Detection and characterization of serine and threonine hydroxyl protons in Bacillus circulans xylanase by NMR spectroscopy

Hydroxyl protons on serine and threonine residues are not well characterized in protein structures determined by both NMR spectroscopy and X-ray crystallography. In the case of NMR spectroscopy, this is in large part because hydroxyl proton signals are usually hidden under crowded regions of ¹H-NMR spectra and remain undetected by conventional heteronuclear correlation approaches that rely on strong one-bond ¹H–¹⁵N or ¹H–¹³C couplings. However, by filtering against protons directly bonded to ¹³C or ¹⁵N nuclei, signals from slowly-exchanging hydroxyls can be observed in the ¹H-NMR spectrum of a uniformly ¹³C/¹⁵N-labeled protein. Here we demonstrate the use of a simple selective labeling scheme in combination with long-range heteronuclear scalar correlation experiments as an easy and relatively inexpensive way to detect and assign these hydroxyl proton signals. Using auxtrophic Escherichia coli strains, we produced Bacillus circulans xylanase (BcX) labeled with ¹³C/¹⁵N-serine or ¹³C/¹⁵N-threonine. Signals from two serine and three threonine hydroxyls in these protein samples were readily observed via ³J_C–OH couplings in long-range ¹³C-HSQC spectra. These scalar couplings (~5–7 Hz) were measured in a sample of uniformly ¹³C/¹⁵N-labeled BcX using a quantitative ¹³C/¹⁵N-filtered spin-echo difference experiment. In a similar approach, the threonine and serine hydroxyl hydrogen exchange kinetics were measured using a ¹³C/¹⁵N-filtered CLEANEX-PM pulse sequence. Collectively, these experiments provide insights into the structural and dynamic properties of several serine and threonine hydroxyls within this model protein.     

Structure and localization of an essential transmembrane segment of the proton translocation channel of yeast H-V-ATPase

Vacuolar (H⁺)-ATPase (V-ATPase) is a proton pump present in several compartments of eukaryotic cells to regulate physiological processes. From biochemical studies it is known that the interaction between arginine 735 present in the seventh transmembrane (TM7) segment from subunit a and specific glutamic acid residues in the subunit c assembly plays an essential role in proton translocation. To provide more detailed structural information about this protein domain, a peptide resembling TM7 (denoted peptide MTM7) from Saccharomyces cerevisiae (yeast) V-ATPase was synthesized and dissolved in two membrane-mimicking solvents: DMSO and SDS. For the first time the secondary structure of the putative TM7 segment from subunit a is obtained by the combined use of CD and NMR spectroscopy. SDS micelles reveal an α-helical conformation for peptide MTM7 and in DMSO three α-helical regions are identified by 2D ¹H-NMR. Based on these conformational findings a new structural model is proposed for the putative TM7 in its natural environment. It is composed of 32 amino acid residues that span the membrane in an α-helical conformation. It starts at the cytoplasmic side at residue T719 and ends at the luminal side at residue W751. Both the luminal and cytoplasmatic regions of TM7 are stabilized by the neighboring hydrophobic transmembrane segments of subunit a and the subunit c assembly from V-ATPase.     

A high-resolution 1H-NMR investigation of the histidine-binding protein J of Salmonella Typhimurium: Substrate-induced conformational changes

High-resolution ¹ H-NMR spectroscopy at 600 MHz has been used to investigate the conformational transitions of the histidine-binding protein J of Salmonella Typhinmrium in solution as a function of pH and of l-histidine concentration. The dissociation constant for the binding of l-histidine to histidine-binding protein J increases from 6.0 × 10^?8 to 5.1 × 10^?7 M in going from pH 5.57 to 8.00. The conformation of this protein as observed by ¹H-NMR also changes over this range of pH. However, when l-histidine is bound, the changes in conformation with pH are much smaller. Also, the pk for the single histidyl residue in histidine-binding protein J changes from 6.75 in the absence of l-histidine to 6.52 when l-histidine is bound. Earlier work in this laboratory resulted in the identification of several proton resonances believed to be at or near the l-histidine-binding site. Two of these resonances have been assigned to a tyrosine and the single histidyl residue in the histidine-binding protein J molecule.     

