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1.
Nanotechnology ; 35(33)2024 May 30.
Article in English | MEDLINE | ID: mdl-38759638

ABSTRACT

Memristive devices offer essential properties to become a part of the next-generation computing systems based on neuromorphic principles. Organic memristive devices exhibit a unique set of properties which makes them an indispensable choice for specific applications, such as interfacing with biological systems. While the switching rate of organic devices can be easily adjusted over a wide range through various methods, controlling the switching potential is often more challenging, as this parameter is intricately tied to the materials used. Given the limited options in the selection conductive polymers and the complexity of polymer chemical engineering, the most straightforward and accessible approach to modulate switching potentials is by introducing specific molecules into the electrolyte solution. In our study, we show polyaniline (PANI)-based device switching potential control by adding nucleotide-free analogue of vitamin B12, aquacyanocobinamide, to the electrolyte solution. The employed concentrations of this molecule, ranging from 0.2 to 2 mM, enabled organic memristive devices to achieve switching potential decrease for up to 100 mV, thus providing a way to control device properties. This effect is attributed to strong aromatic interactions between PANI phenyl groups and corrin macrocycle of the aquacyanocobinamide molecule, which was supported by ultraviolet-visible spectra analysis.


Subject(s)
Aniline Compounds , Vitamin B 12 , Aniline Compounds/chemistry , Vitamin B 12/chemistry , Vitamin B 12/analogs & derivatives
2.
Nature ; 629(8013): 886-892, 2024 May.
Article in English | MEDLINE | ID: mdl-38720071

ABSTRACT

Cobalamin (vitamin B12, herein referred to as B12) is an essential cofactor for most marine prokaryotes and eukaryotes1,2. Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics2-4. Here we show that two bacterial B12 auxotrophs can salvage different B12 building blocks and cooperate to synthesize B12. A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B12 auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B12. Release of B12 by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B12 by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B12. These complex microbial interactions of ligand cross-feeding and joint B12 biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B12 producers. These findings add new players to our understanding of B12 supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems.


Subject(s)
Alteromonadaceae , Ligands , Rhodobacteraceae , Vitamin B 12 , Atlantic Ocean , Coculture Techniques , Microbial Interactions , Prophages/genetics , Prophages/growth & development , Prophages/metabolism , Vitamin B 12/biosynthesis , Vitamin B 12/chemistry , Vitamin B 12/metabolism , Alteromonadaceae/growth & development , Alteromonadaceae/metabolism , Rhodobacteraceae/cytology , Rhodobacteraceae/metabolism , Rhodobacteraceae/virology , Ribonucleosides/metabolism , Cobamides/metabolism , Ecosystem
3.
Int J Biol Macromol ; 268(Pt 2): 131902, 2024 May.
Article in English | MEDLINE | ID: mdl-38692532

ABSTRACT

Vitamin B12 is a group of biologically active cobalamin compounds. In this study, we investigated the inhibitory effects of methylcobalamin (MeCbl) and hydroxocobalamin acetate (OHCbl Acetate) on protein tyrosine phosphatase 1B (PTP1B). MeCbl and OHCbl Acetate exhibited an IC50 of approximately 58.390 ± 2.811 µM and 8.998 ± 0.587 µM, respectively. The Ki values of MeCbl and OHCbl Acetate were 25.01 µM and 4.04 µM respectively. To elucidate the inhibition mechanism, we conducted a 500 ns Gaussian accelerated molecular dynamics (GaMD) simulation. Utilizing PCA and tICA, we constructed Markov state models (MSM) to examine secondary structure changes during motion. Our findings revealed that the α-helix at residues 37-42 remained the most stable in the PTP1B-OHCbl Acetate system. Furthermore, upon binding of OHCbl Acetate or MeCbl, the WPD loop of PTP1B moved inward to the active pocket, forming a closed conformation and potentially obstructs substrate entry. Protein-ligand interaction analysis and MM-PBSA showed that OHCbl Acetate exhibited lower binding free energy and engaged in more residue interactions with PTP1B. In summary, our study confirmed the substantial inhibitory activity of OHCbl Acetate against PTP1B, with its inhibitory potency notably surpassing that of MeCbl. We demonstrated potential molecular mechanisms of OHCbl Acetate inhibiting PTP1B.


