Structural and Functional Analysis of the Amorphous Calcium Carbonate-Binding Protein Paramyosin in the Shell of the Pearl Oyster, Pinctada fucata.

Amorphous calcium carbonate (ACC) is an important precursor phase for the formation of aragonite crystals in the shells of Pinctada fucata. To identify the ACC-binding protein in the inner aragonite layer of the shell, extracts from the shell were used in the ACC-binding experiments. Semiquantitative analyses using liquid chromatography-mass spectrometry revealed that paramyosin was strongly associated with ACC in the shell. We discovered that paramyosin, a major component of the adductor muscle, was included in the myostracum, which is the microstructure of the shell attached to the adductor muscle. Purified paramyosin accumulates calcium carbonate and induces the prism structure of aragonite crystals, which is related to the morphology of prism aragonite crystals in the myostracum. Nuclear magnetic resonance measurements revealed that the Glu-rich region was bound to ACC. Activity of the Glu-rich region was stronger than that of the Asp-rich region. These results suggest that paramyosin in the adductor muscle is involved in the formation of aragonite prisms in the myostracum.

Exploring an Artificial Metabolic Route in Fusarium sporotrichioides: Production and Characterization of 7-Hydroxy T-2 Toxin.

An artificial metabolic route to an unnatural trichothecene was designed by taking advantage of the broad substrate specificities of the T-2 toxin biosynthetic enzymes of Fusarium sporotrichioides. By feeding 7-hydroxyisotrichodermin, a shunt pathway metabolite of F. graminearum, to a trichodiene synthase-deficient mutant of F. sporotrichioides, 7-hydroxy T-2 toxin (1) was obtained as the final metabolite. Such an approach may have future applications in the metabolic engineering of a variety of fungal secondary metabolites. The toxicity of 7-hydroxy T-2 toxin was 10 times lower than that of T-2 toxin in HL-60 cells.

DPFGSE-MDEC-J-resolved COSY: An efficient method for selectively measuring proton-proton spin coupling constants of the multiplet signals.

Natural products such as polyketides often possess various spin systems, consisting of a methine group directly bonded to a methyl group (e.g., ─CHA ─CHB (CH3 )─CHC ─). The methine proton HB splits into a broadened multiplet by coupling with several vicinal protons, rendering analysis difficult of n JH-H with respect to HB in double-quantum filtered COSY or exclusive COSY. For the purpose of measuring n JH-H in the aforesaid spin system, we have developed new techniques, named multifrequency homo-decoupling (MDEC)-J-resolved COSY and DPFGSE-MDEC-J-resolved COSY. This method incorporates MDEC pulse scheme into J-resolved COSY for the selective decouple of individual methyl groups, avoiding decoupling of the target protons resonating in methyl region. Determinations of n JH-H of the multiplet signals can easily be performed using the proposed pulse sequence.

NMR-based analysis of the chemical composition of Japanese persimmon aqueous extracts.

Japanese persimmon (Diospyros kaki L.) is recognized as an outstanding source of biologically active compounds relating to many health benefits. In the present study, NMR spectroscopy provided a comprehensive metabolic overview of Japanese persimmon juice. Detailed signal assignments of Japanese persimmon juice were carried out using various 2D NMR techniques incorporated with broadband water suppression enhanced through T1 effects (BB-WET) or WET sequences, and 26 components, including minor components, were identified. In addition, most components were quantitatively evaluated by the integration of signals using conventional (1) H NMR and BB-WET NMR. This is the first detailed analysis combined with quantitative characterization of chemical components using NMR for Japanese persimmon. Copyright © 2015 John Wiley & Sons, Ltd.

