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1.
J Phys Chem Lett ; 15(20): 5382-5389, 2024 May 23.
Article in English | MEDLINE | ID: mdl-38738984

ABSTRACT

Metronidazole is a prospective hyperpolarized MRI contrast agent with potential hypoxia sensing utility for applications in cancer, stroke, neurodegenerative diseases, etc. We demonstrate a pilot procedure for production of ∼30 mM hyperpolarized [15N3]metronidazole in aqueous media by using a phase-separated SABRE-SHEATH hyperpolarization method, with nitrogen-15 polarization exceeding 2.2% on all three 15N sites achieved in less than 2 min. The 15N polarization T1 of ∼12 min is reported for the 15NO2 group at the clinically relevant field of 1.4 T in the aqueous phase, demonstrating a remarkably long lifetime of the hyperpolarized state. The produced aqueous solution of [15N3]metronidazole that contained only ∼100 µM of residual Ir was deemed biocompatible via validation through the MTT colorimetric test for assessing cell metabolic activity using human embryotic kidney HEK293T cells. This low-cost and ultrafast hyperpolarization procedure represents a major advance for the production of a biocompatible HP [15N3]metronidazole (and potentially other hyperpolarized drugs) formulation for MRI sensing applications.


Subject(s)
Metronidazole , Water , Humans , Metronidazole/chemistry , Metronidazole/pharmacology , HEK293 Cells , Water/chemistry , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Hydrogen/chemistry , Nitrogen Isotopes/chemistry , Magnetic Resonance Imaging/methods , Contrast Media/chemistry
2.
Molecules ; 28(3)2023 Jan 25.
Article in English | MEDLINE | ID: mdl-36770865

ABSTRACT

The present work investigates the potential for enhancing the NMR signals of DNA nucleobases by parahydrogen-based hyperpolarization. Signal amplification by reversible exchange (SABRE) and SABRE in Shield Enables Alignment Transfer to Heteronuclei (SABRE-SHEATH) of selected DNA nucleobases is demonstrated with the enhancement (ε) of 1H, 15N, and/or 13C spins in 3-methyladenine, cytosine, and 6-O-guanine. Solutions of the standard SABRE homogenous catalyst Ir(1,5-cyclooctadeine)(1,3-bis(2,4,6-trimethylphenyl)imidazolium)Cl ("IrIMes") and a given nucleobase in deuterated ethanol/water solutions yielded low 1H ε values (≤10), likely reflecting weak catalyst binding. However, we achieved natural-abundance enhancement of 15N signals for 3-methyladenine of ~3300 and ~1900 for the imidazole ring nitrogen atoms. 1H and 15N 3-methyladenine studies revealed that methylation of adenine affords preferential binding of the imidazole ring over the pyrimidine ring. Interestingly, signal enhancements (ε~240) of both 15N atoms for doubly labelled cytosine reveal the preferential binding of specific tautomer(s), thus giving insight into the matching of polarization-transfer and tautomerization time scales. 13C enhancements of up to nearly 50-fold were also obtained for this cytosine isotopomer. These efforts may enable the future investigation of processes underlying cellular function and/or dysfunction, including how DNA nucleobase tautomerization influences mismatching in base-pairing.


Subject(s)
Imidazoles , Magnetic Resonance Imaging , Magnetic Resonance Spectroscopy , Nitrogen Isotopes/chemistry , DNA
3.
J Phys Chem Lett ; 13(44): 10253-10260, 2022 Nov 10.
Article in English | MEDLINE | ID: mdl-36301252

ABSTRACT

Magnetic resonance imaging (MRI) provides unique information about the internal structure and function of living organisms in a non-invasive way. The use of conventional proton MRI for the observation of real-time metabolism is hampered by the dominant signals of water and fat, which are abundant in living organisms. Heteronuclear MRI in conjunction with the hyperpolarization methods does not encounter this issue. In this work, we polarized 15N nuclei of [15N1]fampridine (a drug used for the treatment of multiple sclerosis) to the level of 4% in nuclear magnetic resonance (NMR) experiments and 0.7% in MRI studies using spin-lock-induced crossing combined with signal amplification by reversible exchange. Consequently, three-dimensional 15N MRI of the hyperpolarized 15N-labeled drug was acquired in 0.1 s with a signal-to-noise ratio of 70. In addition, the NMR signal enhancements for 15N-enriched fampridine and fampridine with a natural abundance of 15N nuclei were compared and an explanation for their difference was proposed.


