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 H 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 H ligand signals, which resonate across the entire H spectral width.

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

NMR screening methods based on F spin-spin relaxation time (F-T) 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 F NMR analysis. It was shown that F-T was more sensitive in monitoring the binding affinity to the target protein than F spin-lattice relaxation time (F-T).

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.

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

The H{F} 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, H 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.

Myrindole A, an Antimicrobial Bis-indole from a Marine Sponge sp.

Myrindole A, a bis-indole alkaloid, was isolated from the deep-sea sponge sp. The high degree of unsaturation of the molecule complicated the assignment of its structure by standard 2D-NMR experiments but was ultimately achieved by a combination of H-N-HMBC and 1,-ADEQUATE experiments as well as the comparison of measured and calculated CD spectra. Myrindole A showed antimicrobial activity against Gram-positive and Gram-negative bacteria.

Analysis of Binding Mode of 2'-GMP to Proteins Using H/P NMR Spectroscopy.

H/P NMR techniques were applied to analyze the binding mode of guanosine 2'-monophosphate (2'-GMP) to histone. To date, no structures of the complex comprising 2'-GMP and histone have been deposited in Protein Data Bank. Because the P nucleus can be a selective marker of phosphorylated compounds, the combined use of H and P NMR spectroscopy has been applied to investigate these molecular interactions.

Author Correction: Formation of gold nanoparticles by glycolipids of Lactobacillus casei.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Identification of Binding Epitopes of a Fluorinated Compound Bound to Proteins Using H and F NMR Spectroscopy.

H/F NMR-based screening methods were applied to a human serum albumin-fleroxacin complex. Fleroxacin contains three fluorine atoms in a molecule, which is suitable as a model fluorinated compound for NMR analysis with H and F detection. The F{H} and H{H} saturation transfer difference spectra were acquired and the H/F spin-lattice relaxation rates were measured with and without any selective irradiation of protein resonance to identify the binding epitopes of fleroxacin.

NMR-based metabolic profiling and comparison of Japanese persimmon cultivars.

Persimmons are a traditional, autumnal, and healthy fruit commonly consumed in Japan and East Asia based on the saying, "a persimmon a day keeps the doctor away." The differences in metabolites among five major Japanese persimmon cultivars were investigated using a nuclear magnetic resonance (NMR)-based metabolomics approach. By using a broadband water suppression enhanced through T effects (WET) method for the sensitive detection of minor metabolites, better discrimination among cultivars and more informative details regarding their metabolic differences have been achieved compared to those achieved in conventional H NMR sequences.

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., ─CH ─CH (CH )─CH ─).

Solution-state structures of the cellulose model pullulan in lithium chloride/N,N-dimethylacetamide.

Pullulan is soluble in both N,N-dimethylacetamide (DMAc) and LiCl/DMAc. Here, the solution-state structures of pullulan in these two solvents were studied by size-exclusion chromatography with multi-angle laser light scattering (SEC/MALLS) and nuclear magnetic resonance (NMR) analyses. SEC/MALLS and off-line refractive index analyses revealed that the hydroxy groups of pullulan interact with LiCl in DMAc, as observed previously for cellulose.

Formation of gold nanoparticles by glycolipids of Lactobacillus casei.

Gold nanoparticles have particular properties distinct from those of bulk gold crystals, and such nanoparticles are used in various applications in optics, catalysis, and drug delivery. Many reports on microbial synthesis of gold nanoparticles have appeared. However, the molecular details (reduction and dispersion) of such synthesis remain unclear.

Use of NMR-Based Metabolomics To Chemically Characterize the Roasting Process of Chicory Root.

Roasted chicory root (Cichorium intybus) has been widely accepted as the most important coffee substitute. In this study, a nuclear magnetic resonance (NMR)-based comprehensive analysis was performed to monitor the substantial changes in the composition of chicory root during the roasting process. A detailed signal assignment of dried raw and roasted chicory roots was carried out using H, C, H-H DQF-COSY, H-C edited-HSQC, H-C CT-HMBC, and H-C HSQC-TOCSY NMR spectra.

Exploring Peptide Ligase Orthologs in Actinobacteria-Discovery of Pseudopeptide Natural Products, Ketomemicins.

We recently identified a novel peptide ligase (PGM1), an ATP-grasp-ligase, that catalyzes amide bond formation between (S)-2-(3,5-dihydroxy-4-methoxyphenyl)-2-guanidinoacetic acid and ribosomally supplied oligopeptides in pheganomycin biosynthesis. This was the first example of an ATP-grasp-ligase utilizing peptides as nucleophiles. To explore the potential of this type of enzyme, we performed a BLAST search and identified many orthologs.

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).

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.

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.

Analysis of the components of hard resin in hops (Humulus lupulus L.) and structural elucidation of their transformation products formed during the brewing process.

The resins from hops (Humulus lupulus L.), which add the bitter taste to beer, are classified into two main sub-fractions, namely, soft and hard resins. α- and β-Acids in soft resin and their transformation during the wort boiling process are well-studied; however, other constituents in resins, especially hard resin, have been unidentified.

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.

A pilot study of NMR-based sensory prediction of roasted coffee bean extracts.

Nuclear magnetic resonance (NMR) spectroscopy can be considered a kind of "magnetic tongue" for the characterisation and prediction of the tastes of foods, since it provides a wealth of information in a nondestructive and nontargeted manner. In the present study, the chemical substances in roasted coffee bean extracts that could distinguish and predict the different sensations of coffee taste were identified by the combination of NMR-based metabolomics and human sensory test and the application of the multivariate projection method of orthogonal projection to latent structures (OPLS). In addition, the tastes of commercial coffee beans were successfully predicted based on their NMR metabolite profiles using our OPLS model, suggesting that NMR-based metabolomics accompanied with multiple statistical models is convenient, fast and accurate for the sensory evaluation of coffee.

Structural determination of a nivalenol glucoside and development of an analytical method for the simultaneous determination of nivalenol and deoxynivalenol, and their glucosides, in wheat.

Trichothecene mycotoxins such as nivalenol and deoxynivalenol frequently contaminate foodstuffs. Recently, several trichothecene glucosides have been found in trichothecene-contaminated foods, and information about their chemistry, toxicity, and occurrence is required. In this study, a glucoside of nivalenol was isolated from nivalenol-contaminated wheat and was identified as nivalenol-3-O-β-D-glucopyranoside.

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-).