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Journal of the American Society For... Jun 2024Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has evolved as an essential technique in structural proteomics. The use of ion mobility separation (IMS) coupled...
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has evolved as an essential technique in structural proteomics. The use of ion mobility separation (IMS) coupled to HDX-MS has increased the applicability of the technique to more complex systems and has been shown to improve data quality and robustness. The first step when running any HDX-MS workflow is to confirm the sequence and retention time of the peptides resulting from the proteolytic digestion of the nondeuterated protein. Here, we optimized the collision energy ramp of HDMS experiments for membrane proteins using a Waters SELECT SERIES cIMS-QTOF system following an HDX workflow using Phosphorylase B, XylE transporter, and Smoothened receptor (SMO) as model systems. Although collision energy (CE) ramp 10-50 eV gave the highest amount of positive identified peptides when using Phosphorylase B, XylE, and SMO, results suggest optimal CE ramps are protein specific, and different ramps can produce a unique set of peptides. We recommend cIMS users use different CE ramps in their HDMS experiments and pool the results to ensure maximum peptide identifications. The results show how selecting an appropriate CE ramp can change the sequence coverage of proteins ranging from 4 to 94%.
PubMed: 38842540
DOI: 10.1021/jasms.4c00093 -
The Journal of Physical Chemistry. A Jun 2024Glycolaldehyde, an important prebiotic molecule, along with its monodeuterated species and its higher energy tautomer, ()-1,2-ethenediol, has been detected in the...
Glycolaldehyde, an important prebiotic molecule, along with its monodeuterated species and its higher energy tautomer, ()-1,2-ethenediol, has been detected in the interstellar medium. Although the elemental D/H ratio in the universe is only ∼1.6 × 10, the deuterium relative abundance in interstellar molecules might be by far larger than this. As such, it provides a remarkable and almost unique diagnostic tool. In particular, it might help elucidate the reaction mechanisms that lead to the formation of the so-called complex organic molecules. It is therefore crucial to extend the census of the interstellar deuterated molecules. To this aim, in this work, we present for the first time a spectroscopic investigation of the rotational spectra of the CHDOD-CHO bideuterated variant of glycolaldehyde and of mono- and bideuterated species of ()-1,2-ethenediol (CHOD═CHOD, CHOD═CHOH, and CHOH═CHOD rotamers). For each species, more than a hundred transitions have been assigned. Their analysis led to the accurate determination of all rotational constants as well as quartic and sextic centrifugal distortion terms, thus providing spectroscopic line catalogs suitable for supporting astronomical searches. In addition, the rotational constants of the bideuterated glycolaldehyde isotopologue studied in this work allowed us to improve the semiexperimental equilibrium structure determination for this molecule.
PubMed: 38842131
DOI: 10.1021/acs.jpca.4c02533 -
Journal of the American Society For... Jun 2024Nucleoside ions that were furnished on ribose with a 2'--acetyl radical group were generated in the gas phase by multistep collision-induced dissociation of precursor...
Nucleoside ions that were furnished on ribose with a 2'--acetyl radical group were generated in the gas phase by multistep collision-induced dissociation of precursor ions tagged with radical initiator groups, and their chemistry was investigated in the gas phase. 2'--Acetyladenosine cation radicals were found to undergo hydrogen transfer to the acetoxyl radical from the ribose ring positions that were elucidated using specific deuterium labeling of 1'-H, 2'-H, and 4'-H and in the N-H and O-H exchangeable positions, favoring 4'-H transfer. Ion structures and transition-state energies were calculated by a combination of Born-Oppenheimer molecular dynamics and density functional theory and used to obtain unimolecular rate constants for competitive hydrogen transfer and loss of the acetoxyl radical. Migrations to the acetoxyl radical of ribose hydrogens 1'-H, 2'-H, 3'-H, and 4'-H were all exothermic, but product formation was kinetically controlled. Both Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations indicated preferential migration of 4'-H in a qualitative agreement with the deuterium labeling results. The hydrogen migrations displayed substantial isotope effects that along with quantum tunneling affected the relative rate constants and reaction branching ratios. UV-vis action spectroscopy indicated that the cation radicals from 2'--acetyladenosine consisted of a mixture of isomers. Radical-driven dissociations were also observed for protonated guanosine, cytosine, and thymidine conjugates. However, for those nucleoside ions and cation radicals, the dissociations were dominated by the loss of the nucleobase or formation of protonated nucleobase ions.
PubMed: 38842116
DOI: 10.1021/jasms.4c00198 -
Chemical Communications (Cambridge,... Jun 2024The synthesis of deuterated -difluoroalkenes selective deuterodefluorination of β-CF-cinnamates using a nickel catalyst has been reported for the first time....