Subject(s)
Magnetic Resonance Imaging , Protons , Magnetic Resonance Spectroscopy/methods , Magnetic Resonance Imaging/methods , Nitrogen Isotopes/chemistry
4.
Anal Chem ; 94(6): 2981-2987, 2022 02 15.
Article in English | MEDLINE | ID: mdl-35107978

ABSTRACT

Compound-specific stable isotope analysis (CSIA) is a unique analytical technique for determining small variations in isotope ratios of light isotopes in analytes from complex mixtures. A problem of CSIA using gas chromatography (GC) and liquid chromatography-isotope ratio mass spectrometry (LC-IRMS) is that any structural information of the analytes is lost due to the processes involved in determining the isotope ratio. To obtain the isotopic composition of, for example, carbon from organic compounds, all carbon in each analyte is quantitatively converted to CO2. For GC-IRMS, open split GC-IRMS-MS couplings have been described that allow additional acquisition of structural information of analytes and interferences. Structural analysis using LC-IRMS is more difficult and requires additional technical and instrumental efforts. In this study, LC was combined for the first time with simultaneous analysis by IRMS and high-resolution mass spectrometry (HRMS), enabling the direct identification of unknown or coeluting species. We have thoroughly investigated and optimized the coupling and showed how technical problems, arising from instrumental conditions, can be overcome. To this end, it was successfully demonstrated that a consistent split ratio between IRMS and HRMS could be obtained using a variable postcolumn flow splitter. This coupling provided reproducible results in terms of resulting peak areas, isotope values, and retention time differences for the two mass spectrometer systems. To demonstrate the applicability of the coupling, we chose to address an important question regarding the purity of international isotope standards. In this context, we were able to confirm that the USGS41 reference material indeed contains substantial amounts of pyroglutamic acid as suggested previously in the literature. Moreover, the replacement material, USGS41a, still has significant amounts of pyroglutamic acid as impurity, rendering some caution necessary when using this material for isotopic calibration.


Subject(s)
Carbon Isotopes , Carbon Isotopes/analysis , Chromatography, Liquid/methods , Gas Chromatography-Mass Spectrometry/methods , Mass Spectrometry/methods , Nitrogen Isotopes/chemistry
5.
Nat Commun ; 13(1): 880, 2022 02 15.
Article in English | MEDLINE | ID: mdl-35169118

ABSTRACT

The impacts of enhanced nitrogen (N) deposition on the global forest carbon (C) sink and other ecosystem services may depend on whether N is deposited in reduced (mainly as ammonium) or oxidized forms (mainly as nitrate) and the subsequent fate of each. However, the fates of the two key reactive N forms and their contributions to forest C sinks are unclear. Here, we analyze results from 13 ecosystem-scale paired 15N-labelling experiments in temperate, subtropical, and tropical forests. Results show that total ecosystem N retention is similar for ammonium and nitrate, but plants take up more labelled nitrate ([Formula: see text]%) ([Formula: see text]) than ammonium ([Formula: see text]%) while soils retain more ammonium ([Formula: see text]%) than nitrate ([Formula: see text]%). We estimate that the N deposition-induced C sink in forests in the 2010s  is [Formula: see text] Pg C yr-1, higher than previous estimates because of a larger role for oxidized N and greater rates of global N deposition.


Subject(s)
Ammonium Compounds/analysis , Carbon Sequestration/physiology , Environmental Restoration and Remediation , Forests , Nitrates/analysis , Trees/metabolism , Environment , Nitrogen Isotopes/chemistry , Nitrogen Oxides/analysis , Soil/chemistry
6.
PLoS One ; 16(12): e0251834, 2021.
Article in English | MEDLINE | ID: mdl-34874953

