Correlation NMR Spectroscopy Research Articles

Kinetic Control of Thiamin Diphosphate Activation in Enzymes Studied by Proton−Nitrogen Correlated NMR Spectroscopy

Proton-nitrogen correlated NMR studies were performed on thiamin diphosphate, which has been specifically labeled with (15)N at the 4'-amino group. After reconstitution of the labeled coenzyme with the apoenzymes of both wild-type pyruvate decarboxylase from Zymomonas mobilis and the E50Q variant, a high-field shift of the (15)N signal of approximately 4 ppm is observed at pH 5.9 when compared to that of the free coenzyme, indicating a higher electron density at the 4'-amino nitrogen in the enzyme-bound state. The pH dependence of the chemical shift of the (15)N signals in the (1)H-(15)N heteronuclear single-quantum coherence NMR spectra reveals typical titration curves for the free as well as the reconstituted coenzyme with nearly identical chemical shift end points. The midpoints of the transitions are at pH 5.3 and 5.0 for the free and enzyme-bound coenzyme, respectively. We conclude that the tremendous rate acceleration of C2-H deprotonation in ThDP enzymes is mainly the result of the enforced V conformation of the cofactor in the active site being perfectly suited to allowing intramolecular acid-base catalysis.

The preparation and analysis of fluoro-polyphosphates by 19F, 31P, 2D 19F– 31P HETCOR and 2D 31P– 31P COSY NMR

A complex mixture of fluoro-polyphosphates (FPPs) and polyphosphates was prepared by heating a mixture of NaF and sodium tripolyphosphate (STPP) at 600 °C in nitrogen atmosphere. Two-dimensional 31P– 19F heteronuclear correlation spectroscopy (HETCOR) NMR was developed in identifying the atomic connection between F and P in the mixed FPPs. 19F, 31P and 31P– 31P correlation spectroscopy (COSY) NMR methods were employed to identify the components of the mixture and measure the chain length of each FPP ingredient. NMR results clearly demonstrated that the mixture contains four kinds of fluoro-phosphates with different chain length of polyphosphate, which are monofluoro-phosphate (MFP), monofluoro-dipolyphosphate (MFDPP), monofluoro-tripolyphosphate (MFTPP) and difluoro-tripolyphosphate (DFTPP). Other phosphates and polyphosphates also were found in the mixture.

Comparison of cell‐based and cell‐free protocols for producing target proteins from theArabidopsis thalianagenome for structural studies

We describe a comparative study of protein production from 96 Arabidopsis thaliana open reading frames (ORFs) by cell-based and cell-free protocols. Each target was carried through four pipeline protocols used by the Center for Eukaryotic Structural Genomics (CESG), one for the production of unlabeled protein to be used in crystallization trials and three for the production of 15N-labeled proteins to be analyzed by 1H-15N NMR correlation spectroscopy. Two of the protocols involved Escherichia coli cell-based and two involved wheat germ cell-free technology. The progress of each target through each of the protocols was followed with all failures and successes noted. Failures were of the following types: ORF not cloned, protein not expressed, low protein yield, no cleavage of fusion protein, insoluble protein, protein not purified, NMR sample too dilute. Those targets that reached the goal of analysis by 1H-15N NMR correlation spectroscopy were scored as HSQC+ (protein folded and suitable for NMR structural analysis), HSQC+/- (protein partially disordered or not in a single stable conformational state), HSQC- (protein unfolded, misfolded, or aggregated and thus unsuitable for NMR structural analysis). Targets were also scored as X- for failing to crystallize and X+ for successful crystallization. The results constitute a rich database for understanding differences between targets and protocols. In general, the wheat germ cell-free platform offers the advantage of greater genome coverage for NMR-based structural proteomics whereas the E. coli platform when successful yields more protein, as currently needed for crystallization trials for X-ray structure determination.

