Mapping Post-translational Modifications of Histones H2A, H2B and H4 in Schizosaccharomyces pombe

Core histones are known to carry a variety of post-translational modifications (PTMs), including acetylation, phosphorylation, methylation and ubiquitination, which play important roles in the epigenetic control of gene expression. The nature and biological functions of these PTMs in histones from plants, animals and budding yeast have been extensively investigated. In contrast, the corresponding studies for fission yeast were mainly focused on histone H3. In the present study, we applied LC-nano-ESI-MS/MS, coupled with multiple protease digestion, to identify PTMs in histones H2A, H2B and H4 from Schizosaccharomyces pombe (S. pombe), the typical model organism of fission yeast. Various protease digestions provided high sequence coverage for PTM mapping, and accurate mass measurement of fragment ions allowed for unambiguous differentiation of acetylation from tri-methylation. Many modification sites conserved in other organisms were identified in S. pombe. In addition, some unique modification sites, including N-terminal acetylation in H2A and H2B as well as K123 acetylation in H2A.β, were observed. Our results provide a comprehensive picture of the PTMs of histones H2A, H2B and H4 in S. pombe, which serves as a foundation for future investigations on the regulation and functions of histone modifications in this important model organism.     

Vitamin B12-derivatives-enzyme cofactors and ligands of proteins and nucleic acids

B(12)-cofactors play important roles in the metabolism of microorganisms, animals and humans. Microorganisms are the only natural sources of B(12)-derivatives, and the latter are "vitamins" for other B(12)-requiring organisms. Some B(12)-dependent enzymes catalyze complex isomerisation reactions, such as methylmalonyl-CoA mutase. They need coenzyme B(12), an organometallic B(12)-derivative, to induce enzymatic radical reactions. Another group of widely relevant enzymes catalyzes the transfer of methyl groups, such as methionine synthase, which uses methylcobalamin as cofactor. This tutorial review covers structure and reactivity of B(12)-derivatives and structural aspects of their interactions with proteins and nucleotides, which are crucial for the efficient catalysis by the important B(12)-dependent enzymes, and for achieving and regulating uptake and transport of B(12)-derivatives.     

Synthesis of Mixed Dinucleotides by Mechanochemistry

We report the synthesis of vitamin B1, B2, and B3 derived nucleotides and dinucleotides generated either through mechanochemical or solution phase chemistry. Under the explored conditions, adenosine and thiamine proved to be particularly amenable to milling conditions. Following optimization of the chemistry related to the formation pyrophosphate bonds, mixed dinucleotides of adenine and thiamine (vitamin B1), riboflavin (vitamin B2), nicotinamide riboside and 3-carboxamide 4-pyridone riboside (both vitamin B3 derivatives) were generated in good yields. Furthermore, we report an efficient synthesis of the MW+4 isotopologue of NAD⁺ for which deuterium incorporation is present on either side of the dinucleotidic linkage, poised for isotopic tracing experiments by mass spectrometry. Many of these mixed species are novel and present unexplored possibilities to simultaneously enhance or modulate cofactor transporters and enzymes of independent biosynthetic pathways.     

New developments in the field of vitamin B12: enzymatic reactions dependent upon corrins and coenzyme B12.

Simple corrins such as vitamin B₁₂ and vitamin B₁₂ coenzyme catalyze a variety of unusual enzymatic reactions of which some are still without analogy in organic or organometallic chemistry. The mechanisms of these reactions are currently the subject of lively discussion. The present review focuses attention on new ideas about the mode of action of vitamin B₁₂ coenzymes in enzymatic reactions.     

New Developments in the Field of Vitamin B12: Reactions of the Cobalt Atom in Corrins and in Vitamin B12 Model Compounds

Studies with vitamin B₁₂ model compounds such as the cobaloximes provide a basis for the understanding of the mode of action of corrinoid coenzymes in enzymatic reactions. They also widen our knowledge of the properties and reactions of organocobalt compounds. The present article outlines the most important nonenzymatic reactions of cobalt in vitamin B₁₂ and in model compounds of the cobaloxime type.     