ABSTRACT

Structural characterization of the SARS-CoV-2 full length nsp1 protein will be an essential tool for developing new target-directed antiviral drugs against SARS-CoV-2 and for further understanding of intra- and intermolecular interactions of this protein. As a first step in the NMR studies of the protein, we report the 1H, 13C and 15N resonance backbone assignment as well as the Cß of the apo form of the full-lengthSARS-CoV-2 nsp1 including the folded domain together with the flaking N- and C- terminal intrinsically disordered fragments. The 19.8 kD protein was characterized by high-resolution NMR. Validation of assignment have been done by using two different mutants, H81P and K129E/D48E as well as by amino acid specific experiments. According to the obtained assignment, the secondary structure of the folded domain in solution was almost identical to its previously published X-ray structure as well as another published secondary structure obtained by NMR, but some discrepancies have been detected. In the solution SARS-CoV-2 nsp1 exhibited disordered, flexible N- and C-termini with different dynamic characteristics. The short peptide in the beginning of the disordered C-terminal domain adopted two different conformations distinguishable on the NMR time scale. We propose that the disordered and folded nsp1 domains are not fully independent units but are rather involved in intramolecular interactions. Studies of the structure and dynamics of the SARS-CoV-2 mutant in solution are on-going and will provide important insights into the molecular mechanisms underlying these interactions.


Subject(s)
Magnetic Resonance Spectroscopy/methods , SARS-CoV-2/metabolism , Viral Nonstructural Proteins/chemistry , Amino Acid Sequence , COVID-19/pathology , COVID-19/virology , Carbon-13 Magnetic Resonance Spectroscopy , Humans , Mutation , Nitrogen Isotopes/chemistry , Protein Structure, Secondary , Proton Magnetic Resonance Spectroscopy , SARS-CoV-2/isolation & purification , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/metabolism
7.
Rapid Commun Mass Spectrom ; 35(24): e9204, 2021 Dec 30.
Article in English | MEDLINE | ID: mdl-34549474

ABSTRACT

RATIONALE: Lipid correction models use elemental carbon-to-nitrogen ratios to estimate the effect of lipids on δ13 C values and provide a fast and inexpensive alternative to chemically removing lipids. However, the performance of these models varies, especially in whole-body invertebrate samples. The generation of tissue-specific lipid correction models for American lobsters, both an ecologically and an economically important species in eastern North America, will aid ecological research of this species and our understanding of the function of these models in invertebrates. METHOD: We determined the δ13 C and δ15 N values before and after lipid extraction in muscle and digestive glands of juvenile and adult lobster. We assessed the performance of four commonly used models (nonlinear, linear, natural logarithm (LN) and generalized linear model (GLM)) at estimating lipid-free δ13 C values based on the non-lipid-extracted δ13 C values and elemental C:N ratios. The accuracy of model predictions was tested using paired t-tests, and the performance of the different models was compared using the Akaike information criterion score. RESULTS: Lipid correction models accurately estimated post-lipid-extraction δ13 C values in both tissues. The nonlinear model was the least accurate for both tissues. In muscle, the three other models performed well, and in digestive glands, the LN model provided the most accurate estimates throughout the range of C:N values. In both tissues, the GLM estimates were not independent of the post-lipid-extraction δ13 C values, thus reducing their transferability to other datasets. CONCLUSIONS: Whereas previous work found that whole-body models poorly estimated the effect of lipids in invertebrates, we show that tissue-specific lipid correction models can generate accurate and precise estimates of lipid-free δ13 C values in lobster. We suggest that the tissue-specific logarithmic models presented here are the preferred models for accounting for the effect of lipid on lobster isotope ratios.


Subject(s)
Carbon Isotopes/chemistry , Lipids/chemistry , Nephropidae/chemistry , Animals , Carbon Isotopes/metabolism , Digestive System/chemistry , Digestive System/metabolism , Lipid Metabolism , Mass Spectrometry , Muscles/chemistry , Muscles/metabolism , Nephropidae/metabolism , Nitrogen Isotopes/chemistry , Nitrogen Isotopes/metabolism , Shellfish/analysis
8.
J Phys Chem Lett ; 12(32): 7701-7707, 2021 Aug 19.
Article in English | MEDLINE | ID: mdl-34355903

ABSTRACT

The resolving power of solid-state nuclear magnetic resonance (NMR) crystallography depends heavily on the accuracy of computational predictions of NMR chemical shieldings of candidate structures, which are usually taken to be local minima in the potential energy. To test the limits of this approximation, we systematically study the importance of finite-temperature and quantum nuclear fluctuations for 1H, 13C, and 15N shieldings in polymorphs of three paradigmatic molecular crystals: benzene, glycine, and succinic acid. The effect of quantum fluctuations is comparable to the typical errors of shielding predictions for static nuclei with respect to experiments, and their inclusion improves the agreement with measurements, translating to more reliable assignment of the NMR spectra to the correct candidate structure. The use of integrated machine-learning models, trained on first-principles energies and shieldings, renders rigorous sampling of nuclear fluctuations affordable, setting a new standard for the calculations underlying NMR structure determinations.