Synthesis of novel copoly(ether ether ketones): Property evaluation and microstructure analysis by NMR

AbstractA series of copolymers were prepared by the reaction of various bisphenols with a 50:50 molar ratio of two bisfluoro compounds, 4,4′‐bis(1‐fluoro‐2‐trifluoromethyl benzyl) benzene and 4,4′‐difluorobenzophenone. The synthesized polymers were well characterized for their thermal, mechanical, and electrical performances. The copolymers showed a better set of properties than their analogous homopolymers derived from 4,4′‐bis(1‐fluoro‐2‐trifluoromethyl benzyl) benzene and bisphenols. The microstructures of the copolymers were analyzed by 1H‐, 13C‐, 19F‐, distortionless enhancement by polarization transfer 90, two‐dimensional 1H–1H homonuclear correlation spectroscopy, and 13C–1H correlation spectroscopy NMR techniques. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 1292–1305, 2005

Selective Chemical Shift Assignment of B800 and B850 Bacteriochlorophylls in Uniformly [13C,15N]-Labeled Light-Harvesting Complexes by Solid-State NMR Spectroscopy at Ultra-High Magnetic Field

The electronic ground states of the bacteriochlorophyll a type B800 and type B850 in the light-harvesting 2 complex of Rhodopseudomonas acidophila strain 10050 have been characterized by magic angle spinning (MAS) dipolar (13)C-(13)C correlation NMR spectroscopy. Uniformly [(13)C,(15)N] enriched light-harvesting 2 (LH2) complexes were prepared biosynthetically, while [(13)C,(15)N]-B800 LH2 complexes were obtained after reconstitution of apoprotein with uniformly [(13)C,(15)N]-enriched bacteriochlorophyll cofactors. Extensive sets of isotropic (13)C NMR chemical shifts were obtained for each bacteriochlorin ring species in the LH2 protein. (13)C isotropic shifts in the protein have been compared to the corresponding shifts of monomeric BChl a dissolved in acetone-d(6). Density functional theory calculations were performed to estimate ring current effects induced by adjacent cofactors. By correction for the ring current shifts, the (13)C shift effects due to the interactions with the protein matrix were resolved. The chemical shift changes provide a clear evidence for a global electronic effect on the B800 and B850 macrocycles, which is attributed to the dielectrics of the protein environment, in contrast with local effects due to interaction with specific amino acid residues. Considerable shifts of -6.2 < Deltasigma < +5.8 ppm are detected for (13)C nuclei in both the B800 and the B850 bacteriochlorin rings. Because the shift effects for the B800 and B850 are similar, the polarization of the electronic ground states induced by the protein environment is comparable for both cofactors and corresponds with a red shift of approximately 30 nm relative to the monomeric BChl dissolved in acetone-d(6). The electronic coupling between the B850 cofactors due to macrocycle overlap is the predominant mechanism behind the additional red shift in the B850.

Demonstration of co-polymerization in melamine–urea–formaldehyde reactions using 15N NMR correlation spectroscopy

Melamine–urea–formaldehyde resins are very important commercially, yet little is known about their structures, and the techniques that have been available to examine this are quite limited. In this manuscript we describe the use of 1H– 15N HMQC NMR spectroscopy and the development of a doubly-selective 1H– 15N– 13C CP INEPT NMR experiment, to establish for the first time that melamine and urea co-polymerize with formaldehyde and to identify the 1H, 15N and 13C chemical shifts of the bridging units. This methodology makes it possible to examine co-condensation in industrial preparations of melamine–urea–formaldehyde resins, in order to correlate structure and function and optimize the manufacturing process.

A solid-state NMR application of the anomeric effect in carbohydrates: galactosamine, glucosamine, and N-acetyl-glucosamine

Simple 2D 13C/ 15N heteronuclear correlation solid-state NMR spectroscopy was implemented to resolve the 15N resonances of the α and β anomers of three amino monosaccharides: galactosamine (GalN), glucosamine hydrochloride (GlcN), and N-acetyl-glucosamine (GlcNAc) labeled specifically with 13C 1/ 15N spin pairs. Although the 15N resonances could not be distinguished in normal 1D spectra, they were well resolved in 2D double CP/MAS correlation spectra by taking advantage of the 13C spectral resolution. The α and β resonances shifted apart by 3–5 ppm in their 13C chemical shifts, and differed by 1–2 ppm in the extended 15N dimension. Aside from this, the detection of other 13C/ 15N correlations over short distances was also achieved arising from the C 2, C 3 and CO carbons present in natural abundance. 2D double CP/MAS chemical shift correlation NMR spectroscopy is a simple and powerful technique to characterize the anomeric effect of amino monosaccharides. Applications of the 2D method reveal well-resolved 15N and 13C chemical shifts might be useful for structural determination on carbohydrates of biological significance, such as glycopeptide or glycolipids.