Subject(s)
Molecular Dynamics Simulation , Protein Tyrosine Phosphatase, Non-Receptor Type 1 , Vitamin B 12 , Protein Tyrosine Phosphatase, Non-Receptor Type 1/antagonists & inhibitors , Protein Tyrosine Phosphatase, Non-Receptor Type 1/chemistry , Protein Tyrosine Phosphatase, Non-Receptor Type 1/metabolism , Vitamin B 12/chemistry , Vitamin B 12/analogs & derivatives , Vitamin B 12/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Humans , Molecular Docking Simulation , Protein Binding , Kinetics , Structure-Activity Relationship
4.
Molecules ; 29(9)2024 May 01.
Article in English | MEDLINE | ID: mdl-38731585

ABSTRACT

The techniques used to detect and quantify cyanocobalamin (vitamin B12) vary considerably in terms of detection sensitivity, from the most sensitive, based on radioisotopes and mass spectrometry (MS) with limits of detection (LOD) in fg mL-1, to fluorescence (FL) and surface plasmon resonance (SPR) biosensors with LOD values in the range of a few µg mL-1. For accurate quantification of an analyte present at trace levels in complex biological matrices, a selective separation and enrichment step is required to overcome matrix interferences and ensure sufficient detection sensitivity. In this study, iron oxide magnetic nanoparticles (IONPs) were used for the extraction and initial preconcentration of cyanocobalamin (vitamin B12). In the dependence of the magnetization on the H-field (hysteresis loop), no coercivity and remanence values were found at 300 K, indicating the superparamagnetic properties of the tested IONPs. Perfluorinated acids were used as amphiphilic agents to allow the sorption of cyanocobalamin onto the IONPs. FT-IR/ATR spectroscopy was used to confirm the sorption of cyanocobalamin on the IONPs. The influence of the addition of a homologous series of perfluorinated acids such as trifluoroacetic acid (TFAA), heptafluorobutyric acid (HFBA), and trichloroacetic acid (TCAA) to the extraction mixture was tested considering their type, mass, and time required for effective sorption. The adsorption kinetics and isotherm, described by the Freundlich and Langmuir equations, were analyzed. The maximum adsorption capacity (qm) exceeded 6 mg g-1 and was 8.9 mg g-1 and 7.7 mg g-1 for HFBA and TCAA, respectively, as the most efficient additives. After the desorption process using aqueous KH2PO4 solution, the sample was finally analyzed spectrophotometrically and chromatographically. The IONP-based method was successfully applied for the isolation of cyanocobalamin from human urine samples. The results showed that the developed approach is simple, cheap, accurate, and efficient for the determination of traces of cyanocobalamin in biological matrices.


Subject(s)
Magnetic Iron Oxide Nanoparticles , Vitamin B 12 , Vitamin B 12/chemistry , Vitamin B 12/analysis , Adsorption , Magnetic Iron Oxide Nanoparticles/chemistry , Limit of Detection , Porosity , Spectroscopy, Fourier Transform Infrared
5.
J Biol Chem ; 300(5): 107289, 2024 May.
Article in English | MEDLINE | ID: mdl-38636663

ABSTRACT

Vitamin B12 (cobalamin or Cbl) functions as a cofactor in two important enzymatic processes in human cells, and life is not sustainable without it. B12 is obtained from food and travels from the stomach, through the intestine, and into the bloodstream by three B12-transporting proteins: salivary haptocorrin (HC), gastric intrinsic factor, and transcobalamin (TC), which all bind B12 with high affinity and require proteolytic degradation to liberate Cbl. After intracellular delivery of dietary B12, Cbl in the aquo/hydroxocobalamin form can coordinate various nucleophiles, for example, GSH, giving rise to glutathionylcobalamin (GSCbl), a naturally occurring form of vitamin B12. Currently, there is no data showing whether GSCbl is recognized and transported in the human body. Our crystallographic data shows for the first time the complex between a vitamin B12 transporter and GSCbl, which compared to aquo/hydroxocobalamin, binds TC equally well. Furthermore, sequence analysis and structural comparisons show that TC recognizes and transports GSCbl and that the residues involved are conserved among TCs from different organisms. Interestingly, haptocorrin and intrinsic factor are not structurally tailored to bind GSCbl. This study provides new insights into the interactions between TC and Cbl.