Subject(s)
Benzene/chemistry , Glycine/chemistry , Succinic Acid/chemistry , Carbon Isotopes/chemistry , Crystallography/methods , Hydrogen/chemistry , Machine Learning , Magnetic Resonance Spectroscopy , Nitrogen Isotopes/chemistry
9.
Proc Natl Acad Sci U S A ; 118(33)2021 08 17.
Article in English | MEDLINE | ID: mdl-34373325

ABSTRACT

Carnivorous plants consume animals for mineral nutrients that enhance growth and reproduction in nutrient-poor environments. Here, we report that Triantha occidentalis (Tofieldiaceae) represents a previously overlooked carnivorous lineage that captures insects on sticky inflorescences. Field experiments, isotopic data, and mixing models demonstrate significant N transfer from prey to Triantha, with an estimated 64% of leaf N obtained from prey capture in previous years, comparable to levels inferred for the cooccurring round-leaved sundew, a recognized carnivore. N obtained via carnivory is exported from the inflorescence and developing fruits and may ultimately be transferred to next year's leaves. Glandular hairs on flowering stems secrete phosphatase, as seen in all carnivorous plants that directly digest prey. Triantha is unique among carnivorous plants in capturing prey solely with sticky traps adjacent to its flowers, contrary to theory. However, its glandular hairs capture only small insects, unlike the large bees and butterflies that act as pollinators, which may minimize the conflict between carnivory and pollination.


Subject(s)
Alismatales/physiology , Carnivorous Plant/physiology , Inflorescence/physiology , Nitrogen Isotopes/metabolism , Animals , Drosophila/chemistry , Ecosystem , Nitrogen/metabolism , Nitrogen Isotopes/chemistry
10.
Rapid Commun Mass Spectrom ; 35(21): e9173, 2021 Sep 15.
Article in English | MEDLINE | ID: mdl-34382255

ABSTRACT

RATIONALE: Around the world biosecurity measures are being strengthened to prevent the spread of pests and diseases across national and international borders. Quarantine protocols that involve sample sterilisation have potential effects on sample integrity. The consequences of sterilisation methods such as gamma (γ)-irradiation on the elemental and chemical properties of biological samples have not been widely examined. METHODS: We tested the effect of γ-irradiation (50 kGy) on the stable carbon and nitrogen isotope compositions (δ13 C and δ15 N values) and elemental concentrations (C % and N %) of common biological samples (fish, plants and bulk soils). The analysis used a continuous flow system consisting of a Delta V Plus isotope ratio mass spectrometer connected with a Thermo Flash 1112 elemental analyser via a ConFlo IV interface. Results were compared using two one-sided tests (TOST) to test for statistical similarity between paired samples. RESULTS: There was no change in the δ15 N values or N % of γ-irradiated samples, and only small changes to the δ13 C values of consumers (range: 0.01‰ to 0.04‰), producers (-0.02‰ to 0.04‰) and sediments (0‰ to 0.07‰). The magnitude of change in δ13 C values was greatest at low carbon concentrations but appeared negligible when measured against replicated sample analysis and the combined analytical uncertainty (i.e., 0.10‰). The C % values of irradiated samples were higher for consumers (0.23%) and lower for producers and sediments (0.04% and 0.05%, respectively) which may have implications for certain types of biological material. CONCLUSIONS: Routine γ-irradiation has little effect on the stable carbon and nitrogen isotope compositions of common biological samples and marginal effects on carbon elemental concentrations. This is unlikely to warrant concerns since the observed difference is typically of a magnitude lower than other sources of potential uncertainty.


Subject(s)
Biosecurity , Carbon Isotopes/analysis , Gamma Rays , Mass Spectrometry/methods , Nitrogen Isotopes/analysis , Animals , Carbon Isotopes/chemistry , Fishes , Nitrogen Isotopes/chemistry , Plants/chemistry , Plants/radiation effects , Soil , Sterilization
11.
Angew Chem Int Ed Engl ; 60(43): 23207-23211, 2021 10 18.
Article in English | MEDLINE | ID: mdl-34432359

