The application of "excitation sculpting" in the construction of selective one-dimensional homonuclear coherence-transfer experiments

NMR analysis of the Fischer-Tropsch wastewater: Combination of 1D selective gradient TOCSY, 2D DOSY and qNMR

The Fischer-Tropsch (FT) process is a practical approach to convert synthesis gas (CO and H₂) into hydrocarbons and oxygenates, and these product mixtures are usually well-characterized. However, the analysis of Fischer-Tropsch waste water (FTW) is still somewhat underdeveloped and the exact composition of FTW remains unclear. Herein, various qualitative NMR techniques, especially diffusion-ordered spectroscopy (DOSY) and one dimension (1D) selective gradient total correlation spectroscopy (SelTOCSY) were strategically applied in the analysis of FTW. The NMR results show that the DOSY technique can pseudo-separate most of components in complex mixtures over the diffusion dimension. The SelTOCSY technique is used as a supporting method in the cases where the DOSY technique cannot clearly distinguish overlapped signals. Moreover, the quantitative ¹H NMR (qNMR) was further used to quantify the components of the sample. These routine and advanced qualitative and quantitative NMR technique utilized here provide a fast, effective and feasible method for the identification of complex mixtures in FTW, which might be a powerful and fast alternative to gas chromatography or high performance liquid chromatography for FTW research.

Interaction of Avibactam with Class B Metallo-β-Lactamases

β-Lactamases are the most important mechanisms of resistance to the β-lactam antibacterials. There are two mechanistic classes of β-lactamases: the serine β-lactamases (SBLs) and the zinc-dependent metallo-β-lactamases (MBLs). Avibactam, the first clinically useful non-β-lactam β-lactamase inhibitor, is a broad-spectrum SBL inhibitor, which is used in combination with a cephalosporin antibiotic (ceftazidime). There are multiple reports on the interaction of avibactam with SBLs but few such studies with MBLs. We report biochemical and biophysical studies on the binding and reactivity of avibactam with representatives from all 3 MBL subfamilies (B1, B2, and B3). Avibactam has only limited or no activity versus MBL-mediated resistance in pathogens. Avibactam does not inhibit MBLs and binds only weakly to most of the MBLs tested; in some cases, avibactam undergoes slow hydrolysis of one of its urea N-CO bonds followed by loss of CO₂, in a process different from that observed with the SBLs studied. The results suggest that while the evolution of MBLs that more efficiently catalyze avibactam hydrolysis should be anticipated, pursuing the development of dual-action SBL and MBL inhibitors based on the diazabicyclooctane core of avibactam may be productive.

Incorporation of selective population transfer and homo-spin decoupling into selective one-dimensional experiments

The incorporation of selective population transfer (SPT) and homo-spin decoupling (HSD) into selective one-dimensional (1D) experiments has been shown to be very useful in obtaining information on the elucidation of the structure of organic compounds. To demonstrate this, the determination of the relative configuration of the sugar moiety of Mi-saponins has been presented.

Simplifying DOSY spectra with selective TOCSY edited preparation

Diffusion-ordered NMR spectroscopy, while quite powerful, is limited by its inability to resolve signals that are severely overlapped in the proton spectrum. We present here a DOSY experiment that uses selective TOCSY as an editing/preparation period. With this method, well-resolved signals of the analytes are selectively excited and the magnetization subsequently transferred by isotropic mixing to resonances buried in the matrix background, which are then resolved by the ensuing DOSY sequence. Key to the success of our proposed method is the incorporation of a highly effective zero-quantum filter into the selective TOCSY preparation period, which prevents zero-quantum coherence from being carried into the DOSY part of the pulse sequence. Further improvement in spectral resolution can be obtained by expanding the proposed experiment into a 3D sequence and utilizing the homonuclear decoupling feature of the BASHD-TOCSY technique. Both pulse sequences were found to greatly simplify the DOSY spectrum of a 'dirty' sucrose/raffinose mixture, as the complex matrix background is no longer present to obscure or overlap with the signals of interests. Furthermore, complete resolution of the relevant signals was achieved with the 3D sequence.