The use of two-dimensional correlated spectroscopy to obtain new assignments in the high-resolution 1H nuclear magnetic resonance spectrum of the biantennary complex oligosaccharide isolated from human serum transferrin by hydrazinolysis

The asialo biantennary complex type oligosaccharide from human serum transffrrin was isolated by hydrazinolysis, a method which results in the quantitative release of the intact oligosaccharide free of all amino acids. The ¹H-NMR chemical shifts of the previously assigned anomeric and H-2 protons from the peripheral residues of the glycopeptide are identical to the corresponding values for the reduced oligosaccharide. The chemical shift of GlcNAc-1 H-1 proton in the reduced oligosaccharide was assigned by selective deuteration. Proton J connectivities were determined using two-dimensional ¹H-¹H correlated high resolution NMR spectroscopy. Twelve new assignments were made within the central envelope of the NMR spectrum and a further six were tentatively proposed. The ability to assign proton resonances in this way should allow further conformational studies of the oligosaccharide using nuclear Overhauser effects between the relevant assigned protons on different saccharide residues (Homans, S.W., Dwek, R.A., Fernandes, D.L. and Rademacher, T.W. (1982) FEBS Lett. 150, 503–506).     

Determination of iduronic acid and glucuronic acid in sulfated chondroitin/dermatan hybrid chains by <Superscript>1</Superscript>H-nuclear magnetic resonance spectroscopy

The relative proportion of L-iduronic acid (IdoA) and D-glucuronic acid (GlcA) is of great importance for the structure–function relationship of chondroitin sulfate (CS)/dermatan sulfate (DS). However, determination of the isotypes of uronic acid residues in CS/DS is still a challenge, due to the instability of free uronic acid released by chemical degradation and its conversion to unsaturated uronic acid by digestion with bacterial eliminase. ¹H-Nuclear magnetic resonance (NMR) spectroscopy is a promising tool with which to address this issue, but the traditional method based on the assignment of the ring proton signals of IdoA and GlcA residues still has drawbacks such as the serious overlap of signals in the ¹H-NMR spectrum of CS/DS polysaccharides. We found that the proton signals of the N-acetyl group of N-acetyl-D-galactosamines in CS and DS could be clearly distinguished and accurately integrated in the one-dimensional (1D) ¹H-NMR spectrum. Based on this finding, here we report a novel, sensitive, and nondestructive 1D ¹H-NMR-based method to determine the proportion of IdoA and GlcA residues in CS/DS hybrid chains. The contributions of Fuchuan Li and Shuhei Yamada should be considered equal.     

Determination of three-dimensional solution structure of waglerin I,a toxin from Trimeresurus wagleri,using 2D-NMR and molecular dynamics simulation

The solution conformation of a synthetic snake venom toxin waglerin I, has been determined by using proton nuclear magnetic resonance spectroscopy. By y a combination of various two-dimensional NMR techniques, the ¹H-NMR spectrum of waglerin I was completely assigned. A set of 247 interproton distance restraints was derived from nuclear Overhauser enhancement (NOE) measurements. These NOE constraints, in addition to the 2 dihedral angle restraints (from coupling constant measurements) and 7 ω torsion angle restraints for prolines, formed the basis of three-dimensional structure determined by molecular dynamics techniques. The 19 structures that were obtained satisfy the experimental restraints, and display small deviation from idealized covalent geometry. Analysis of converged structures indicates that the toxin has no special secondary structure. In the solution structure of waglerin I, the central ring region is well defined but the N- and C-termini possesses more disorder.     

Application of BATMAN and BAYESIL for quantitative <Superscript>1</Superscript>H-NMR based metabolomics of urine: discriminant analysis of lean,obese, and obese-diabetic rats

Introduction

BATMAN and BAYESIL are software tools, which can provide a solution for automated metabolite quantifications based on the proton nuclear magnetic resonance (¹H-NMR) spectral data of bio-fluids. However, their specific application for the quantitative ¹H-NMR based metabolomics of urine has not been investigated.

Objectives

The aim of this study is to evaluate the performance of BATMAN and BAYESIL in the quantitative metabolite analysis of urine based on its ¹H-NMR spectra.