Subject(s)
Glutathione , Rats , Transcobalamins , Vitamin B 12 , Animals , Crystallography, X-Ray , Glutathione/metabolism , Glutathione/analogs & derivatives , Glutathione/chemistry , Protein Binding , Transcobalamins/metabolism , Transcobalamins/chemistry , Vitamin B 12/metabolism , Vitamin B 12/analogs & derivatives , Vitamin B 12/chemistry
6.
Chembiochem ; 25(10): e202400184, 2024 May 17.
Article in English | MEDLINE | ID: mdl-38573110

ABSTRACT

Genetic aberrations of the maternal UBE3A allele, which encodes the E3 ubiquitin ligase E6AP, are the cause of Angelman syndrome (AS), an imprinting disorder. In most cases, the maternal UBE3A allele is not expressed. Yet, approximately 10 percent of AS individuals harbor distinct point mutations in the maternal allele resulting in the expression of full-length E6AP variants that frequently display compromised ligase activity. In a high-throughput screen, we identified cyanocobalamin, a vitamin B12-derivative, and several alloxazine derivatives as activators of the AS-linked E6AP-F583S variant. Furthermore, we show by cross-linking coupled to mass spectrometry that cobalamins affect the structural dynamics of E6AP-F583S and apply limited proteolysis coupled to mass spectrometry to obtain information about the regions of E6AP that are involved in, or are affected by binding cobalamins and alloxazine derivatives. Our data suggest that dietary supplementation with vitamin B12 can be beneficial for AS individuals.


Subject(s)
Angelman Syndrome , Ubiquitin-Protein Ligases , Vitamin B 12 , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/chemistry , Ubiquitin-Protein Ligases/genetics , Angelman Syndrome/genetics , Angelman Syndrome/drug therapy , Angelman Syndrome/metabolism , Humans , Allosteric Regulation/drug effects , Vitamin B 12/metabolism , Vitamin B 12/chemistry , Vitamin B 12/pharmacology
7.
J Phys Chem B ; 128(6): 1428-1437, 2024 Feb 15.
Article in English | MEDLINE | ID: mdl-38301132

ABSTRACT

Polarized time-resolved X-ray absorption spectroscopy at the Co K-edge is used to probe the excited-state dynamics and photolysis of base-off methylcobalamin and the excited-state structure of base-off adenosylcobalamin. For both molecules, the final excited-state minimum shows evidence for an expansion of the cavity around the Co ion by ca. 0.04 to 0.05 Å. The 5-coordinate base-off cob(II)alamin that is formed following photodissociation has a structure similar to that of the 5-coordinate base-on cob(II)alamin, with a ring expansion of 0.03 to 0.04 Å and a contraction of the lower axial bond length relative to that in the 6-coordinate ground state. These data provide insights into the role of the lower axial ligand in modulating the reactivity of B12 coenzymes.


Subject(s)
Coenzymes , Vitamin B 12 , X-Ray Absorption Spectroscopy , Vitamin B 12/chemistry , Photolysis
8.
Molecules ; 28(22)2023 Nov 07.
Article in English | MEDLINE | ID: mdl-38005191