Extending the limits of the selective 1D NOESY experiment with an improved selective TOCSY edited preparation function

Compared to its 2D counterpart, the selective 1D NOESY experiment offers greatly simplified spectral interpretation and is invaluable to the structure elucidation of small-to-medium sized molecules, although its application is limited to well-resolved resonances only. The doubly selective 1D TOCSY-NOESY experiment allows the 1D NOESY experiment to be extended to resonances within overlapped spectral regions. However, existing methods do not address the critical issue of zero-quantum interference, which leads to severe anti-phase distortions to the line shape of scalar coupled spins and often complicates the identification of weak NOE enhancements. In this communication, we describe an improved selective TOCSY edited preparation (STEP) function and its application to the selective 1D NOESY experiment. The STEP function incorporates a novel zero-quantum filter introduced by Thrippleton and Keeler [Angew. Chem. Int. Ed. 42 (2003) 3938], which permits essentially complete suppression of zero-quantum coherence in a single scan. Residual anti-phase distortions due to spin-state mixing are removed using the double difference methodology reported by Shaka et al. [45th Experimental NMR Conference, Pacific Grove, USA, 2004]. The combined use of these techniques ensures that the final spectra are free of distortions, which is crucial to the reliable detection of weak NOE enhancements. Although employed as an additional preparation period in the example demonstrated here, the STEP function affords a general editing tool for spectral simplification and can be applied to a range of experiments.

A new selective population transfer experiment using a double pulsed field gradient spin-echo

A new pulse sequence is proposed for the determination of scalar coupling correlation in small- and medium-sized organic compounds. The method uses a combination of the double pulsed field gradient spin-echo (DPFGSE) and the selective population transfer (SPT) techniques and is shown to be useful in the analysis of complex spectra with many overlapped signals. The usefulness of this method in the structural elucidation of natural substances is demonstrated using strychnine and digitoxin as examples.

Structural characterization of the N-terminal mineral modification domains from the molluscan crystal-modulating biomineralization proteins, AP7 and AP24

The AP7 and AP24 proteins represent a class of mineral-interaction polypeptides that are found in the aragonite-containing nacre layer of mollusk shell (H. rufescens). These proteins have been shown to preferentially interfere with calcium carbonate mineral growth in vitro. It is believed that both proteins play an important role in aragonite polymorph selection in the mollusk shell. Previously, we demonstrated the 1-30 amino acid (AA) N-terminal sequences of AP7 and AP24 represent mineral interaction/modification domains in both proteins, as evidenced by their ability to frustrate calcium carbonate crystal growth at step edge regions. In this present report, using free N-terminal, C(alpha)-amide "capped" synthetic polypeptides representing the 1-30 AA regions of AP7 (AP7-1 polypeptide) and AP24 (AP24-1 polypeptide) and NMR spectroscopy, we confirm that both N-terminal sequences possess putative Ca (II) interaction polyanionic sequence regions (2 x -DD- in AP7-1, -DDDED- in AP24-1) that are random coil-like in structure. However, with regard to the remaining sequences regions, each polypeptide features unique structural differences. AP7-1 possesses an extended beta-strand or polyproline type II-like structure within the A11-M10, S12-V13, and S28-I27 sequence regions, with the remaining sequence regions adopting a random-coil-like structure, a trait common to other polyelectrolyte mineral-associated polypeptide sequences. Conversely, AP24-1 possesses random coil-like structure within A1-S9 and Q14-N16 sequence regions, and evidence for turn-like, bend, or loop conformation within the G10-N13, Q17-N24, and M29-F30 sequence regions, similar to the structures identified within the putative elastomeric proteins Lustrin A and sea urchin spicule matrix proteins. The similarities and differences in AP7 and AP24 N-terminal domain structure are discussed with regard to joint AP7-AP24 protein modification of calcium carbonate growth.