The synthesis of deuterated -difluoroalkenes selective deuterodefluorination of β-CF-cinnamates using a nickel catalyst has been reported for the first time. Commercially available deuterated formic acid is a cheap and convenient deuterium source. The nickel-catalyst showed high selectivity for monodefluorination and avoided competitive reactions such as multiple defluorination or hydrogenation.
PubMed: 38842110
DOI: 10.1039/d4cc00918e -
International Journal of Biological... Jun 2024Low molecular weight heparin and synthetic mimetics such as fondaparinux show different binding kinetics, protease specificity, and clinical effects. A combination of...
Low molecular weight heparin and synthetic mimetics such as fondaparinux show different binding kinetics, protease specificity, and clinical effects. A combination of allosteric and template-mediated bridging mechanisms have been proposed to explain the differences in rate acceleration and specificity. The difficulty in working with heterogeneous heparin species has rendered a crystallographic interpretation of the differences in antithrombin activation between mimetics and natural heparin inaccessible. In this study, we examine the allosteric changes in antithrombin caused by binding fondaparinux, enoxaparin and depolymerized natural heparins using millisecond hydrogen deuterium exchange mass spectrometry (TRESI-HDX MS) and relate these conformational changes to complex stability in the gas phase using collision induced unfolding (CIU). This exploration reveals that in addition to the dynamic changes caused by fondaparinux, long chain heparins reduce structural flexibility proximal to Arg393, the cleavable residue in the reactive centre loop of the protein. These local changes in protein dynamics are associated with an increase in overall complex stability that increases with heparin chain length. Ultimately, these results shed light on the molecular mechanisms underlying differences in activity and specificity between heparin mimetics and natural heparins.
PubMed: 38838881
DOI: 10.1016/j.ijbiomac.2024.132868 -
Journal of Medicinal Chemistry Jun 2024To fully explore the potential of F-labeled l-fluoroalanine for imaging cancer and other chronic diseases, a simple and mild radiosynthesis method has been established...
To fully explore the potential of F-labeled l-fluoroalanine for imaging cancer and other chronic diseases, a simple and mild radiosynthesis method has been established to produce optically pure l-3-[F]fluoroalanine (l-[F]FAla), using a serine-derivatized, five-membered-ring sulfamidate as the radiofluorination precursor. A deuterated analogue, l-3-[F]fluoroalanine-d (l-[F]FAla-d), was also prepared to improve metabolic stability. Both l-[F]FAla and l-[F]FAla-d were rapidly taken up by 9L/lacZ, MIA PaCa-2, and U87MG cells and were shown to be substrates for the alanine-serine-cysteine (ASC) amino acid transporter. The ability of l-[F]FAla, l-[F]FAla-d, and the d-enantiomer, d-[F]FAla-d, to image tumors was evaluated in U87MG tumor-bearing mice. Despite the significant bone uptake was observed for both l-[F]FAla and l-[F]FAla-d, the latter had enhanced tumor uptake compared to l-[F]FAla, and d-[F]FAla-d was not specifically taken up by the tumors. The enhanced tumor uptake of l-[F]FAla-d compared with its nondeuterated counterpart, l-[F]FAla, warranted the further biological investigation of this radiotracer as a potential cancer imaging agent.
Topics: Fluorine Radioisotopes; Animals; Humans; Positron-Emission Tomography; Deuterium; Cell Line, Tumor; Mice; Radiopharmaceuticals; Neoplasms; Mice, Nude; Alanine; Tissue Distribution
PubMed: 38838188
DOI: 10.1021/acs.jmedchem.4c00774 -
Chemphyschem : a European Journal of... Jun 2024The peripherical protons of the dye molecule hypericin can undergo structural interconversion (tautomerization) between different isomers through separated by a low...
The peripherical protons of the dye molecule hypericin can undergo structural interconversion (tautomerization) between different isomers through separated by a low energy barrier with rates that depends sensitively on the interaction with local chemical environment defined by the nature of host material. We investigate the deuterium (D) isotope effect of hypericin tautomerism at the single-molecule level to avoid ensemble averaging in different polymer matrices by a combined spectroscopic and computational approach. In the 'innocent' PMMA matrix only intramolecular isotope effects on the internal conversion channel and tautomerization are observed; while PVA specifically interacts with the probe via H- and D-bonding. This establishes a single molecular picture on intra- and intermolecular nano-environment effects to control chromophore photophysics and -chemistry.
PubMed: 38837881
DOI: 10.1002/cphc.202400374 -
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 -
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