ABSTRACT

In this overview, the latest achievements in dietary origins, absorption mechanism, bioavailability assay, health advantages, cutting-edge encapsulation techniques, fortification approaches, and innovative highly sensitive sensor-based detection methods of vitamin B12 (VB12) were addressed. The cobalt-centered vitamin B is mainly found in animal products, posing challenges for strict vegetarians and vegans. Its bioavailability is highly influenced by intrinsic factor, absorption in the ileum, and liver reabsorption. VB12 mainly contributes to blood cell synthesis, cognitive function, and cardiovascular health, and potentially reduces anemia and optic neuropathy. Microencapsulation techniques improve the stability and controlled release of VB12. Co-microencapsulation of VB12 with other vitamins and bioactive compounds enhances bioavailability and controlled release, providing versatile initiatives for improving bio-functionality. Nanotechnology, including nanovesicles, nanoemulsions, and nanoparticles can enhance the delivery, stability, and bioavailability of VB12 in diverse applications, ranging from antimicrobial agents to skincare and oral insulin delivery. Staple food fortification with encapsulated and free VB12 emerges as a prominent strategy to combat deficiency and promote nutritional value. Biosensing technologies, such as electrochemical and optical biosensors, offer rapid, portable, and sensitive VB12 assessment. Carbon dot-based fluorescent nanosensors, nanocluster-based fluorescent probes, and electrochemical sensors show promise for precise detection, especially in pharmaceutical and biomedical applications.


Subject(s)
Food, Fortified , Vitamin B 12 , Animals , Vitamin B 12/chemistry , Delayed-Action Preparations , Vitamins , Insulin/chemistry
9.
J Photochem Photobiol B ; 245: 112751, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37441852

ABSTRACT

CarH is a cobalamin-based photoreceptor which has attracted significant interest due to its complex mechanism involving its organometallic coenzyme-B12 chromophore. While several experimental and computational studies have sought to understand CarH's mechanism of action, there are still many aspects of the mechanism which remain unclear. While light is needed to activate the Co-C5' bond, it is not entirely clear whether reaction pathway involves singlet or triplet diradical states. A recent experimental study implicated triplet pathway and importance of intersystem crossing (ISC) as a viable mechanistic route for photoproduct formation in CarH. Herein, a combined quantum mechanics/molecular mechanics approach (QM/MM) was used to explore the involvement of triplet states in CarH. Two possibilities were explored. The first possibility involved photo-induced homolytic cleavage of the Co-C5' where the radical pair (RP) would deactivate to a triplet state (T0) on the ground state potential energy surface (PES). However, a pathway for the formation of the photoproduct, 4',5'-anhydroadenosine (anhAdo), on the triplet ground state PES was not energetically feasible. The second possibility involved exploring a manifold of low-lying triplet excited states computed using TD-DFT within the QM/MM framework. Viable crossings of triplet excited states with singlet excited states were identified using semiclassical Landau-Zener theory and the effectiveness of spin-orbit coupling by El-Sayed rules. Several candidates along both the Co-NIm potential energy curve (PEC) and Co-C5'/Co-NIm PES were identified, which appear to corroborate experimental findings and implicate the possible role of triplet states in CarH.


Subject(s)
Quantum Theory , Vitamin B 12 , Vitamin B 12/chemistry
10.
J Biol Inorg Chem ; 28(6): 571-581, 2023 09.
Article in English | MEDLINE | ID: mdl-37479902

ABSTRACT

Cyanocobalamin (CNCbl), a medicinal form of vitamin B12, is resistant to glutathione (GSH), and undergoes intracellular processing via reductive decyanation producing the Co(II)-form of Cbl (Cbl(II)) mediated by the CblC-protein. Alteration of the CblC-protein structure might inhibit CNCbl processing. Here, we showed that introducing a bromine atom to the C10-position of the CNCbl corrin ring facilitates its reaction with GSH leading to the formation of Cbl(II) and cyanide dissociation. In a neutral medium, the reaction between C10-Br-CNCbl and GSH proceeds via the complexation of the reactants further leading to dimethylbenzimidazole (DMBI) substitution and electron transfer from GSH to the Co(III)-ion. The reaction is accelerated upon the GSH thiol group deprotonation. The key factors explaining the higher reactivity of C10-Br-CNCbl compared with unmodified CNCbl towards GSH are increasing the electrode potential of CNCbl two-electron reduction upon meso-bromination and the substantial labilization of DMBI, which was shown by comparing their reactions with cyanide and the pKa values of DMBI protonation (pKa base-off). Aquacobalamin (H2OCbl) brominated at the C10-position of the corrin reacts with GSH to give Cbl(II) via GSH complexation and subsequent reaction of this complex with a second GSH molecule, whereas unmodified H2OCbl generates glutathionyl-Cbl, which is resistant to further reduction by GSH.