Identification of a "glycine-loop"-like coiled structure in the 34 AA Pro,Gly,Met repeat domain of the biomineral-associated protein, PM27

Fracture resistance in biomineralized structures has been linked to the presence of proteins, some of which possess sequences that are associated with elastic behavior. One such protein superfamily, the Pro,Gly-rich sea urchin intracrystalline spicule matrix proteins, form protein-protein supramolecular assemblies that modify the microstructure and fracture-resistant properties of the calcium carbonate mineral phase within embryonic sea urchin spicules and adult sea urchin spines. In this report, we detail the identification of a repetitive keratin-like "glycine-loop"- or coil-like structure within the 34-AA (AA: amino acid) N-terminal domain, (PGMG)(8)PG, of the spicule matrix protein, PM27. The identification of this repetitive structural motif was accomplished using two capped model peptides: a 9-AA sequence, GPGMGPGMG, and a 34-AA peptide representing the entire motif. Using CD, NMR spectrometry, and molecular dynamics simulated annealing/minimization simulations, we have determined that the 9-AA model peptide adopts a loop-like structure at pH 7.4. The structure of the 34-AA polypeptide resembles a coil structure consisting of repeating loop motifs that do not exhibit long-range ordering. Given that loop structures have been associated with protein elastic behavior and protein motion, it is plausible that the 34-AA Pro,Gly,Met repeat sequence motif in PM27 represents a putative elastic or mobile domain.

The core oligosaccharide component from Mannheimia (Pasteurella) haemolytica serotype Al lipopolysaccharide contains L-glycero-D-manno- and D-glycero-D-manno-heptoses: Analysis of the structure and conformation by high-resolution NMR spectroscopy

Previous studies from our laboratory have indicated that the lipopolysaccharide (LPS) from Mannheimia haemolytica serotype A1 contains both L-glycero-D-manno-heptose and D-glycero-D-manno-heptose residues. NMR methods making use of 1D 1H selective excitation and 2D (1H, 13C) and (1H, 31P) heteronuclear experiments were used for the structural determination of the major core oligosaccharide components of the deacylated low-molecular-mass LPS obtained following sequential treatment with anhydrous hydrazine and aq KOH. The core oligosaccharide region was found to be composed of a branched octasaccharide linked to the deacylated lipid A moiety via a 3-deoxy-4-phospho-D-manno-oct-2-ulosonate residue having the structure,[Formula: see text]Heterogeneity was found to be present at several linkages. NMR methods were devised to distinguish between the diastereomeric forms of the heptose residues. Synthesized monosaccharides of L-D- and D-D-heptose were used as model compounds for analysis of the 1H and 13C NMR chemical shifts and proton coupling constants. Molecular modeling using a Monte Carlo method for conformational analysis of saccharides was used to determine the conformation of the inner core of the oligosaccharide and to establish the stereochemical relationships between the heptoses.Key words: LPS, NMR, conformation, oligosaccharide, heptose.

Model peptide studies of sequence regions in the elastomeric biomineralization protein, Lustrin A. I. The C-domain consensus-PG-, -NVNCT-motif

The lustrin superfamily represents a unique group of biomineralization proteins localized between layered aragonite mineral plates (i.e., nacre layer) in mollusk shell. Recent atomic force microscopy (AFM) pulling studies have demonstrated that the lustrin-containing organic nacre layer in the abalone, Haliotis rufescens, exhibits a typical sawtooth force-extension curve with hysteretic recovery. This force extension behavior is reminiscent of reversible unfolding and refolding in elastomeric proteins such as titin and tenascin. Since secondary structure plays an important role in force-induced protein unfolding and refolding, the question is, What secondary structure(s) exist within the major domains of Lustrin A? Using a model peptide (FPGKNVNCTSGE) representing the 12-residue consensus sequence found near the N-termini of the first eight cysteine-rich domains (C-domains) within the Lustrin A protein, we employed CD, NMR spectroscopy, and simulated annealing/minimization to determine the secondary structure preferences for this sequence. At pH 7.4, we find that the 12-mer sequence adopts a loop conformation, consisting of a "bend" or "turn" involving residues G3-K4 and N7-C8-T9, with extended conformations arising at F1-G3; K4-V6; T9-S10-G11 in the sequence. Minor pH-dependent conformational effects were noted for this peptide; however, there is no evidence for a salt-bridge interaction between the K4 and E12 side chains. The presence of a loop conformation within the highly conserved -PG-, -NVNCT- sequence of C1-C8 domains may have important structural and mechanistic implications for the Lustrin A protein with regard to elastic behavior.