ABSTRACT

Cellular DNA is composed of four canonical nucleosides (dA, dC, dG and T), which form two Watson-Crick base pairs. In addition, 5-methylcytosine (mdC) may be present. The methylation of dC to mdC is known to regulate transcriptional activity. Next to these five nucleosides, the genome, particularly of stem cells, contains three additional dC derivatives, which are formed by stepwise oxidation of the methyl group of mdC with the help of Tet enzymes. These are 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC). It is believed that fdC and cadC are converted back into dC, which establishes an epigenetic control cycle that starts with methylation of dC to mdC, followed by oxidation and removal of fdC and cadC. While fdC was shown to undergo intragenomic deformylation to give dC directly, a similar decarboxylation of cadC was postulated but not yet observed on the genomic level. By using metabolic labelling, we show here that cadC decarboxylates in several cell types, which confirms that both fdC and cadC are nucleosides that are directly converted back to dC within the genome by C-C bond cleavage.


Subject(s)
DNA/metabolism , Deoxycytidine/analogs & derivatives , Genome/physiology , Animals , CHO Cells , Cricetulus , DNA/chemistry , Decarboxylation , Deoxycytidine/chemistry , Deoxycytidine/metabolism , Deuterium/chemistry , Mice , Nitrogen Isotopes/chemistry
12.
Plant J ; 107(4): 1260-1276, 2021 08.
Article in English | MEDLINE | ID: mdl-34152049

ABSTRACT

Determining which proteins are actively synthesized at a given point in time and extracting a representative sample for analysis is important to understand plant responses. Here we show that the methionine (Met) analogue homopropargylglycine (HPG) enables Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT) of a small sample of the proteins being synthesized in Arabidopsis plants or cell cultures, facilitating their click-chemistry enrichment for analysis. The sites of HPG incorporation could be confirmed by peptide mass spectrometry at Met sites throughout protein amino acid sequences and correlation with independent studies of protein labelling with 15 N verified the data. We provide evidence that HPG-based BONCAT tags a better sample of nascent plant proteins than azidohomoalanine (AHA)-based BONCAT in Arabidopsis and show that the AHA induction of Met metabolism and greater inhibition of cell growth rate than HPG probably limits AHA incorporation at Met sites in Arabidopsis. We show HPG-based BONCAT provides a verifiable method for sampling, which plant proteins are being synthesized at a given time point and enriches a small portion of new protein molecules from the bulk protein pool for identification, quantitation and subsequent biochemical analysis. Enriched nascent polypeptides samples were found to contain significantly fewer common post-translationally modified residues than the same proteins from whole plant extracts, providing evidence for age-related accumulation of post-translational modifications in plants.


Subject(s)
Alkynes/chemistry , Arabidopsis Proteins/chemistry , Arabidopsis Proteins/isolation & purification , Arabidopsis/chemistry , Glycine/analogs & derivatives , Proteomics/methods , Alanine/analogs & derivatives , Alanine/chemistry , Arabidopsis/cytology , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Gene Ontology , Glycine/chemistry , Mass Spectrometry , Methionine/chemistry , Methionine/metabolism , Nitrogen Isotopes/chemistry , Plant Cells , Protein Processing, Post-Translational
13.
J Phys Chem Lett ; 12(18): 4392-4399, 2021 May 13.
Article in English | MEDLINE | ID: mdl-33939920

ABSTRACT

The amino-terminal-copper-and-nickel-binding (ATCUN) motif, a tripeptide sequence ending with a histidine, confers important functions to proteins and peptides. Few high-resolution studies have been performed on the ATCUN motifs of membrane-associated proteins and peptides, limiting our understanding of how they stabilize Cu2+/Ni2+ in membranes. Here, we leverage solid-state NMR to investigate metal-binding to piscidin-1 (P1), a host-defense peptide featuring F1F2H3 as its ATCUN motif. Bound to redox ions, P1 chemically and physically damages pathogenic cell membranes. We design 13C/15N correlation experiments to detect and assign the deprotonated nitrogens produced and/or shifted by Ni2+-binding. Occupying multiple chemical states in P1-apo, H3 and the neighboring H4 respond to metalation by populating only the τ-tautomer. H3, as a proximal histidine, directly coordinates the metal, compared to the distal H4. Density functional theory calculations reflect this noncanonical arrangement and point toward cation-π interactions between the F1/F2/H4 aromatic rings and metal. These structural findings, which are relevant to other ATCUN-containing membrane peptides, could help design new therapeutics and materials for use in the areas of drug-resistant bacteria, neurological disorders, and biomedical imaging.