Conformation analysis of d-glucaric acid in deuterium oxide by NMR based on its JHH and JCH coupling constants.

d-Glucaric acid (GA) is an aldaric acid and consists of an asymmetric acyclic sugar backbone with a carboxyl group positioned at either end of its structure (i.e., the C1 and C6 positions). The purpose of this study was to conduct a conformation analysis of flexible GA as a solution in deuterium oxide by NMR spectroscopy, based on J-resolved conformation analysis using proton-proton ((3) JHH ) and proton-carbon ((2) JCH and (3) JCH ) coupling constants, as well as nuclear overhauser effect spectroscopy (NOESY). The (2) JCH and (3) JCH coupling constants were measured using the J-resolved heteronuclear multiple bond correlation (HMBC) NMR technique. NOESY correlation experiments indicated that H2 and H5 were in close proximity, despite the fact that these protons were separated by too large distance in the fully extended form of the chain structure to provide a NOESY correlation. The validities of the three possible conformers along the three different bonds (i.e., C2C3, C3C4, and C4C5) were evaluated sequentially based on the J-coupling values and the NOESY correlations. The results of these analyses suggested that there were three dominant conformers of GA, including conformer 1, which was H2H3:gauche, H3H4:anti, and H4H5:gauche; conformer 2, which was H2H3:gauche, H3H4:anti, and H4H5:anti; and conformer 3, which was H2H3:gauche, H3H4: gauche, and H4H5:anti. These results also suggested that all three of these conformers exist in equilibrium with each other. Lastly, the results of the current study suggested that the conformational structures of GA in solution were 'bent' rather than being fully extended. Copyright © 2016 John Wiley & Sons, Ltd.

Achievement of 1 H-19 F heteronuclear experiments using the conventional spectrometer with a shared single high band amplifier.

The (1)H-(19) F heteronuclear NMR experiments were achieved using the conventional spectrometer equipped with a single high band amplifier and a (1)H/(19)F/(13) C double-tuned probe. Although double high band amplifiers are generally required to perform such experiments, a simple modification of pathway in the conventional spectrometer was capable of acquiring various (1)H-(19)F heteronuclear spectra. The efficiency of the present technique was demonstrated in an application for (19)F{(1)H} and (1)H{(19)F} saturation transfer difference experiments.

BASHD-J-resolved-HMBC, an efficient method for measuring proton-proton and heteronuclear long-range coupling constants.

Natural products often possess various spin systems consisting of a methine group directly bonded to a methyl group (e.g. -CHa-CHb(CH3)-CHc-). The methine proton Hb splits into a broadened multiplet by coupling with several vicinal protons, rendering analysis difficult of (n)JC-H with respect to Hb in the J-resolved HMBC-1. In purpose of the reliable and easy measurements of (n)JC-H and (n)JH-H in the aforesaid spin system, we have developed a new technique, named BASHD-J-resolved-HMBC. This method incorporates band selective homo decoupled pulse and J-scaling pulse into HMBC. In this method, high resolution cross peaks can be observed along the F1 axis by J-scaling pulse, and band selective homo decoupled pulse simplified multiplet signals. Determinations of (n)JC-H and (n)JH-H of multiplet signals can easily be performed using the proposed pulse sequence.

Broadband WET: a novel technique for quantitative characterization of minor components in foods.

NMR analysis of foods frequently suffers from a problem of dynamic range, which limits the detection of minor components due to the huge signals of water and major components such as sugars. In the present study, we propose a new method named as 'broadband WET'. This pulse scheme was applied to persimmon fruit juice for saturating the resonances of water and sugars, which covered a broad bandwidth. In comparison with the conventional solvent suppression methods such as WET and DPFGSE-WATERGATE, it was shown that broadband WET provided highly selective suppression of resonances covering an extensive bandwidth and quantitative signals of minor components without distortion. The proposed method is suitable to detect quantitative signals of the minor components with a high sensitivity.

NMR screening method based on 19F spin-spin relaxation time for analyses of fluorinated compound bound to proteins.

NMR screening methods based on 19F spin-spin relaxation time (19F-T2) were applied to fluorinated compounds bound to human serum albumin. Diflunisal and fleroxacin (the fluorinated compounds) contain two and three fluorine atoms per molecule, respectively, and are suitable as the model system for 19F NMR analysis. It was shown that 19F-T2 was more sensitive in monitoring the binding affinity to the target protein than 19F spin-lattice relaxation time (19F-T1). The comparisons of 19F signal intensities acquired at different echo times using 19F-T2 pulse sequence were also shown to be an effective means of assessing complex formation for fluorinated compounds.

Optimization of reverse NOE pumping experiments in the analysis of complex systems with densely crowded NMR spectra.