Fluorescent coumarin-labeled nucleotides to measure ADP release from actomyosin

Several coumarin-labeled nucleotides have been synthesized, based on 2'(3')-O-(2-aminoethyl)carbamoyl-ATP (edaATP). The fluorescent coumarins coupled with the free amino group are 7-diethylaminocoumarin-3-carboxylic acid (to give deac-edaATP), coumarin 343 (but-edaATP) and 7-ethylamino-8-bromocoumarin-3-carboxylic acid (mbc-edaATP). The carbamoyl linkage of these nucleotide analogs undergoes interconversion between 2'- and 3'-hydroxyl attachment very slowly, so that the 2'- and 3'-isomers were separated and stored with minimal equilibration. 3'-Deac-edaADP had fluorescence excitation and emission maxima at 430 nm and 477 nm, with a fluorescence quantum yield of 0.012. The equivalent data for 3'-but-edaADP are 445 nm, 494 nm, and 0.51, respectively, and for 3'-mbc-edaADP, 405 nm, 464 nm, and 0.62. The interaction with skeletal myosin subfragment 1 was measured in the absence and presence of actin. In each case the fluorescence was decreased when bound to subfragment 1, 3-fold for 3'-deac-edaADP, 7-fold for 3'-but-edaADP, and 11-fold for 3'-mbc-edaADP. Steady-state ATPase measurements and the kinetics of binding and release of nucleotides were similar to those reported for the natural nucleotide. Large fluorescence changes could be observed for the release of these analogs from actomyosin subfragment 1, enabling a direct measurement of the kinetics of this process. In the case of 3'-deac-edaADP a rate constant of 474 s(-1) was measured (at pH 7.0, 20 degrees C, and low ionic strength).

Model peptide studies of sequence repeats derived from the intracrystalline biomineralization protein, SM50. II. Pro,Asn-rich tandem repeats

In the biomineralization process, a number of Pro-rich proteins participate in the formation of three-dimensional supramolecular structures. One such protein superfamily, the Pro,Gly-rich sea urchin intracrystalline spicule matrix proteins, form protein-protein supramolecular assemblies that modify the microstructure of the inorganic mineral phase (calcite) within embryonic sea urchin spicules and adult sea urchin spines. These proteins represent a useful model for understanding Pro sequence usage and the resulting generation of extended or "open" structures for protein-protein and/or protein-crystal recognition. In the sea urchin spicule matrix protein, SM50 (Strongylocentrotus purpuratus), there exists an unusual 20-residue Pro,Asn-containing repeat, &bond;PNNPNNPNPNNPNNPNNPNPbond which links the upstream 15-residue C-terminal domain and the downstream 211-residue beta-spiral repeat domain. To define the structural preferences of this 20-residue repeat, we created a 20-residue N- and C-terminal "capped" peptidomimetic of this sequence. Using far-uv CD dichroism, CH(alpha) and alpha-(15)N conformational shifts, (3)J(NH-CHalpha) coupling constants, sequential d(NN(i, i + 1)) rotating frame nuclear Overhauser effect connectivities, d(alphaN(i, i + 1))/d(NN(i, i + 1)) intensity ratios, amide temperature shift coefficients, amide solvent exchange, and simulated annealing refinement protocols, we have determined that this 20-residue repeat motif adopts an extended "twist" structure consisting of turn- and coil-like regions. These findings are consistent with previous studies, which have shown that Pro-rich tandem repeats adopt extended, flexible structures in solution. We hypothesize that this 20-residue repeat may fulfill the role of a mineral-binding domain, a protein-protein docking domain, or as an internal "molecular spacer" for the SM50 protein during spicule biocomposite formation.