Subject(s)
Halogenation , Vitamin B 12 , Vitamin B 12/chemistry , Cyanides , Glutathione
11.
Inorg Chem ; 62(32): 12762-12772, 2023 Aug 14.
Article in English | MEDLINE | ID: mdl-37463115

ABSTRACT

Understanding the diverse reactivities of vitamin B12 and its derivatives, collectively called cobalamins, requires detailed knowledge of their geometric and electronic structures. Electronic absorption (Abs) and resonance Raman (rR) spectroscopies have proven invaluable in this area, particularly when used in concert with computational techniques such as density functional theory (DFT). There remain, however, lingering uncertainties in the computational description of electronic excited states of cobalamins, particularly surrounding the vibronic coupling that impacts the Abs bandshapes and gives rise to rR enhancement of vibrational modes. Past computational analyses of the vibrational spectra of cobalamins have either neglected rR enhancement or calculated rR enhancement for only a small number of modes. In the present study, we used the recently developed ORCA_ASA computational tool in conjunction with the popular B3LYP and BP86 functionals to predict Abs bandshapes and rR spectra for vitamin B12. The ORCA_ASA/B3LYP-computed Abs envelope in the visible spectral region and rR spectra of vitamin B12 agree remarkably well with our experimental data, while BP86 fails to reproduce both. This finding represents a significant advance in our understanding of how these two commonly used density functionals differently model the electronic properties of cobalamins. Guided by the computed frequencies for the Co-C stretching and Co-C-N bending modes, we identified, for the first time, isotope-sensitive features in our rR spectra of 12CNCbl and 13CNCbl that can be assigned to these modes. A normal coordinate analysis of the experimentally determined Co-C stretching and Co-C-N bending frequencies indicates that the Co-C force constant for vitamin B12 is 2.67 mdyn/Å, considerably larger than the Co-C force constants reported for alkylcobalamins.


Subject(s)
Spectrum Analysis, Raman , Vitamin B 12 , Vitamin B 12/chemistry , Vibration , Vitamins
12.
Front Biosci (Elite Ed) ; 15(2): 10, 2023 05 05.
Article in English | MEDLINE | ID: mdl-37369571

ABSTRACT

BACKGROUND: Information on the contents of both vitamin B12 and folate in edible seaweeds is limited, of which deficiencies disrupt methionine biosynthesis to accumulate homocysteine as a risk factor of cardiovascular diseases. METHODS: Both vitamins were determined in commercially available edible seaweed products using high-performance liquid chromatography. RESULTS: Dried purple laver (Neopyropia yezoensis) products contain higher levels of vitamin B12 (approximately 30-60 µg/100 g dry weight) and folate compounds (approximately 880-1300 µg/100 g dry weight) than other seaweed products, such as kombu (Saccharina japonica), hijiki (Sargassum fusiformis), and wakame (Undaria pinnatifida). 5-methyltetrahydrofolate was the major folate compound in purple laver products. 5-formyltetrahydrofolate was found at a moderate level, whereas tetrahydrofolate, 5,10-metenyltetrahydrofolate, 10-formyltetrahydrofolate, and folic acid were found to be minor folate compounds. CONCLUSIONS: These findings suggest that dried purple laver (nori) products are suitable sources of vitamin B12 and folate compounds for humans, especially vegetarians.