Subject(s)
Antimicrobial Cationic Peptides/chemistry , Copper/chemistry , Fish Proteins/chemistry , Nickel/chemistry , Carbon Isotopes/chemistry , Cations, Divalent/chemistry , Density Functional Theory , Magnetic Resonance Spectroscopy , Nitrogen Isotopes/chemistry , Protein Binding , Protein Conformation , Structure-Activity Relationship
14.
J Am Soc Mass Spectrom ; 32(6): 1538-1544, 2021 Jun 02.
Article in English | MEDLINE | ID: mdl-34028260

ABSTRACT

The aggregation process of α-synuclein (α-syn) is substantial in the pathogenesis of Parkinson's disease. Indolinone derivatives are inhibitors of α-syn aggregates and can be used as PET-based radiotracers for imaging α-syn fibrils. However, no investigations on the metabolism of indolinone derivatives have been reported until now. In the present research, a 13C and 15N isotope labeling strategy was developed to synthesize compound [13C2,15N]-(Z)-1-(4-aminobenzyl)-3-((E)-(3-phenyl)allylidene)indolin-2-one (M0'), which was then used in a study of metabolism in hepatocytes. The metabolites were characterized using accurate mass and characteristic ion measurements. In the metabolic system, compound M0' was the main component (accounting for 97.5% of compound-related components) after incubation in hepatocytes for 3 h, which indicated that compound M0' possessed great metabolic stability. Seven metabolites have been successfully verified by UPLC/Q TOF MS in metabolic studies, including hydroxyl M0' (M1'), hydroxyl and methylated M0' (M2'), N-acetylated M0' (M3'), sulfate of hydroxyl M0' (M4'), the glucose conjugate of M0' (M5'), glucuronide conjugate of M0' (M6'), and glucuronide conjugate of hydroxyl M0' (M7'). The study on metabolism provides the important information to develop effective α-syn aggregate inhibitors and new PET-tracer-related indolinone derivatives.


Subject(s)
Mass Spectrometry/methods , Oxindoles/chemistry , Carbon Isotopes/chemistry , Cell Line , Chromatography, High Pressure Liquid/methods , Hepatocytes/drug effects , Hepatocytes/metabolism , Humans , Isotope Labeling , Nitrogen Isotopes/chemistry
15.
Sci Rep ; 11(1): 6804, 2021 03 24.
Article in English | MEDLINE | ID: mdl-33762670

ABSTRACT

Cytochrome c (cyt c) is widely used as a model protein to study (i) folding and stability aspects of the protein folding problem and (ii) structure-function relationship from the evolutionary point of view. Databases of cyts c now contain 285 cyt c sequences from different organisms. A sequence alignment of all these proteins with respect to horse cyt c led to several important conclusions. One of them is that Leu94 is always conserved in all 30 mammalian cyts c. It is known that mutation L94G of the wild type (WT) horse cyt c is destabilizing and mutant exists as molten globule under the native condition (buffer pH 6 and 25 °C). We have expressed and purified uniformly labeled (13C and 15N) and unlabeled WT horse cyt c and its L94G mutant. We report that labeling does not affect the thermodynamic stability of proteins. To support this conclusion, the secondary and tertiary structure of each protein in labeled and unlabeled forms was determined by conventional techniques (UV-Vis absorption and circular dichroism spectroscopy).


Subject(s)
Cytochromes c/metabolism , Animals , Carbon Isotopes/chemistry , Circular Dichroism , Cytochromes c/chemistry , Cytochromes c/genetics , Horses , Hydrogen-Ion Concentration , Isotope Labeling , Mutagenesis, Site-Directed , Nitrogen Isotopes/chemistry , Protein Folding , Protein Stability , Protein Structure, Quaternary , Spectrophotometry, Ultraviolet , Thermodynamics
16.
J Chromatogr A ; 1639: 461932, 2021 Feb 22.
Article in English | MEDLINE | ID: mdl-33535117