Methods

BATMAN and BAYESIL were used for automated metabolite quantification based on the ¹H-NMR spectra of the urine from the lean, obese and obese-diabetic rat groups. PLS-DA model was used to discriminate the three different groups based on the results from the quantifications.

Results

BATMAN was found to be superior to BAYESIL in identifying and quantifying the metabolites in the urine samples, owing to its flexibility that allows users to define and adjust the relevant signals of the pure standard metabolites in the database in order to fit the signals in the samples, a necessary step since variations and peak shift are natural in most ¹H-NMR spectra. The results of BATMAN also agreed well with that of the manual deconvolution method, which indicated the higher accuracy in metabolite quantification, despite the need of pre-processing and longer processing time than BAYESIL. However, in the case where the problems in baseline correction and peak shift of ¹H-NMR spectra are absent, the use of BAYESIL is more advantageous. Application of quantitative ¹H-NMR based metabolomics of the urine showed that PLS-DA model derived from BATMAN could satisfactorily discriminate the lean, obese, and obese-diabetic rat groups.

Conclusion

Both BATMAN and BAYESIL are useful for the quantitative automation of urine metabolites based on its ¹H-NMR spectra. The results from BATMAN method is superior to BAYESIL but require expertise in spectroscopy and longer computer time. Both methods help in simplifying the interpretation of metabolite status in the VIP analysis.

     

Structure of the Ring Cleavage Product of 1-Hydroxy-2-Naphthoate, an Intermediate of the Phenanthrene-Degradative Pathway of Nocardioides sp. Strain KP7

1-Hydroxy-2-naphthoate (compound I) is a metabolite of the phenanthrene-degradative pathway in Nocardioides sp. strain KP7. This singly hydroxylated aromatic compound is cleaved by 1-hydroxy-2-naphthoate dioxygenase. In this study, the structure of the ring cleavage product generated by the action of homogeneous 1-hydroxy-2-naphthoate dioxygenase was determined upon separation by high-performance liquid chromatography at pH 2.5 by using nuclear magnetic resonance (NMR) and mass spectroscopic techniques. The ring cleavage product at this pH existed in equilibrium between two forms, 2-oxo-3-(3-oxo-1,3-dihydro-1-isobenzofuranyl)propanoate (compound III) and 2,2-dihydroxy-3-(3-oxo-1,3-dihydro-1-isobenzofuranyl)propanoate (compound IV). After the pH of the solution was raised to 7.5, the structure of the major species became (E)-4-(2-carboxylatophenyl)-2-oxo-3-butenoate (compound II; common name, trans-2′-carboxybenzalpyruvate), which was in equilibrium with compound III. Direct monitoring of the enzymatic formation of the ring cleavage product by ¹H-NMR in a deuterated potassium phosphate buffer (pH 7.5) detected only compound II as a product, and the proton on carbon 3 of compound II was not exchanged with deuterium. Thus, compound II is likely to be the first stable product of dioxygenation of 1-hydroxy-2-naphthoate.     

Segment TM7 from the cytoplasmic hemi-channel from VO-H-V-ATPase includes a flexible region that has a potential role in proton translocation

A 900-MHz NMR study is reported of peptide sMTM7 that mimics the cytoplasmic proton hemi-channel domain of the seventh transmembrane segment (TM7) from subunit a of H⁺-V-ATPase from Saccharomyces cerevisiae. The peptide encompasses the amino acid residues known to actively participate in proton translocation. In addition, peptide sMTM7 contains the amino acid residues that upon mutation cause V-ATPase to become resistant against the inhibitor bafilomycin. 2D TOCSY and NOESY ¹H-¹H NMR spectra are obtained of sMTM7 dissolved in d₆-DMSO and are used to calculate the three-dimensional structure of the peptide. The NMR-based structures and corresponding dynamical features of peptide sMTM7 show that sMTM7 is composed of two α-helical regions. These regions are separated by a flexible hinge of two residues. The hinge acts as a ball-and-joint socket and both helical segments move independently with respect to one another. This movement in TM7 is suggested to cause the opening and closing of the cytoplasmic proton hemi-channel and enables proton translocation.     