N-Chloroacyl-6-O-triphenylmethylchitosans: Useful Intermediates for Synthetic Modifications of Chitosan

An efficient synthetic route was developed for the mild chloroacylation of chitosan with different chloroacyl chlorides. Full N-chloroacylation was obtained with this procedure without any O-acylation, and products having lower degrees of substitution can also be produced. Organo-soluble 6-O-triphenylmethylchitosan was used as a starting material for the acylation reactions. The resulting N-chloroacyl-6-O-triphenylmethylchitosan intermediates were also organo-soluble and characterized by FT-IR. N-Methylpiperazine moieties were attached to make end products that were sufficiently soluble for characterization by NMR and also to prove that the present intermediates could be used for further modifications. The end products were fully characterized by 1H NMR, 13C NMR, and 2D 1H-13C heteronuclear single-quantum correlation NMR spectroscopy. The degrees of substitution were determined by 1H NMR. Molecular weight determination by GPC-LS displayed a significant degradation of the polymer. The weight-average molar masses (M(w)) of the end products ranged from 29.6 to 49.4 kDa, when the M(w) of the starting material was 144.2 kDa.

Biosynthetic site-specific 13 C labeling of the light-harvesting 2 protein complex: A model for solid state NMR structure determination of transmembrane proteins

Partly biosynthetic site-directed isotopically (13)C enriched photosynthetic light-harvesting 2(LH2) complexes have been prepared from Rhodopseudomonas acidophila strain 10050 by using chemically labeled [1,2,3,4-(13)C], [1,4-(13)C] and [2,3-(13)C] succinic acid as a precursor in the growth medium. Two-dimensional proton driven spin diffusion (PDSD) solid state NMR correlation spectroscopy has been used to trace each individual (13)C isotope from the labeled succinic acid precursor to its destination into the protein and into the embedded major light-absorbing bacteriochlorophyll cofactors. For both the residues of the protein and for the cofactors distinct labeling patterns have been deduced, for protein complexes prepared from [1,4-(13)C]-succinic acid or [2,3-(13)C]-succinic labeled media. All residues, except isoleucine and leucine, have been labeled almost homogeneously by the succinic acid precursor. Carbonyl carbons in the protein backbone were labeled by [1,4-(13)C]-succinic acid, while the Calpha and Cbeta carbons of the residues were labeled by [2,3 (13)C]-succinic acid. Leucine and isoleucine residues were labeled using a uniformly labeled amino acid mixture in the medium. The pattern labeling yields an increase of the resolution and less spectral crowding. The partial labeling technique in combination with conventional solid state NMR methods at ultra high magnetic fields provides an attractive route to resolve chemical shifts for alpha-helical transmembrane protein structures.

Trans-β-Nitrostyrene Derivatives as Slow-Binding Inhibitors of Protein Tyrosine Phosphatases

Protein tyrosine phosphatases (PTPs) catalyze the hydrolysis of phosphotyrosyl (pY) proteins to produce tyrosyl proteins and inorganic phosphate. Specific PTPs inhibitors provide useful tools for studying PTP function in signal transduction processes and potential treatment for human diseases such as diabetes, inflammation, and cancer. In this work, trans-beta-nitrostyrene (TBNS) and its derivatives are found to be slow-binding inhibitors against protein tyrosine phosphatases PTP1B, SHP-1, and Yop with moderate potencies (K(I*) = 1-10 microM). Competition experiments with a substrate (pNPP) and iodoacetate indicate that TBNS is active site-directed. The mechanism of inhibition was investigated by UV-vis absorption spectroscopy, (1)H-(13)C heteronuclear single-quantum correlation NMR spectroscopy, and site-directed mutagenesis. These studies suggested a mechanism in which TBNS acts a pY mimetic and binds to the PTP active site to form an initial noncovalent E.I complex, followed by nucleophilic attack on the TBNS nitro group by Cys-215 of PTP1B to form a reversible, covalent adduct as the tighter E.I* complex. TBNS derivatives represent a new class of neutral pY mimetic inhibitors of PTPs.