ABSTRACT

Position-specific isotope analysis by Nuclear Magnetic Resonance spectrometry was employed to study the 13C intramolecular isotopic fractionation associated with the migration of organic substrates through different stationary phases chromatography columns. Liquid chromatography is often used to isolate compounds prior to their isotope analysis and this purification step potentially alters the isotopic composition of target compounds introducing a bias in the later measured data. Moreover, results from liquid chromatography can yield the sorption parameters needed in reactive transport models that predict the transport and fate of organic contaminants to in the environment. The aim of this study was to use intramolecular isotope analysis to study both 13C and 15N isotope effects associated with the elution of paracetamol (acetaminophen) through different stationary phases and to compare them to effects observed previously for vanillin. Results showed very different intramolecular isotope fractionation profiles depending on the chemical structure of the stationary phase. The data also demonstrate that both the amplitude and the distribution of measured isotope effects depend on the nature of the non-covalent interactions involved in the migration process. Results provided by theoretical calculation performed during this study also confirmed the direct link between observed intramolecular isotope fractionation and the nature of involved intermolecular interactions. It is concluded that the nature of the stationary phase through which the substrate passes has a major impact on the intramolecular isotopic composition of organic compounds isolated by chromatography methods..


Subject(s)
Acetaminophen/analysis , Carbon Isotopes/chemistry , Chromatography, Liquid/methods , Nitrogen Isotopes/chemistry , Carbon-13 Magnetic Resonance Spectroscopy , Cellulose/chemistry , Charcoal/chemistry , Chemical Fractionation , Reproducibility of Results , Silica Gel/chemistry , Solvents/chemistry
17.
Magn Reson Chem ; 59(3): 237-246, 2021 03.
Article in English | MEDLINE | ID: mdl-32603513

ABSTRACT

An important step in the process of protein research by NMR is the assignment of chemical shifts. In the coat protein of IKe bacteriophage, there are 53 residues making up a long helix resulting in relatively high spectral ambiguity. Assignment thus requires the collection of a set of three-dimensional (3D) experiments and the preparation of sparsely labeled samples. Increasing the dimensionality can facilitate fast and reliable assignment of IKe and of larger proteins. Recent progress in nonuniform sampling techniques made the application of multidimensional NMR solid-state experiments beyond 3D more practical. 4D 1 H-detected experiments have been demonstrated in high-fields and at spinning speeds of 60 kHz and higher but are not practical at spinning speeds of 10-20 kHz for fully protonated proteins. Here, we demonstrate the applicability of a nonuniformly sampled 4D 13 C/15 N-only correlation experiment performed at a moderate field of 14.1 T, which can incorporate sufficiently long acquisition periods in all dimensions. We show how a single CANCOCX experiment, supported by several 2D carbon-based correlation experiments, is utilized for the assignment of heteronuclei in the coat protein of the IKe bacteriophage. One sparsely labeled sample was used to validate sidechain assignment of several hydrophobic-residue sidechains. A comparison to solution NMR studies of isolated IKe coat proteins embedded in micelles points to key residues involved in structural rearrangement of the capsid upon assembly of the virus. The benefits of 4D to a quicker assignment are discussed, and the method may prove useful for studying proteins at relatively low fields.


Subject(s)
Bacteriophage IKe/chemistry , Capsid Proteins/analysis , Capsid/chemistry , Capsid Proteins/chemistry , Carbon-13 Magnetic Resonance Spectroscopy , Micelles , Nitrogen Isotopes/chemistry , Nuclear Magnetic Resonance, Biomolecular , Protein Conformation, alpha-Helical
18.
Magn Reson Chem ; 59(2): 99-107, 2021 02.
Article in English | MEDLINE | ID: mdl-32761649

ABSTRACT

Solid-state nuclear magnetic resonance is a promising technique to probe bone mineralization and interaction of collagen protein in the native state. However, many of the developments are hampered due to the low sensitivity of the technique. In this article, we report solid-state nuclear magnetic resonance (NMR) experiments using the newly developed BioSolids CryoProbe™ to access its applicability for elucidating the atomic-level structural details of collagen protein in native state inside the bone. We report here approximately a fourfold sensitivity enhancement in the natural abundance 13 C spectrum compared with the room temperature conventional solid-state NMR probe. With the advantage of sensitivity enhancement, we have been able to perform natural abundance 15 N cross-polarization magic angle spinning (CPMAS) and two-dimensional (2D) 1 H-13 C heteronuclear correlation (HETCOR) experiments of native collagen within a reasonable timeframe. Due to high sensitivity, 2D 1 H/13 C HETCOR experiments have helped in detecting several short and long-range interactions of native collagen assembly, thus significantly expanding the scope of the method to such challenging biomaterials.