Synthesis and photophysical investigation of Schiff base as a Mg2+ and Zn2+ fluorescent chemosensor and its application

In view of the fluorescent switching properties and anti-fatigue properties of diarylethene, a diarylethene fluorescent chemosensor for the immediate detection of zinc ion (Zn²⁺) and magnesium ion (Mg²⁺) in acetonitrile was synthesized in this article. The structure of 1o was determined by performing spectroscopy and elemental analysis. The presence of Zn²⁺ or Mg²⁺ made the chemosensor 1o show an obvious “turn-on” fluorescent signal (bright yellow-green for Mg²⁺ and bright cyan for Zn²⁺). The fluorescent change caused by the 1:1 binding of 1o and Zn²⁺ or Mg²⁺ might be due to hindering the excited-state intramolecular proton transfer (ESIPT) process, which were bolstered by Benesi–Hildebrand analysis, Job's plot curves, proton nuclear magnetic resonance (¹H-NMR) titration and mass spectrometry. The limits of detection were acquired from the standard curve plots for Mg²⁺ at 44.6 nM and for Zn²⁺ at 14 nM. Based on the fluorescent behaviors, a logic gate was constructed with the emission intensity at 528/518 nm as output signal, the ultraviolet-visible (UV-vis) lights, Mg²⁺/Zn²⁺ and EDTA as input signals. Exogenous Zn²⁺ and Mg²⁺ fluorescent bioimaging were performed on Hela cells with 1o , indicating its potential application in biodiagnostic analysis. In particular, 1o was manufactured into test paper, and Zn²⁺ or Mg²⁺ can be conveniently, efficiently and qualitatively identified by the fluorescent color variation of the test strips.     

NMR solution structure of gramicidin A complex with caesium cations

The conformation of the 1:1 complex of [Val¹] gramicidin A with caesium cations has been determined in methanol/chloroform (1:1) solution by 2-dimensional ¹H-NMR spectroscopy. The molecular structure was found to be a right-handed antiparallel double helical dimer ↑↓ππ_LD^7.2 with 7.2 residues per turn, which incorporates two caesium cations.     

Proton NMR visible mobile lipid signals in sensitive and multidrug-resistant K562 cells are modulated by rafts

Background  

Most cancer cells are characterized by mobile lipids visible on proton NMR (¹H-NMR), these being comprised mainly of methyl and methylene signals from lipid acyl chains. Erythroleukemia K562 cells show narrow signals at 1.3 and 0.9 ppm, corresponding to mobile lipids (methylene and methyl, respectively), which are reduced when K562 cells are multidrug resistant (MDR). While the significance of the mobile lipids is unknown, their subcellular localization is still a matter of debate and may lie in the membrane or the cytoplasm. In this study, we investigate the role of cholesterol in the generation of mobile lipid signals.     

Extracellular polysaccharides of cowpea rhizobia: compositional and functional studies

Polysaccharides excreted by cowpea Rhizobium strains JLn(c) and RA-1 were mixtures of complex acidic exopolysaccharides and low molecular weight neutral glucans. These polymers were fractionated using gel filtration chromatography. Purified fractions of the acidic heteropolymer reacted with peanut agglutinin to give precipitin bands when subjected to Ouchterlony gel diffusion. The acidic exopolysaccharide was found to contain mainly glucose, galactose, glucuronic acid, mannose and fucose. The non-carbohydrate substituents of the acidic heteropolymer were pyruvate, acetate and uronate which were identified by infrared and proton nuclear magnetic resonance spectroscopy as well as by chemical analysis.Abbreviations EPS Extracellular polysaccharide - YEM yeast extract mannitol - PNA peanut agglutination - ¹H-NMR proton nuclear magnetic resonance     

Structural properties of a peptide derived from H-V-ATPase subunit a

The 3D structure of a peptide derived from the putative transmembrane segment 7 (TM7) of subunit a from H⁺-V-ATPase from Saccharomyces cerevisiae has been determined by solution state NMR in SDS. A stable helix is formed from L736 up to and including Q745, the lumenal half of the putative TM7. The helical region extends well beyond A738, as was previously suggested based on NMR studies of a similar peptide in DMSO. The pKa of both histidine residues that are important for proton transport was measured in water and in SDS. The differences that are found demonstrate that the histidine residues interact with the SDS polar heads. In detergent, circular dichroism data indicate that the secondary structure of the peptide depends on the pH and the type of detergent used. Using solid-state NMR, it is shown that the peptide is immobile in phospholipid bilayers, which means that it is probably not a single transmembrane helix in these samples. The environment is important for the structure of TM7, so in subunit a it is probably held in place by the other transmembrane helices of this subunit.     