Molybdenum: biological activity and metabolism

Molybdenum and tungsten are available to all organisms, with molybdenum having the far greater abundance and availability. Molybdenum occurs in a wide range of metalloenzymes in bacteria, fungi, algae, plants and animals, while tungsten was found to be essential only for a limited range of bacteria. In order to gain biological activity, molybdenum has to be complexed by a pterin compound, thus forming a molybdenum cofactor. In this article I will review the way that molybdenum takes from uptake into the cell, via formation of the molybdenum cofactor and its storage, to the final modification of molybdenum cofactor and its insertion into apo-metalloenzymes.     

维生素B1、B6与金属离子关系的光化学研究

分别研究了必需微量元素铁、锌、铜、锰、硒、常量元素钙、镁、非必需元素铝、锂，有毒元素尔，铅，镉对维生素B1、B6的紫外吸收光谱的影响，并对其机理进行了初步探讨。所得结果对于金属离子与维生素B1、B6的关系及其在人体中的生化、生理功能和生物有效性提供了一定的理论依据。     

Determination of vitamin B5 in human urine by high-performance liquid chromatography coupled with mass spectrometry

In the present work, we have developed a simple and rapid liquid chromatography/mass spectrometry (LC/MS) method for the identification and quantification of vitamin B5 in human urine. Urine was spiked with vitamin B5 internal standard, hopantenic acid (HOPA), and then diluted with the LC mobile phase prior to its analysis by LC/MS. The quantification was performed in single ion monitoring mode. The calibration curve was linear (r2 = 0.999) between 0.25 to 10 microg/mL. With a limit of detection of 0.1 microg/mL the method was sensitive enough to determine low levels of vitamin B5 in urine. The overall quantitative efficiency of the method was evaluated by spiking urine samples with four different concentrations of vitamin B5; the intra-assay coefficient of variation was below 5% and the recoveries were between 96 to 108%. The results of the present study show that the proposed method is selective and sensitive enough for the quantification of vitamin B5 in urine.     

Enzyme catalysis of 1,2-amino shifts: the cooperative action of B6, B12, and aminomutases

Ab initio molecular orbital theory is used to investigate 1,2-amino shifts catalyzed by aminomutases, coenzyme B12, and vitamin B6 (in the form of pyridoxal 5'-phosphate or PLP). Our calculations suggest essential catalytic roles for each of B12, B6, and the enzyme in aminomutase-catalyzed reactions. In the first place, coenzyme B12 provides a source of abstracting radicals, allowing the rearrangement reaction to take place on the radical surface. The involvement of radicals is supported by comparison of experimental and theoretical electron paramagnetic resonance parameters. Next, B6 allows the enzyme to lower the barrier height by introducing a double bond (allowing a low-energy intramolecular rearrangement pathway) and by providing a suitable site for partial protonation (preventing overstabilization of the reaction intermediate which could lead to enzyme inactivation). The PLP hydroxyl group is also identified as an important participant in these reactions. Finally, the enzyme holds the various reaction components in place and is the source of acidic functional groups that can provide partial protonation.     

Toward catalytically active oligonucleotides: synthesis of a flavin nucleotide and its incorporation into DNA

[reaction--see text] The synthesis of a vitamin B(2)-derived flavin-nucleotide is described. A combined H-phosphonate/phosphoramidite protocol was developed for the first incorporation of flavin coenzymes into a DNA stack. The coenzyme-DNA is predicted to have novel biosensing and catalytic properties.     

Vitamin B1 as a scavenger of reactive oxygen species photogenerated by vitamin B2

Kinetics and mechanism of photoprocesses generated by visible light-irradiation of the system riboflavin (Rf, vitamin B2) plus Thiamine (Th) and Thiamine pyrophosphate (ThDP), representing vitamin B1, was studied in pH 7 water. A weak dark complex vitamin B2-vitamin B1, with a mean value of 4 ± 0.4 M(-1) is formed. An intricate mechanism of competitive reactions operates upon photoirradiation, being the light only absorbed by Rf. Th and ThDP quench excited singlet and triplet states of Rf, with rate constants in the order of 10(9) and 10(6 ) M(-1 ) s(-1), respectively. With Vitamin B1 in a concentration similar to that of dissolved molecular oxygen in water, the quenching of triplet excited Rf by the latter is highly predominant, resulting in the generation of O(2)((1)Δ(g)). Superoxide radical anion was not detected under work conditions. A relatively slow O(2)((1)Δ(g))-mediated photodegradation of Th and ThDP was observed. Nevertheless, Th and especially ThDP behave as efficient physical deactivators of O(2)((1)Δ(g)). The thiazol structure in vitamin B1 appears as a good scavenger of this reactive oxygen species. This characteristic, that presents at vitamin B1 as a potential photoprotector of biological entities against O(2)((1)Δ(g)) attack, was been experimentally confirmed employing the protein lisozime as a photo-oxidizable target.     