We present an optimization of Reverse NOE-pumping (RNP) in order to observe the 1H signals of ligands bound to proteins. Although various ligand-based NMR screening methods have been proposed, the most frequently used method has been Saturation-Transfer Difference (STD), owing to the relatively easy setup of experiments. Yet the critical point of STD is the selective irradiation of protein without irradiating ligand, and thus the STD technique is unable to observe 1H ligand signals, which resonate across the entire 1H spectral width. In the present study, the RNP experiment has been improved to develop an effective NMR-based screening technique. The optimized RNP spectra reveal less subtraction artifacts and phase distortion than the original RNP spectra, indicating its applicability to any type of ligand molecules.

Glycolytic intermediates induce amorphous calcium carbonate formation in crustaceans.

It has been thought that phosphorus in biominerals made of amorphous calcium carbonate (ACC) might be related to ACC formation, but no such phosphorus-containing compounds have ever been identified. Crustaceans use ACC biominerals in exoskeleton and gastroliths so that they will have easy access to calcium carbonate inside the body before and after molting. We have identified phosphoenolpyruvate and 3-phosphoglycerate, intermediates of the glycolytic pathway, in exoskeleton and gastroliths and found them important for stabilizing ACC.

Determination of strain-specific wall teichoic acid structures in Lactobacillus plantarum reveals diverse α-D-glucosyl substitutions and high structural uniformity of the repeating units.

The structural diversity of wall teichoic acid (WTA) was investigated using biochemical and NMR analyses among 19 strains of Lactobacillus plantarum, of which seven were previously established to contain a glycerol-type backbone, whereas the remaining 12 strains possess ribitol-containing WTA. Despite the fact that the WTAs consisted of identical components, namely phosphoric acid, alditol (glycerol or ribitol) and glucose, comparative analysis of the (1)H and (13)C NMR spectra indicated the presence of six different structures, based on the observed differences in the anomeric signals of glucose residues. To determine the six WTA structures, their repeating units were prepared by alkaline hydrolysis, followed by fractionation on HPLC, and analysis by NMR spectroscopy using synthetic molecules as a reference. The structures of the six isolates were established as 1-α-D-glucosyl-sn-glycerol 3-phosphate, 1-α-D-kojibiosyl-sn-glycerol 3-phosphate, 1-α-D-nigerosyl-sn-glycerol 3-phosphate, 4-α-D-kojibiosylribitol 1-phosphate and 1,5-linked di-(2,4-di-α-D-glucosylribitol) phosphate. The backbone structures appeared to be 3,6'-linked poly(1-α-D-glucosyl-sn-glycerol phosphate) for the glycerol-type WTA and 1,5-linked poly(ribitol phosphate) for the ribitol-containing WTA. Moreover, in the analysis of the alkaline hydrolysates on HPLC, only single structures of repeating units were released from each WTA, indicating the high structural uniformity of the WTA in each strain. Notably, analyses of lipoteichoic acid isolated from representative strains harbouring the six different WTAs revealed the universal presence of a 1,3-linked poly(glycerol phosphate) chain, substituted at C-2 of the glycerol residues with glucose residues. These findings provide fundamental information on WTA structural variability in Lb. plantarum, which seems likely to play a pivotal role in the physiology of this bacterial species.

Selective COSY-J-resolved-HMBC, a new method for improving sensitivity of cross peaks of methine proton signals attached to a methyl group.

Improved pulse sequences for measuring long-range C-H coupling constants ((n)J(C-H)), named selective COSY-J-resolved HMBC-1 and -2, have been developed. In the spin systems, such as -CH(C)-CH(A)(CH(3))-CH(B)-, a methine proton H(A) splits into a multiplet owing to several vicinal couplings with protons, resulting in attenuation of its cross-peak intensity. Therefore, the measurements of (n)J(C-H) with H(A) are generally difficult in the J-resolved HMBC or selective J-resolved HMBC spectrum. With the aim of accurate measurements of (n)J(C-H) in such a spin system, we have developed new pulse sequences, which transfer the magnetization of a methyl group to its adjacent methine proton. The proposed pulse sequences successfully enable to enhance the sensitivity of H(A) cross peak in comparison with the selective J-resolved HMBC pulse sequence.

BASHD-J-resolved-COSY: a new method for measuring proton-proton spin coupling constants of multiplet signals.