Morpholine Degradation Pathway of Mycobacterium aurum MO1: Direct Evidence of Intermediates by In Situ 1H Nuclear Magnetic Resonance

Resting Mycobacterium aurum MO1 cells were incubated with morpholine, a waste from the chemical industry. The kinetics of biodegradation was monitored by using in situ nuclear magnetic resonance (NMR). The incubation medium was directly analyzed by ¹H NMR. This technique allowed the unambiguous identification of two intermediates of the metabolic pathway involved in the biodegradation process, glycolate and 2-(2-aminoethoxy)acetate. The latter compound, which was not commercially available, was synthesized, in three steps, from 2-(2-aminoethoxy)ethanol. Quantitative analysis of the kinetics of degradation of morpholine was performed by integrating the signals of the different metabolites in ¹H-NMR spectra. Morpholine was degraded within 10 h. The intermediates increased during the first 10 h and finally disappeared after 20 h incubation. Assays of degradation were also carried out with glycolate and ethanolamine, hypothetical intermediates of the morpholine degradation pathway. They were degraded within 4 and 8 h, respectively. Until now, no tool for direct detection of intermediates or even morpholine has been available, consequently, only hypothetical pathways have been proposed. The approach described here gives both qualitative and quantitative information about the metabolic routes used in morpholine degradation by M. aurum MO1. It could be used to investigate many biodegradative processes.     

Identification of Thr29 as a Critical Phosphorylation Site That Activates the Human Proton Channel Hvcn1 in Leukocytes

Voltage-gated proton channels and NADPH oxidase function cooperatively in phagocytes during the respiratory burst, when reactive oxygen species are produced to kill microbial invaders. Agents that activate NADPH oxidase also enhance proton channel gating profoundly, facilitating its roles in charge compensation and pH_i regulation. The “enhanced gating mode” appears to reflect protein kinase C (PKC) phosphorylation. Here we examine two candidates for PKC-δ phosphorylation sites in the human voltage-gated proton channel, H_V1 (Hvcn1), Thr²⁹ and Ser⁹⁷, both in the intracellular N terminus. Channel phosphorylation was reduced in single mutants S97A or T29A, and further in the double mutant T29A/S97A, by an in vitro kinase assay with PKC-δ. Enhanced gating was evaluated by expressing wild-type (WT) or mutant H_V1 channels in LK35.2 cells, a B cell hybridoma. Stimulation by phorbol myristate acetate enhanced WT channel gating, and this effect was reversed by treatment with the PKC inhibitor GF109203X. The single mutant T29A or double mutant T29A/S97A failed to respond to phorbol myristate acetate or GF109203X. In contrast, the S97A mutant responded like cells transfected with WT H_V1. We conclude that under these conditions, direct phosphorylation of the proton channel molecule at Thr²⁹ is primarily responsible for the enhancement of proton channel gating. This phosphorylation is crucial to activation of the proton conductance during the respiratory burst in phagocytes.     

Anaerobic C1 Metabolism of the O-Methyl-14C-Labeled Substituent of Vanillate

The O-methyl substituents of aromatic compounds constitute a C₁ growth substrate for a number of taxonomically diverse anaerobic acetogens. In this study, strain TH-001, an O-demethylating obligate anaerobe, was chosen to represent this physiological group, and the carbon flow when cells were grown on O-methyl substituents as a C₁ substrate was determined by ¹⁴C radiotracer techniques. O-[methyl-¹⁴C]vanillate (4-hydroxy-3-methoxy-benzoate) was used as the labeled C₁ substrate. The data showed that for every O-methyl carbon converted to [¹⁴C]acetate, two were oxidized to ¹⁴CO₂. Quantitation of the carbon recovered in the two products, acetate and CO₂, indicated that acetate was formed in part by the fixation of unlabeled CO₂. The specific activity of ¹⁴C in acetate was 70% of that in the O-methyl substrate, suggesting that only one carbon of acetate was derived from the O-methyl group. Thus, it is postulated that the carboxyl carbon of the product acetate is derived from CO₂ and the methyl carbon is derived from the O-methyl substituent of vanillate. The metabolism of O-[methyl-¹⁴C]vanillate by strain TH-001 can be described as follows: 3¹⁴CH₃OC₇H₅O₃ + CO₂ + 4H₂O → ¹⁴CH₃COOH + 2¹⁴CO₂ + 10H⁺ + 10e^- + 3HOC₇H₅O₃.     