Synthesis of imidazolo analogues of the oxidation-reduction cofactor pyrroloquinoline quinone (PQQ)

Parallel syntheses of 2-hydro-, 2-methyl-, and 2-methoxycarbonylimidazo-7,9-dimethoxycarbonyl analogues of the oxidation-reduction cofactor pyrroloquinoline quinone [4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylic acid] have been developed. The properties of the imidazolo analogues in relation to the corresponding pyrrole analogues will be important in assessing the origins of catalysis and biological activity in the cofactor, which has recently been shown to be a vitamin.     

Discovering nature's diverse pathways to vitamin B12: a 35-year odyssey

The chronology of the discoveries along the pathway of vitamin B(12) biosynthesis is reviewed from a personal perspective, including discussion of the most recent finding that two pathways to B(12) exist-one aerobic and one anaerobic-which differ mainly in the ring contraction mechanisms that convert porphyrin to corrin.     

The diverse roles of flavin coenzymes--nature's most versatile thespians

Flavin coenzymes play a variety of roles in biological systems. This Perspective highlights the chemical versatility of flavins by reviewing research on five flavoenzymes that have been studied in our laboratory. Each of the enzymes discussed in this review [the acyl-CoA dehydrogenases (ACDs), CDP-6-deoxy-l-threo-d-glycero-4-hexulose-3-dehydrase reductase (E3), CDP-4-aceto-3,6-dideoxygalactose synthase (YerE), UDP-galactopyranose mutase (UGM), and type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2)] utilizes flavin in a distinct role. In particular, the catalytic mechanisms of two of these enzymes, UGM and IDI-2, may involve novel flavin chemistry.     

New techniques and strategies in drug discovery

Great success has been witnessed in last decades, some new techniques and strategies have been widely used in drug discovery. In this roadmap, several representative techniques and strategies are highlighted to show recent advances in this filed. (A) A DOX protocol has been developed for accurate protein-ligand binding structure prediction, in which first principle method was used to rank the binding poses. Validation against crystal structures have found that DOX prediction achieved an impressive success rate of 99%, indicating significant improvement over molecular docking method. (B) Virtual target profiling is a compound-centric strategy enabling a parallel implementation of interrogating compounds against various targets in a single screen, which has been used in hit/lead identification, drug repositioning, and mechanism-of-action studies. Current and emerging methods for virtual target profiling are briefly summarized herein. (C) Research on targeted autophagy to treat diseases has received encouraging progress. However, due to the complexity of autophagy and disease, experimental and in silico methods should be performed synergistically for the entire process. This part focuses on in silico methods in autophagy research to promote their use in medicinal research. (D) Histone deacetylases (HDACs) play important roles in various biological functions through the deacetylation of lysine residues. Recent studies demonstrated that HDACs, which possess low deacetylase activities, exhibited more efficient defatty-acylase activities. Here, we review the defatty-acylase activity of HDACs and describe examples for the design of isoform selective HDAC inhibitor. (E) The FDA approval of three kinase allosteric inhibitors and some others entering clinical study has spurred considerable interests in this targeted drug discovery area. (F) Recent advances are reviewed in structure-based design of novel antiviral agents to combat drug resistance. (G) Since nitric oxide (NO) exerts anticancer activity depending on its concentration, optimal levels of NO in cancer cells is desirable. In this minireview, we briefly describe recent advances in the research of NO-based anticancer agents by our group and present some opinions on the future development of these agents. (H) The field of photoactivation strategies have been extensively developed for controlling chemical and biological processes with light. This review will summarize and provide insight into recent research advances in the understanding of photoactivatable molecules including photoactivatable caged prodrugs and photoswitchable molecules.     