Subject(s)
Seaweed , Vitamin B 12 , Humans , Vitamin B 12/analysis , Vitamin B 12/chemistry , Folic Acid , Seaweed/chemistry , Vitamins/analysis , Chromatography, High Pressure Liquid
13.
Food Chem ; 424: 136435, 2023 Oct 30.
Article in English | MEDLINE | ID: mdl-37244193

ABSTRACT

This study aimed to explore the interaction mechanism between soybean lipophilic protein (LP) and vitamin B12 and the potential of LP as a vitamin B12 carrier. The results of spectroscopy indicated that the interaction between vitamin B12 and LP changed the conformation of LP and exposed hydrophobic groups largely. The results of molecular docking revealed that vitamin B12 interacted with LP through a hydrophobic pocket embedded on the surface of LP. With the enhancement of the interaction between LP and vitamin B12, the particle size of the LP-vitamin B12 complex gradually decreased to 588.31 nm and the absolute value of zeta potential gradually increased to 26.82 mV. Meanwhile, the LP-vitamin B12 complex showed excellent physicochemical properties and digestive characteristics. The present work enriched the means of vitamin B12 protection and provided a theoretical basis for applying the LP-vitamin B12 complex in food systems.


Subject(s)
Glycine max , Vitamin B 12 , Vitamin B 12/chemistry , Glycine max/metabolism , Soybean Proteins , Molecular Docking Simulation , Vitamins , Digestion
14.
Molecules ; 28(6)2023 Mar 10.
Article in English | MEDLINE | ID: mdl-36985516

ABSTRACT

EGCG is a catechin known for its antioxidant and anti-inflammatory characteristics. Vitamin B12 is an essential vitamin found in animal-derived products, and its deficiency may cause serious health problems such as anemia. The effectiveness of both catechin and vitamin B12 depends on their stability and bioavailability, which can be lost during industrial processes due to degradation when exposed to external factors. A potential solution to this issue is the microencapsulation, which protects the compounds from external agents. The current study aims to microencapsulate EGCG and vitamin B12 in a polymer matrix of biological origin, zein. Microencapsulation was performed using an electrospinning technique, and different concentrations of zein (1-30% w/v) and active compound (0.5-5% w/w) were tested, resulting in the production of micro/nanoparticles, fibers, or the mixture of both. The microstructures were analyzed and characterized in terms of morphology, release profile and kinetics, and encapsulation efficiency. High encapsulation efficiencies were obtained, and the highest were found in the samples with 1% w/w of active substance and 30% w/v of zein. Controlled release studies were conducted in deionized water and in an ethanolic solution, and five kinetic models were applied to the release profiles. The results indicated that the Weibull model was the best fit for the majority of results.


Subject(s)
Catechin , Zein , Animals , Zein/chemistry , Catechin/chemistry , Vitamin B 12/chemistry , Antioxidants/chemistry
15.
J Inorg Biochem ; 242: 112154, 2023 05.
Article in English | MEDLINE | ID: mdl-36871417

ABSTRACT

The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B12, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B12-dependent enzymes is also given for the reader's convenience.


Subject(s)
Cobalt , Vitamin B 12 , Cobalt/chemistry , Ligands , Vitamin B 12/chemistry , Oxidation-Reduction , Chemistry, Inorganic
16.
ACS Synth Biol ; 12(3): 898-903, 2023 03 17.
Article in English | MEDLINE | ID: mdl-36795971

ABSTRACT

CRISPR/Cas systems have been widely used in the precise and traceless genetic engineering of bacteria. Sinorhizobium meliloti 320 (SM320) is a Gram-negative bacterium with a low efficiency of homologous recombination but a strong ability to produce vitamin B12. Here, a CRISPR/Cas12e-based genome engineering toolkit, CRISPR/Cas12eGET, was constructed in SM320. The expression level of CRISPR/Cas12e was tuned through promoter optimization and the use of a low copy plasmid to adjust Cas12e cutting activity to the low homologous recombination efficiency of SM320, resulting in improved transformation and precision editing efficiencies. Furthermore, the accuracy of CRISPR/Cas12eGET was improved by deleting the ku gene involved in NHEJ repair in SM320. This advance will be useful for metabolic engineering and basic research on SM320, and it further provides a platform to develop the CRISPR/Cas system in strains where the efficiency of homologous recombination is low.