Subject(s)
Bone Matrix/chemistry , Collagen/chemistry , Animals , Carbon Isotopes/chemistry , Femur/chemistry , Goats , Nitrogen Isotopes/chemistry , Nuclear Magnetic Resonance, Biomolecular/methods
19.
Protein Expr Purif ; 178: 105785, 2021 02.
Article in English | MEDLINE | ID: mdl-33152458

ABSTRACT

Isotope-labeled proteins are expected to be used as internal standard proteins in the field of protein quantification by isotope dilution mass spectrometry (ID/MS). To achieve the absolute quantification of Cystatin C (Cys C) based on ID/MS, we aims to obtain 15N isotope-labeled recombinant Cys C (15N-Cys C) protein. Firstly, the Cys C gene was optimized based on the preferred codons of Escherichia coli, and inserted into the pET-28a(+) expression plasmid. Then, the plasmid was transformed into TOP10 and BL21 strains, and 15N-Cys C was expressed in M9 medium using 15N as the only nitrogen source. 15N-Cys C was detected by SDS-PAGE, protein immunoblotting and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). The characteristic peptides obtained from 15N-Cys C were analyzed by a Q Exactive Plus MS system. Results showed that 53.06% of the codons were optimized. The codon adaptation index of the Cys C genes increased from 0.31 to 0.95, and the GC content was adjusted from 64.85% to 54.88%. The purity of 15N-Cys C was higher than 95%. MALDI-TOF MS analysis showed that the m/z of 15N-Cys C had changed from 13 449 to 14 850. The characteristic peptides showed that 619.79 m/z (M+2H)2+ was the parent ion of 15N-Cys C and that the secondary ions of 15N-labeled peptides from y+5 to y+9 were 616.27 m/z, 716.33 m/z, 788.39 m/z, 936.43 m/z, and 1052.46 m/z, respectively. In conclusion, we successfully expressed, purified and identified of 15N-Cys C protein in Escheichia coli intended for absolute quantification using ID/MS.


Subject(s)
Cystatin C , Escherichia coli , Gene Expression , Nitrogen Isotopes/chemistry , Cystatin C/biosynthesis , Cystatin C/genetics , Escherichia coli/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Humans , Mass Spectrometry , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics
20.
PLoS One ; 15(10): e0239861, 2020.
Article in English | MEDLINE | ID: mdl-33052915

ABSTRACT

The flanks of the Caucasus Mountains and the steppe landscape to their north offered highly productive grasslands for Bronze Age herders and their flocks of sheep, goat, and cattle. While the archaeological evidence points to a largely pastoral lifestyle, knowledge regarding the general composition of human diets and their variation across landscapes and during the different phases of the Bronze Age is still restricted. Human and animal skeletal remains from the burial mounds that dominate the archaeological landscape and their stable isotope compositions are major sources of dietary information. Here, we present stable carbon and nitrogen isotope data of bone collagen of 105 human and 50 animal individuals from the 5th millennium BC to the Sarmatian period, with a strong focus on the Bronze Age and its cultural units including Maykop, Yamnaya, Novotitorovskaya, North Caucasian, Catacomb, post-Catacomb and late Bronze Age groups. The samples comprise all inhumations with sufficient bone preservation from five burial mound sites and a flat grave cemetery as well as subsamples from three further sites. They represent the Caucasus Mountains in the south, the piedmont zone and Kuban steppe with humid steppe and forest vegetation to its north, and more arid regions in the Caspian steppe. The stable isotope compositions of the bone collagen of humans and animals varied across the study area and reflect regional diversity in environmental conditions and diets. The data agree with meat, milk, and/or dairy products from domesticated herbivores, especially from sheep and goats having contributed substantially to human diets, as it is common for a largely pastoral economy. This observation is also in correspondence with the faunal remains observed in the graves and offerings of animals in the mound shells. In addition, foodstuffs with elevated carbon and nitrogen isotope values, such as meat of unweaned animals, fish, or plants, also contributed to human diets, especially among communities living in the more arid landscapes. The regional distinction of the animal and human data with few outliers points to mobility radii that were largely concentrated within the environmental zones in which the respective sites are located. In general, dietary variation among the cultural entities as well as regarding age, sex and archaeologically indicated social status is only weakly reflected. There is, however, some indication for a dietary shift during the Early Bronze Age Maykop period.


Subject(s)
Agriculture/history , Diet/history , Archaeology/methods , Bone and Bones/chemistry , Carbon Isotopes/chemistry , Collagen/analysis , Grassland , History, Ancient , Humans , Nitrogen Isotopes/chemistry , Russia
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