Well-Defined Glycopolymers from RAFT Polymerization: Poly(methyl 6-O-methacryloyl-α-d-glucoside) and Its Block Copolymer with 2-Hydroxyethyl Methacrylate

The glycomonomer methyl 6-O-methacryloyl-α-d-glucoside was prepared by lipase-catalyzed transesterification of vinyl methacrylate with methyl α-d-glucoside in dry acetonitrile. The desired 6-O regioisomer was obtained in good yield and its structure confirmed by 1H−1H and 1H−13C correlation NMR spectroscopy. Reversible addition−fragmentation chain transfer (RAFT) polymerization of the unprotected monomer was performed directly in aqueous solution using (4-cyanopentanoic acid)-4-dithiobenzoate as the chain transfer agent to give poly(methyl 6-O-methacryloyl-α-d-glucoside) with Mn between 16 and 103 kDa (1H NMR) and polydispersities as low as 1.10. Chain extension of one of these polymers with 2-hydroxyethyl methacrylate afforded the novel hydrophilic−hydrophilic block copolymer poly[(methyl 6-O-methacryloyl-α-d-glucoside)-block-(2-hydroxyethyl methacrylate)].

Delignification mechanism during high-boiling solvent pulping. Part 6: Changes in lignin structure analyzed by 1H-13C correlation 2-D NMR spectroscopy

Abstract In order to investigate the delignification mechanism during high-boiling solvent (HBS) pulping, softwood HBS lignin samples from todo fir (Abies sachalinensis) were analyzed by 1H–13C correlation NMR spectroscopy (HMQC). Nine lignin model compounds that may represent the substructures in HBS lignin were prepared. The 1H and 13C NMR spectral data were compared with HBS lignin samples. The HMQC spectra of HBS lignin samples showed the disappearance of β-O-4 structures. Introduction of a pulping solvent into lignin was plainly observed with new signals in aliphatic regions. Only the erythro β-1 structure was detected in softwood milled wood lignin from todo fir by HMQC spectra. The β-1 structure was very reactive and probably produced the stilbene structure. The β-β and β-5 structures remained in HBS lignin. The 4-O-5 structure was successfully detected by HMQC spectra, and it was found to be stable under the conditions used.

High resolution heteronuclear correlation NMR spectroscopy between quadrupolar nuclei and protons in the solid state

A high resolution two-dimensional solid state NMR experiment is presented that correlates half-integer quadrupolar spins with protons. In this experiment the quadrupolar nuclei evolve during t 1 under a split-t1, FAM-enhanced MQMAS pulse scheme. After each t 1 period ending at the MQMAS echo position, single quantum magnetization is transferred, via a cross polarization process in the mixing time, from the quadrupolar nuclei to the protons. High-resolution proton signals are then detected in the t 2 time domain during wPMLG5* homonuclear decoupling. The experiment has been demonstrated on a powder sample of sodium citrate and 23Na– 1H 2D correlation spectra have been obtained. From the HETCOR spectra and the regular MQMAS spectrum, the three crystallographically inequivalent Na + sites in the asymmetric unit were assigned. This MQMAS- wPMLG HETCOR pulse sequence can be used for spectral editing of half-integer quadrupolar nuclei coupled to protons.

Synthesis and Study of Equilenin Derivatives and Modified Analogs

Modified equilenin analogs were synthesized with a view to examine the relation between the structure and biological properties of steroid estrogens. The 1H and 13C NMR signals of six estra-1,3,5,7,9-pentaenes were completely assigned using homo- and heteronuclear correlation NMR spectroscopy. The structure of equilenin methyl ester was determined by X-ray analysis. Among the synthesized steroids, compounds were found which exhibit hypocholesterinemic activity with no uterotropic and hypertriglyceridemic effects.