Structural investigation of the capsular polysaccharide from Klebsiella serotype K-34 and its characterization by N.M.R. spectroscopy

The repeating unit of the capsular polysaccharide from Klebsiella type K-34 has been established by methylation, partial hydrolysis, and Smith degradation to consist of a hexasaccharide repeating-unit built up of four l-rhamnose, one d-glucose, and one d-galacturonic acid residues. The anomeric configurations of the linkages was determined by proton and ¹³C-n.m.r. spectroscopy at each step of the degradation procedures. Further evidence for the configurations of the glycosidic linkages involved the use of proton T₁ relaxation-times and oxidation by chromium trioxide. The data allowed assignment of the following structure for the repeating unit:     

New ursane-type triterpenes from the root bark of Calotropis procera

As a part of our continuing interest in identifying anticancer drug leads from natural sources, we have investigated the in vitro growth inhibitory effects of the hexane fraction of the root bark of Calotropis procera (Ait) R. Br. (Asclepiadaceae). This study reports the isolation and structure elucidation of four new ursane-type triterpenes named calotroprocerol A (1), calotroproceryl acetate A (2), calotroprocerone A (3) and calotroproceryl acetate B (4) in addition to five known compounds including pseudo-taraxasterol acetate (5), taraxasterol (6), calotropursenyl acetate B (7), stigmasterol (8) and (E)-octadec-7-enoic acid (9). Their structures were established on the basis of 1D and 2D NMR studies (¹H–¹H COSY, HSQC, and HMBC) and HRMS spectral data. The in vitro growth inhibitory activity of the isolated compounds was evaluated against three human cancer cell lines including the A549 non-small cell lung cancer (NSCLC), the U373 glioblastoma (GBM) and the PC-3 prostate cancer cell lines.     

An Arabidopsis mutant deficient in sterol biosynthesis: heterologous complementation by ERG 3 encoding a Δ7-sterol-C-5-desaturase from yeast

The mutant STE 1 was isolated by screening an ethylmethane sulfonate (EMS)-mutagenized population of Arabidopsis thaliana which consisted of 22 000 M₂ plants divided into 1100 pools of 20 plants by gas chromatography of sterols extracted from small leaf samples. STE 1 was characterized by the accumulation of three Δ⁷-sterols concomitantly with the decrease of the three corresponding Δ⁵-sterols which are the end products of the sterol pathway in wild-type leaves. The structure of these Δ⁷-sterols was determined after two steps of purification on HPLC, by gas chromatography coupled with mass spectrometry (GC-MS) and proton nuclear magnetic resonance spectrometry (¹H-NMR). The accumulation of Δ⁷-sterols suggested that the mutant is deficient in the activity of the Δ⁷-sterol-C-5-desaturase. Genetic analysis showed that the accumulation of Δ⁷-sterols was due to a single recessive nuclear mutation. The mutant line STE 1 was backcrossed four times to the wild-type. The resulting STE 1 plants had wild-type morphology and set seeds normally, suggesting that the Δ⁷-sterols in STE 1 are good surrogates of physiologically active Δ⁵-sterols to sustain normal development. STE 1 roots were transformed with the Saccharomyces cerevisiae ERG 3 gene encoding the Δ⁷-sterol-C-5-desaturase under the control of the CaMV 35S promoter. Seven transgenic STE 1 root-derived calli showed an increase in Δ⁵-sterols and a concomitant decrease in Δ⁷-sterols in comparison with STE 1 untransformed root-derived calli. Northern blot analysis using the ERG 3 probe showed a strong expression of ERG 3 in three of the seven transgenic calli. These results suggest that the accumulation of Δ⁷-sterols in the STE 1 mutant is due to a deficiency of the Δ⁷-sterol-C-5-desaturation step in the plant sterol biosynthesis pathway.