrates, high deuterium incorporation, and precise control over the site of deuterium insertion within a molecule such as the benzyl position, allylic position, or any alkyl chain in between, as well as neighboring heteroatoms. This makes it invaluable for synthesizing various deuterium-labeled compounds, especially those with pharmaceutical significance.
PubMed: 38871683
DOI: 10.1038/s41467-024-48590-w -
Pharmacology Research & Perspectives Jun 2024According to the CDC, both Pfizer and Moderna COVID-19 vaccines contain nucleoside-modified messenger RNA (mRNA) encoding the viral spike glycoprotein of severe acute... (Review)
Review
According to the CDC, both Pfizer and Moderna COVID-19 vaccines contain nucleoside-modified messenger RNA (mRNA) encoding the viral spike glycoprotein of severe acute respiratory syndrome caused by corona virus (SARS-CoV-2), administered via intramuscular injections. Despite their worldwide use, very little is known about how nucleoside modifications in mRNA sequences affect their breakdown, transcription and protein synthesis. It was hoped that resident and circulating immune cells attracted to the injection site make copies of the spike protein while the injected mRNA degrades within a few days. It was also originally estimated that recombinant spike proteins generated by mRNA vaccines would persist in the body for a few weeks. In reality, clinical studies now report that modified SARS-CoV-2 mRNA routinely persist up to a month from injection and can be detected in cardiac and skeletal muscle at sites of inflammation and fibrosis, while the recombinant spike protein may persist a little over half a year in blood. Vaccination with 1-methylΨ (pseudouridine enriched) mRNA can elicit cellular immunity to peptide antigens produced by +1 ribosomal frameshifting in major histocompatibility complex-diverse people. The translation of 1-methylΨ mRNA using liquid chromatography tandem mass spectrometry identified nine peptides derived from the mRNA +1 frame. These products impact on off-target host T cell immunity that include increased production of new B cell antigens with far reaching clinical consequences. As an example, a highly significant increase in heart muscle 18-flourodeoxyglucose uptake was detected in vaccinated patients up to half a year (180 days). This review article focuses on medical biochemistry, proteomics and deutenomics principles that explain the persisting spike phenomenon in circulation with organ-related functional damage even in asymptomatic individuals. Proline and hydroxyproline residues emerge as prominent deuterium (heavy hydrogen) binding sites in structural proteins with robust isotopic stability that resists not only enzymatic breakdown, but virtually all (non)-enzymatic cleavage mechanisms known in chemistry.
Topics: Humans; COVID-19; COVID-19 Vaccines; mRNA Vaccines; Pseudouridine; Recombinant Proteins; RNA, Messenger; RNA, Viral; Spike Glycoprotein, Coronavirus; Vaccination; Vaccines, Synthetic
PubMed: 38867495
DOI: 10.1002/prp2.1218 -
Nature Communications Jun 2024Carboxylic acids are widely available and generally inexpensive from abundant biomass feedstocks, and they are suitable and generic coupling partners in synthetic...
Carboxylic acids are widely available and generally inexpensive from abundant biomass feedstocks, and they are suitable and generic coupling partners in synthetic chemistry. Reported herein is an electroreductive coupling of stable and versatile carboxylic acids with (hetero)arenes using protons as the hydrogen source. The application of an earth-abundant titanium catalyst has significantly improved the deoxygenative reduction process. Preliminary mechanistic studies provide insights into the deoxygenative reduction of in-situ generated ketone pathway, and the intermediacy generation of ketyl radical and alkylidene titanocene. Without the necessity of pressurized hydrogen or stoichiometric hydride as reductants, this protocol enables highly selective and straightforward synthesis of various functionalized and structurally diverse alkylbenzenes under mild conditions. The utility of this reaction is further demonstrated through practical and valuable isotope incorporation from readily available deuterium source.
PubMed: 38862567
DOI: 10.1038/s41467-024-49355-1