Structural analysis of cellulose triacetate polymorphs by two-dimensional solid-state 13C–13C and 1H–13C correlation NMR spectroscopies

Abstract For the elucidation of the crystal structures of the two crystalline allomorphs of cellulose triacetate (CTA), namely CTA I and CTA II, two-dimensional (2D) solid-state through-bond 13C–13C and 1H–13C correlations NMR techniques applied to the two crystalline allomorphs of CTA. As a result, the 13C and 1H chemical shifts of the glucopyranose ring of CTA I and CTA II were completely assigned by the 2D NMR spectra of these allomorphs. On the 2D 13C–13C correlation spectrum of CTA II, two sets of the 13C–13C correlations from C1 to C6 were observed. This indicated that the CP/MAS 13C NMR spectrum of CTA II can be characterized by its overlapping of the 13C subspectra of two kinds of 2,3,6-triacetyl-anhydroglucopyranose units and that there are two magnetically non-equivalent sites in the unit cell of CTA II. In the case of CTA I, the numbers of respective 13C and 1H shifts of CTA I agreed with the those of the glucopyranose residue in the allomorph, strongly suggesting that the asymmetric unit of CTA I is only one glucose residue. In addition, conformational differences in the exocyclic C5–C6 bonds between CTA I and CTA II were strongly suggested by the notable differences in the 1H and 13C chemical shifts at the C6 sites of these allomorphs.

Chemoenzymatic synthesis of narrow-polydispersity glycopolymers: poly(6-O-vinyladipoyl-D-glucopyranose).

The glycomonomer 6-O-vinyladipoyl-D-glucopyranose was prepared via lipase catalyzed transesterification of divinyladipate with alpha-D-glucopyranose in dry acetonitrile and acetone. The desired 6-O regioisomer was obtained in good yield, and its structure was confirmed by correlation NMR spectroscopy. Controlled radical polymerization of the unprotected monomer was performed in protic media using both xanthate and dithiocarbamate as chain transfer agents to give poly(6-O-vinyladipoyl-D-glucopyranose) with Mn of 17 and 19 kDa (SEC) respectively and a polydispersity as low as 1.10. To the best of our knowledge, this is the first example of a narrow-polydispersity, poly(vinyl ester)-like glycopolymer.

N-acetylated metabolites in urine: proton nuclear magnetic resonance spectroscopic study on patients with inborn errors of metabolism.

There is no comprehensive analytical technique to analyze N-acetylated metabolites in urine. Many of these compounds are involved in inborn errors of metabolism. In the present study, we examined the potential of proton nuclear magnetic resonance ((1)H-NMR) spectroscopy as a tool to identify and quantify N-acetylated metabolites in urine of patients with various inborn errors of metabolism. We performed (1)H-NMR spectroscopy on a 500 MHz spectrometer. Using a combination of one- and two-dimensional correlation spectroscopy (COSY) (1)H-NMR spectra, we were able to assign and quantify resonances of characteristic N-acetylated compounds products in urine of patients with 13 inborn errors of metabolism. The disease-specific N-acetylated metabolites were excreted at concentrations >100 micromol/mmol of creatinine in the patients' urine. In control urine samples, the concentration of individual N-acetyl-containing compounds was <40 micromol/mmol of creatinine. The combination of one- and two-dimensional COSY NMR spectroscopy led to the correct diagnosis of nine different inborn errors of metabolism. No abnormalities were observed in the spectra of urine from patients with G(M1)- or G(M2)-gangliosidosis. We also determined the (1)H-NMR characteristics of N-acetylated metabolites that may be relevant to human metabolism. (1)H-NMR spectroscopy may be used to identify and quantify N-acetylated metabolites of diagnostic importance for the field of inborn errors of metabolism.