Subject(s)
Gene Editing , Sinorhizobium meliloti , CRISPR-Cas Systems/genetics , Gene Editing/methods , Metabolic Engineering , Plasmids/genetics , Sinorhizobium meliloti/genetics , Vitamin B 12/chemistry
17.
J Biomol Struct Dyn ; 41(8): 3222-3233, 2023 05.
Article in English | MEDLINE | ID: mdl-35261335

ABSTRACT

Many missense mutations/SNPs of the TCN2 gene (which yield Transcobalamin (TC)) were reported in the literature but no study is available about their effect on binding to vitamin B12(B12) at the structural level experimentally nor computationally. Predict the effect of TC missense mutations/SNPs on binding affinity to B12 and characterize their contacts to B12 at the structural level. TC-B12 binding energy difference from the wildtype (ΔΔGmut) was calculated for 378 alanine scanning mutations and 76 ClinVar missense mutations, repeated on two distinct X-ray structures of holoTC namely 2BB5 and 4ZRP. Destabilizing mutations then went through 100 ns molecular dynamics simulation to study their effect on TC-B12 binding at the structural level employing 2BB5 structure. Out of the studied 454 mutations (378 alanine mutations + 76 ClinVar mutations), 19 were destabilizing representing 17 amino acid locations. Mutation energy results show a neutral effect on B12 binding of several missense SNPs reported in the literature including I23V, G94S, R215W, P259R, S348F, L376S, and R399Q. Compared to the wildtype, all the destabilizing mutations have higher average RMSD-Ligand in the last 25% of the MD simulation trajectories and lower average hydrogen bond count while the other parameters vary. Previously reported TCN2 SNPs with an unknown effect on TC-B12 binding were found to have a neutral effect in the current study based on mutation energy calculations. Also, we reported 17 possible amino acids that destabilize TC-B12 binding upon mutation (four listed in ClinVar) and studied their structural effect computationally.


Subject(s)
Polymorphism, Single Nucleotide , Transcobalamins , Humans , Transcobalamins/genetics , Transcobalamins/metabolism , Mutation, Missense , Alanine/genetics , Vitamin B 12/chemistry , Vitamin B 12/metabolism , Amino Acids/genetics
18.
Chemistry ; 29(7): e202202995, 2023 Feb 01.
Article in English | MEDLINE | ID: mdl-36321632

ABSTRACT

TokK is a B12 -dependent radical SAM enzyme involved in the biosynthesis of the ß-lactam antibiotic asparenomycin A. It can catalyze three methylations on different sp3 -hybridized carbon positions to introduce an isopropyl side chain at the ß-lactam ring of pantetheinylated carbapenem. Herein, we report a quantum chemical study of the reaction mechanism of TokK. A stepwise ''push-pull'' radical relay mechanism is proposed for each methylation: a 5'-deoxyadenosine radical first abstracts a hydrogen atom from the substrate in the active site, then methylcobalamin directionally donates a methyl group to the substrate. More importantly, calculations were able to uncover the origin of observed chemoselectivity and stereoselectivity for the first methylation and regioselectivity for the following two methylations. Further detailed distortion/interaction analysis can help to unravel the main factors controlling the selectivities. Our findings of sequential methylations by TokK could have profound implications for studying other B12 -dependent radical SAM enzymes.


Subject(s)
Methyltransferases , beta-Lactams , Methylation , Methyltransferases/metabolism , Catalysis , Models, Theoretical , S-Adenosylmethionine/chemistry , Vitamin B 12/chemistry
19.
Int J Mol Sci ; 23(19)2022 Oct 07.
Article in English | MEDLINE | ID: mdl-36233209