An effective pulse sequence for measuring H-H coupling constants, named BASHD-J-resolved-COSY, has been developed. In the spin systems such as -CH(A)-CH(B)(CH(3))-CH(C)-, a methine proton H(B) splits into a multiplet owing to several vicinal couplings, resulting in attenuation of its cross-peak intensity. Therefore, the measurements of (3)J(H-H) with respect to H(B) are generally difficult in the E-COSY-type experiments. With the aim of accurate measurements of (3)J(H-H) in such a spin system, we have developed a new pulse sequence, which selectively decouples the secondary methyl group. The proposed pulse sequence provides the simplified cross-peak patterns, which are suitable for reliable measurements of (3)J(H-H) in a complicated natural product.

Development of 1H{19F} saturation transfer difference experiments for detection of a fluorinated compound bound to proteins.

The 1H{19F} saturation transfer difference (STD) experiment presented here incorporates the WATERGATE W5 sequence to observe protein-ligand interactions in a human serum albumin (HSA)-fleroxacin complex. In conventional STD experiments, 1H of proteins are first saturated, and the ligands bound to these proteins are then observed. The method proposed here reverses this process: fluorine atoms in fleroxacin are selectively saturated, and saturation transfer then occurs to protons of fleroxacin as well as to those of HSA. The combined use of the present 1H{19F} STD and conventional STD methods is expected to provide better insight in the analysis of the role of fluorine atoms in a fluorinated compound.

NMR and HPLC profiling of bee pollen products from different countries.

Bee pollen, a beehive product collected from flowers by honeybees, contains over 250 biological substances, and has attracted increasing attention as a functional food. However, commercial bee pollen products are often multifloral, and samples from different countries vary significantly. There is no universal standard for objective quality assessment of bee pollen based on its chemical composition. Here, we report metabolomic analysis of 11 bee pollen samples from Spain, China, and Australia for quality control. The characteristics of the samples depend on the sucrose, nucleoside, amino acid, and flavanol concentrations. Bee pollen samples from Spain and Australia had higher sucrose and adenosine concentrations, whereas those from China had higher trigonelline, uridine, and cytidine concentrations. Interestingly, acetic acid was only detected in samples from China. These components can be used to identify the country of origin. The obtained profiles of the samples will contribute to universal standard development for bee pollen products.

Diversity of the early step of the futalosine pathway.

We recently demonstrated that the futalosine pathway was operating in some bacteria for the biosynthesis of menaquinone and that futalosine was converted into dehypoxanthinyl futalosine (DHFL) by an MqnB of Thermus thermophilus. In this study, we found that aminodeoxyfutalosine, which has adenine instead of hypoxanthine in futalosine, was directly converted into DHFL by an MqnB of Helicobacter pylori. Therefore, this step is potentially an attractive target for the development of specific anti-H. pylori drugs.

Maklamicin, an antibacterial polyketide from an endophytic Micromonospora sp.

A new spirotetronate-class polyketide, maklamicin (1), was isolated from the culture extract of an endophytic actinomycete of the genus Micromonospora. The structure and relative configuration of 1 were elucidated by interpretation of NMR and other spectroscopic data, and the absolute configuration was determined using the modified Mosher method. Maklamicin (1) showed strong to modest antimicrobial activity against Gram-positive bacteria.

Selective J-resolved-HMQC-1 and -2, new methods for measuring proton-proton coupling constants in strongly coupled spin systems.

Efficient pulse sequences for measuring (1)H-(1)H coupling constants (JHH) in strongly coupled spin systems, named selective J-resolved-HMQC-1 and -2, have been developed. In the strongly coupled spin systems such as -CH2-CHA(OH)-CHB(OH)-CH2-, measurements of (3)JHAHB are generally difficult owing to the complicated splitting caused by the adjacent CH2 protons. For easier and accurate measurements of (3)JHAHB in such a spin system, a selective excitation pulse is incorporated into the J-resolved HMQC pulse sequence. In the proposed methods, only two strongly coupled protons, HA and HB which are excited by a selective pulse, are observed as J-resolved HMQC signals. The cross peaks of HA and HB appear as doublets owing to (3)JHAHB along the F1 dimension in the selective J-resolved HMQC-1 and -2 experiments. The efficiency of the proposed pulse sequences has been demonstrated in application to the stereochemical studies of the complicated natural product, monazomycin.