In vivo transformations of dihydroartemisinic acid in Artemisia annua plants

[15- 13C 2H 3]-dihydroartemisinic acid ( 2a ) and [15-C 2H 3]-dihydroartemisinic acid ( 2b ) have been fed via the root to intact Artemisia annua plants and their transformations studied in vivo by one-dimensional 2H NMR spectroscopy and two-dimensional 13C– 2H correlation NMR spectroscopy ( 13C– 2H COSY). Labelled dihydroartemisinic acid was transformed into 16 12-carboxy-amorphane and cadinane sesquiterpenes within a few days in the aerial parts of A. annua, although transformations in the root were much slower and more limited. Fifteen of these 16 metabolites have been reported previously as natural products from A. annua. Evidence is presented that the first step in the transformation of dihydroartemisinic acid in vivo is the formation of allylic hydroperoxides by the reaction of molecular oxygen with the Δ 4,5-double bond in this compound. The origin of all 16 secondary metabolites might then be explained by the known further reactions of such hydroperoxides. The qualitative pattern for the transformations of dihydroartemisinic acid in vivo was essentially unaltered when a comparison was made between plants, which had been kept alive and plants which were allowed to die after feeding of the labelled precursor. This, coupled with the observation that the pattern of transformations of 2 in vivo demonstrated very close parallels with the spontaneous autoxidation chemistry for 2 , which we have recently demonstrated in vitro, has lead us to conclude that the main ‘metabolic route’ for dihydroartemisinic acid in A. annua involves its spontaneous autoxidation and the subsequent spontaneous reactions of allylic hydroperoxides which are derived from 2 . There may be no need to invoke the participation of enzymes in any of the later biogenetic steps leading to all 16 of the labelled 11,13-dihydro-amorphane sesquiterpenes which are found in A. annua as natural products.

Spectroscopic Evidence of Si−H End Groups in Dialkylpolysilanes Synthesized via Wurtz Coupling

We demonstrate unambiguously the presence of Si−H end groups in σ-conjugated polysilanes 1−5, with alkyl groups as side chains synthesized via Wurtz coupling by means of IR, 1H, 29Si, and {1H−29Si} heteronuclear correlation NMR spectroscopy. However, there were no detectable Si−Cl, Si−OH, and Si−OR groups that would be associated with end groups of polysilanes. This implies that either such groups are not present or are too small to be detectable by IR and NMR spectra. The presence of Si−H end groups in low as well as high molecular weight polysilanes suggests the sequential existence of silyl radicals and anions in Wurtz coupling reactions and termination reaction involving a radical coupling in the solvent phase as previously described.

1,N2-propanodeoxyguanosine adducts of the 1,3-butadiene metabolite, hydroxymethylvinyl ketone.

1,3-Butadiene (BD) is a rodent and human carcinogen. While several epoxides formed during BD metabolism are mutagenic and may contribute to BD carcinogenicity, another proposed metabolite, hydroxymethylvinyl ketone (HMVK), could also be involved. A significant quantity of HMVK is likely to be formed since it is a proposed intermediate in the metabolism of 3-butene-1,2-diol (BD-diol) to 1,2-dihydroxy-4-(N-acetylcysteinyl)butane, the major mercapturic acid metabolite of BD in humans. In addition, BD-diol is a major BD metabolite in liver perfusion experiments in rodents. By analogy with other alpha,beta-unsaturated carbonyls, HMVK is likely to be mutagenic via formation of promutagenic 1,N(2)-propanodeoxyguanosine adducts. The objective of the current study was to investigate the formation of such adducts in vitro. The reaction between HMVK and dGuo yielded two major products shown to be identical by positive ion electrospray-MS, having protonated molecular ions with m/z consistent with HMVK-derived 1,N(2)-propanodeoxyguanosine (HMVK-dGuo). Rechromatography of each fraction yielded two fractions with retention times identical to those initially isolated, suggesting equilibration between two diastereomers. Two partially resolved sets of (1)H NMR signals were consistent with a 1:1 mixture of diastereomeric C-6-substituted adducts equilibrating slowly on an NMR time-scale. Following deglycosylation, C-6 substitution was verified by two-dimensional correlation NMR spectroscopy, indicating that the initial adducts were formed by Michael addition of dGuo-N1 to the terminal vinyl carbon followed by cyclization to the 1,N(2)-propano structure. Reactions with calf thymus DNA under physiological conditions yielded two sets of products. The first set had HPLC retention times and mass spectra identical to those of the previously characterized C-6-substituted HMVK-dGuo diastereomers. The second set had a molecular ion and fragmentation pattern identical to the C-6-substituted adducts and on this basis were assigned as the diastereomeric C-8 adducts. In addition to detecting HMVK-dGuo in treated DNA, the adducts were also present in control DNA. Overall, our research demonstrates that HMVK can form promutagenic DNA adducts and it therefore has the potential to play a role in BD-associated mutagenicity.