ABSTRACT

Besides its use in medicine, vitamin B12 (cobalamin) and its derivatives have found in numerous applications as catalysts. However, studies related to the activation of oxidants via cobalamin are scant. In this work, we showed how the addition of aquacobalamin (H2OCbl) accelerates the destruction of azo-dye Orange II by peroxymonosulfate (HSO5-) in aqueous solutions. In neutral and weakly alkaline media, the process is initiated by the modification of the corrin macrocycle with HSO5-, which requires the preliminary deprotonation of the aqua-ligand in H2OCbl to give hydroxocobalamin, producing 5,6-dioxo-5,6-secocobalamin or its isomer (14,15-dioxo-14,15-secocobalamin). In acidic solutions, where the concentration of hydroxocobalamin is negligible, the formation of dioxo-seco-species is not observed, and the reaction between H2OCbl and HSO5- results in slow chromophore bleaching. Using terephthalic acid, we demonstrated the formation of hydroxyl radicals in the mixture of H2OCbl with HSO5-, whereas the generation of sulfate radicals was proved by comparing the effects of ethanol and nitrobenzene on Orange II destruction using the H2OCbl/HSO5- system. The reaction mechanism includes the binding of HSO5- to the Co(III) ion of dioxo-secocobalamin, which results in its deprotonation and the labilization of the O-O bond, leading to the formation of sulfate and hydroxyl radicals which further react with Orange II.


Subject(s)
Hydroxocobalamin , Vitamin B 12 , Azo Compounds , Benzenesulfonates , Ethanol , Hydroxocobalamin/pharmacology , Hydroxyl Radical , Ligands , Nitrobenzenes , Oxidants/chemistry , Oxidation-Reduction , Peroxides/chemistry , Sulfates/chemistry , Vitamin B 12/analogs & derivatives , Vitamin B 12/chemistry , Vitamin B 12/pharmacology , Vitamins
20.
J Bone Miner Res ; 37(12): 2443-2455, 2022 12.
Article in English | MEDLINE | ID: mdl-36128889

ABSTRACT

Folate, vitamins B12, B6, and riboflavin are required for one-carbon metabolism and may affect bone health, but no previous randomized trial has investigated all four nutrients in this context. We investigated the effect of low-dose B-vitamins for 2 years on bone mineral density (BMD) in a dual-centered, 2-year randomized controlled trial (RCT) in adults aged ≥50 years. Eligible participants not consuming B-vitamin supplements or fortified foods >4 times weekly were randomized to receive daily either combined folic acid (200 µg), vitamin B12 (10 µg), vitamin B6 (10 mg), and riboflavin (5 mg), or "active" placebo, whereby both the intervention and placebo groups received vitamin D (10 µg). BMD was assessed before and after intervention using dual-energy X-ray absorptiometry (DXA) scanning of the total hip, femoral neck, and lumbar spine (L1 to L4). Of 205 eligible participants randomized, 167 completed the trial in full. B-vitamin intervention resulted in increases in serum folate (p < 0.001), serum B12 (p < 0.001), and plasma pyridoxal-5-phosphate (p < 0.001) and decreases in functional biomarkers of B-vitamin status, erythrocyte glutathione reductase activation coefficient (p < 0.001), serum methylmalonic acid (MMA; p < 0.001), and serum total homocysteine (p < 0.001). B-vitamin intervention had no overall effect on BMD, which declined in both treatment groups by approximately 1% (ranging from -0.7% to -1.4%). However, in participants with lower baseline B12 status (serum B12 <246 pmol/L or MMA ≥0.22 µmol/L), B-vitamin intervention reduced the 2-year BMD decline versus placebo: adjusted mean (95% confidence interval [CI]) change of -0.003 (-0.008, 0.002) versus -0.015 (-0.021, -0.010) g/cm2 at the total hip and -0.004 (-0.010, 0.001) versus -0.013 (-0.018, -0.007) g/cm2 at the femoral neck. In conclusion, the findings indicate that although low-dose B-vitamin intervention for 2 years had no overall effect on BMD, improving B-vitamin status appears to have specific benefits for bone health in adults with lower B12 status. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).


Subject(s)
Bone Density , Vitamin B Complex , Adult , Humans , Bone Density/drug effects , Dietary Supplements , Folic Acid/therapeutic use , Lumbar Vertebrae , Riboflavin/therapeutic use , Vitamin B 12/blood , Vitamin B 12/chemistry , Vitamin B Complex/therapeutic use
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