Comparative single-molecule and ensemble myosin enzymology: sulfoindocyanine ATP and ADP derivatives

Single-molecule and macroscopic reactions of fluorescent nucleotides with myosin have been compared. The single-molecule studies serve as paradigms for enzyme-catalyzed reactions and ligand-receptor interactions analyzed as individual stochastic processes. Fluorescent nucleotides, called Cy3-EDA-ATP and Cy5-EDA-ATP, were derived by coupling the dyes Cy3.29.OH and Cy5.29.OH (compounds XI and XIV, respectively, in, Bioconjug. Chem. 4:105-111)) with 2'(3')-O-[N-(2-aminoethyl)carbamoyl]ATP (EDA-ATP). The ATP(ADP) analogs were separated into their respective 2'- and 3'-O-isomers, the interconversion rate of which was 30[OH(-)] s(-1) (0.016 h(-1) at pH 7.1) at 22 degrees C. Macroscopic studies showed that 2'(3')-O-substituted nucleotides had properties similar to those of ATP and ADP in their interactions with myosin, actomyosin, and muscle fibers, although the ATP analogs did not relax muscle as well as ATP did. Significant differences in the fluorescence intensity of Cy3-nucleotide 2'- and 3'-O-isomers in free solution and when they interacted with myosin were evident. Single-molecule studies using total internal reflection fluorescence microscopy showed that reciprocal mean lifetimes of the nucleotide analogs interacting with myosin filaments were one- to severalfold greater than predicted from macroscopic data. Kinetic and equilibrium data of nucleotide-(acto)myosin interactions derived from single-molecule microscopy now have a biochemical and physiological framework. This is important for single-molecule mechanical studies of motor proteins.

Model peptide studies of sequence repeats derived from the intracrystalline biomineralization protein, SM50. I. GVGGR and GMGGQ repeats

We report solution-state pulsed field gradient nmr studies of a native sequence-derived 23-residue peptidomimetic, N alpha-acetyl-QPGVGGRQPGMGGQPGVGGRQPG-C alpha-amid, that incorporates the prevalent GVGGR and GMGGQ repeats found in the sea urchin embryo intracrystalline spicule matrix protein, SM50 (Strongylocentrotus purpuratus). These repeats are sequence homologues of elastin protein repeats (VPGVG, VGGVG, and APGVGV) and spider dragline silk protein repeats (GPGG, GQGG, and QPGYG). Using rotating frame nuclear Overhauser effect (ROE) connectivities, CH alpha proton conformational shifts, 3JNH-CH alpha coupling constants, amide temperature shift coefficients, and pulsed field gradient ROE spectroscopy solvent exchange measurements, we find that the 23-mer peptidomimetic possesses a multiple beta-turn structure in aqueous solution, in equilibria with an extended or coil structure (60% beta-turn: 40% random coil). The GVGGR sequence adopts a double beta-turn conformation that is stabilized by two hydrogen bonds (R7-->V4, R20-->V17; G6-->G3, G19-->G16). The GMGGQ region adopts a single beta-turn conformation that is stabilized by a hydrogen bond involving residues Q14 and M11. Repeating beta-turn structures, or beta-spirals, may play an important role with regard to matrix assembly, protein stability, molecular elasticity, and/or protein-crystal recognition within the spicule mineralized matrix.

Composite pulsed field gradients with refocused chemical shifts and short recovery time

An improved self-compensating pulsed field gradient (PFG) technique that combines antiphase gradient pairs with broadband frequency-modulated 180 degrees pulses is proposed. The antiphase gradient pairs lead to superb system recovery. In addition, evolution under chemical shift and heteronuclear J coupling are refocused during the PFG, making it appear effectively instantaneous. This new approach makes it possible to obtain high-resolution phase-sensitive 2D spectra for the PFG version of many experiments such as COSY, DQF-COSY, and HSQC without adding extra compensating delays or pulses. While reasonable suppression of unwanted magnetization is achieved, this method also gives satisfactory retention of desired signals. As a bonus, the field-frequency lock is not perturbed during the experiments.