Reflections on the discovery of nature's pathways to vitamin B12

The chronology of the discoveries along the pathway of vitamin B12 biosynthesis is reviewed from a personal perspective, including discussion of the most recent finding that two pathways to B12 exist--one aerobic and one anaerobic--which differ mainly in the ring contraction mechanisms which convert porphyrin to corrin.     

Determination of vitamin B6 vitamers and pyridoxic acid in biological samples.

For the determination of vitamin B6 vitamers (pyridoxal phosphate, pyridoxamine phosphate, pyridoxal, pyridoxine, pyridoxamine) and 4-pyridoxic acid in biological samples such as plasma, cerebrospinal fluid and rat brain regions, a sensitive micromethod using high-performance liquid chromatography (HPLC) with fluorescence detection in combination with post-column derivatization is described. Metaphosphoric acid tissue extracts with deoxypyridoxine as an internal standard were injected into the HPLC system with a binary gradient elution at a flow-rate of 1.2 ml/min. The excitation wavelength of the fluorescence detector was set at 328 nm and the emission wavelength at 393 nm with a 15-nm slit width for the photocell. This method allows the assay of vitamin B6 vitamers within 30 min in one chromatographic run. The present method has been applied extensively for the measurement of vitamin B6 vitamer levels in discrete brain regions of small animals, cells in culture and biopsy samples.     

Determination of Vitamin B3 Vitamer (Nicotinamide) and Vitamin B6 Vitamers in Human Hair Using LC-MS/MS

Water-soluble B vitamins participate in numerous crucial metabolic reactions and are critical for maintaining our health. Vitamin B deficiencies cause many different types of diseases, such as dementia, anaemia, cardiovascular disease, neural tube defects, Crohn’s disease, celiac disease, and HIV. Vitamin B3 deficiency is linked to pellagra and cancer, while niacin (or nicotinic acid) lowers low-density lipoprotein (LDL) and triglycerides in the blood and increases high-density lipoprotein (HDL). A highly sensitive and robust liquid chromatography–tandem mass spectroscopy (LC/MS-MS) method was developed to detect and quantify a vitamin B3 vitamer (nicotinamide) and vitamin B6 vitamers (pyridoxial 5′-phosphate (PLP), pyridoxal hydrochloride (PL), pyridoxamine dihydrochloride (PM), pridoxamine-5′-phosphate (PMP), and pyridoxine hydrochloride (PN)) in human hair samples of the UAE population. Forty students’ volunteers took part in the study and donated their hair samples. The analytes were extracted and then separated using a reversed-phase Poroshell EC-C18 column, eluted using two mobile phases, and quantified using LC/MS-MS system. The method was validated in human hair using parameters such as linearity, intra- and inter-day accuracy, and precision and recovery. The method was then used to detect vitamin B3 and B6 vitamers in the human hair samples. Of all the vitamin B3 and B6 vitamers tested, only nicotinamide was detected and quantified in human hair. Of the 40 samples analysed, 12 were in the range 100–200 pg/mg, 15 in the range 200–500 pg/mg, 9 in the range of 500–4000 pg/mg. The LC/MS-MS method is effective, sensitive, and robust for the detection of vitamin B3 and its vitamer nicotinamide in human hair samples. This developed hair test can be used in clinical examination to complement blood and urine tests for the long-term deficiency, detection, and quantification of nicotinamide.     

Field-portable, high-speed GC/TOFMS

This work is focused on developing a fast gas chromatograph, time-of-flight mass spectrometer (GC/TOFMS) for man-portable field use. The goal is to achieve a total system solution for meeting performance, size, weight, power, cost, and ruggedness requirements for a laboratory in the field. The core technology will also be adaptable to specific applications including real-time point detection for hazardous chemical releases (e.g., chemical weapons), for biological agent signature identification, and for mobile monitoring platforms (e.g., air, ship, truck). Previously we presented results of a feasibility demonstration for a 30-lb field-portable TOFMS system. In this work we present recent progress in integrating a low-power, high-speed GC and show the capability for accurately recording fast GC transients for targeted compound detection using a quadrupole ion trap, time-of-flight instrument (QitTof).