Analysis of phosphorylated metabolites in crayfish extracts by two-dimensional 1H-31P NMR heteronuclear total correlation spectroscopy (heteroTOCSY)

In vivo and extract analyses by one-dimensional 31P NMR have been a key tool in investigating energy-related metabolism. Although many phosphorylated metabolites have been observed, many of them have yet to be identified. This reflects the difficulty in identifying them using 31P NMR alone. Two-dimensional 1H-31P correlation experiments have been shown to be useful for assigning phosphorylated metabolites. To obtain better sensitivity and structure information, 1H-detected 31P-1H heteronuclear total correlation spectroscopy (heteroTOCSY) was implemented and a complete chemical shift assignment for a number of phosphorylated standards was made. The time courses of 1D heteroTOCSY signal intensity versus spin-locking time were established for these standards to aid the optimization of the 2D experiment. This method was applied to crayfish extracts for the assignment of glucose 6-phosphate, alpha-glycerophosphate, ribose 5-phosphate, fructose 1,6-bisphosphate, phosphocholine, phosphoethanolamine, glucose 1-phosphate, glycerophosphoethanolamine, glycerophosphocholine, ATP, ADP, and AMP. An alkyl phosphate, a hexose 1-phosphate, and a UDP-hexose were also observed. These assignments allowed the identification of many changes in the 31P NMR spectra of crayfish extracts elicited by treatment with the organophosphate pesticide chlorpyrifos. The assignment of an in vivo 31P spectrum of a live crayfish was also made based on the extract assignment. This approach should be a powerful tool for examining stress-associated changes in the metabolism of phosphorylated compounds.

Stabilization of a C7 equatorial gamma turn in DMSO-d6 by a ditryptophan crosslink

Covalent crosslinks can control local peptide conformation. In tripeptide sequences of the general formula Cys-Xxx-Cys, cysteine disulfides have been previously shown to enforce a C7 equatorial gamma-turn conformation (also referred to as an inverse gamma-turn). Much less is known about the effects of dityrosine and ditryptophan crosslinks on local peptide structure. In a series of tripeptides, ditryptophan crosslinks were formed using the two-step process of acid-promoted Mannich dimerization followed by oxidative aromatization. In these peptides, with the general formula Trp-Xxx-Trp (Xxx not equal to Gly), ditryptophan crosslinks were found to stabilize a C7 equatorial gamma-turn conformation in DMSO-d6. Rigorous support for a C7 equatorial conformation in the crosslinked sequence Trp-Pro-Trp came from a variety of 1H NMR experiments and molecular modelling. Interproton distances were derived from NOE buildups that were determined through a series of double pulsed field gradient spin echo (DPFGSE) experiments. In addition, the small temperature dependence of the i+2 NH chemical shifts (delta delta/delta T < 2 ppm/degree C) provided further support for the intramolecular hydrogen bond which defines a gamma-turn.

Coherence selection and excitation sculpting using RF-gradients in selective 1D experiments and nonselective 2D experiments

The B0 gradient pulses can be replaced with long high-power pulses (RF-gradients) in z-rotation composite sandwiches. By doing this, practically all B0 gradient-based pulse sequences can be performed with instruments lacking a field gradient accessory. We have implemented RF-gradients into selective 1D and nonselective 2D TOCSY and NOESY experiments. The spectral quality obtained with the RF-gradient method was comparable to that of the B0 method for small- to medium-sized molecules. There are also some advantages in using RF-gradients instead of B0 gradients. There is practically no shift or coupling evolution during RF-gradient pulses. This may be significant in some experiments. Copyright 1998 Academic Press.

Gradient- and sensitivity-enhanced TOCSY experiments

A pulsed field gradient version of the sensitivity-enhanced 2D TOCSY experiment is proposed which yields high-quality spectra with improved sensitivity and a minimum of two scans per t1 increment. For rapid acquisition of 1D TOCSY spectra, the 1D DPFGSE-TOCSY experiment was modified to include phase-encoded multiple-selective excitation followed by a simple spectral editing. Combination of these two building blocks is used in a sensitivity-enhanced 2D analog of the 3D TOCSY-TOCSY experiment which provides an efficient tool for resolving severely overlapped signals of oligomers in short experimental time.