Rapid high-resolution four-dimensional NMR spectroscopy using the filter diagonalization method and its advantages for detailed structural elucidation of oligosaccharides

Carbohydrate isomer resolutionviamulti-site derivatization cyclic ion mobility-mass spectrometry

Cyclic ion mobility-tandem mass spectrometry enhances the separation and identification of small carbohydrate isomers.

A fast approach to 3D HSQC-based spectroscopy based on a Fourier phase encoding of pre-targeted resonances

Multidimensional Nuclear Magnetic Resonance (NMR) provides a unique window into structure and dynamics at an atomic level. Traditionally, given the scan-by-scan time modulation involved in these experiments, the duration of nD NMR increases exponentially with spectral dimensionality. In addition, acquisition times increase as the number of spectral elements being sought in each indirect domain - given by the ratio between the spectral bandwidth being targeted and the resolution desired. These long sampling times can be substantially reduced by exploiting information that is often available from lower-dimensionality acquisitions. This work presents a novel approach that exploits previous 2D information to speed up the acquisition of 3D spectra, based on what we denote as a Time-Optimized FouriEr Encoding (TOFEE) of pre-targeted peaks. Such 3D TOFEE experiments, which present points in common with Hadamard-encoded 3D acquisitions, do not necessarily require more scans than their 2D counterparts. This is here demonstrated based on extensions of 2D Heteronuclear Single-quantum Coherence (HSQC) experiments, to 3D HSQC-TOCSY or 3D HSQC-NOESY acquisitions. The theoretical basis of this new approach is given, and experimental demonstrations are presented on small molecule and protein-based model systems.

Identification of structurally closely related monosaccharide and disaccharide isomers by PMP labeling in conjunction with IM-MS/MS

It remains particularly difficult for gaining unambiguous information on anomer, linkage, and position isomers of oligosaccharides using conventional mass spectrometry (MS) methods. In our laboratory, an ion mobility (IM) shift strategy was employed to improve confidence in the identification of structurally closely related disaccharide and monosaccharide isomers using IMMS. Higher separation between structural isomers was achieved using 1-phenyl-3-methyl-5-pyrazolone (PMP) derivatization in comparison with phenylhydrazine (PHN) derivatization. Furthermore, the combination of pre-IM fragmentation of PMP derivatives provided sufficient resolution to separate the isomers not resolved in the IMMS. To chart the structural variation observed in IMMS, the collision cross sections (CCSs) for the corresponding ions were measured. We analyzed nine disaccharide and three monosaccharide isomers that differ in composition, linkages, or configuration. Our data show that coexisting carbohydrate isomers can be identified by the PMP labeling technique in conjunction with ion-mobility separation and tandem mass spectrometry. The practical application of this rapid and effective method that requires only small amounts of sample is demonstrated by the successful analysis of water-soluble ginseng extract. This demonstrated the potential of this method to measure a variety of heterogeneous sample mixtures, which may have an important impact on the field of glycomics.

Applications of high dimensionality experiments to biomolecular NMR

High dimensionality NMR experiments facilitate resonance assignment and precise determination of spectral parameters such as coupling constants. Sparse non-uniform sampling enables acquisition of experiments of high dimensionality with high resolution in acceptable time. In this review we present and compare some significant applications of NMR experiments of dimensionality higher than three in the field of biomolecular studies in solution.

An update on oligosaccharides and their esters from traditional chinese medicines: chemical structures and biological activities

A great number of naturally occurring oligosaccharides and oligosaccharide esters have been isolated from traditional Chinese medicinal plants, which are used widely in Asia and show prominent curative effects in the prevention and treatment of kinds of diseases. Numerous in vitro and in vivo experiments have revealed that oligosaccharides and their esters exhibited various activities, including antioxidant, antidepressant, cytotoxic, antineoplastic, anti-inflammatory, neuroprotective, cerebral protective, antidiabetic, plant growth-regulatory, and immunopotentiating activities. This review summarizes the investigations on the distribution, chemical structures, and bioactivities of natural oligosaccharides and their esters from traditional Chinese medicines between 2003 and 2013.

Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins

Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins.

Evaluation of ion mobility-mass spectrometry for determining the isomeric heterogeneity of oligosaccharide-alditols derived from bovine submaxillary mucin

Rapid separation and independent analysis of isomeric species are needed for the structural characterization of carbohydrates in glycomics research. Ion mobility-mass spectrometry techniques were used to examine a series of isomeric neutral oligosaccharide-alditols derived from bovine submaxillary mucin. Several analytical techniques were employed: (1) off line separation of the oligosaccharide-alditol mixture by HPLC; (2) direct and rapid evaluation of isomeric heterogeneity of oligosaccharides by electrospray ionization-ion mobility-time of flight mass spectrometry; and (3) mobility-selected MS² and MS³ to evaluate isomeric mobility peaks by dual gate ion mobility-tandem mass spectrometry. Multiple isomeric ion mobility peaks were observed for the majority of oligosaccharide-alditols, which was achieved on the millisecond time scale after LC separation. Fragmentation spectra obtained from the collision-induced dissociation of isomeric precursor ions could be essentially identical, or dramatically different for a given precursor m/z using the dual-gate ion mobility quadrupole ion trap mass spectrometer. This further confirmed the need for rapid physical resolution of isomeric precursor species prior to their tandem mass spectral analysis.

Using NMR to identify and characterize natural products

Over the past 28 years there have been several thousand publications describing the use of 2D NMR to identify and characterize natural products. During this time period, the amount of sample needed for this purpose has decreased from the 20-50 mg range to under 1 mg. This has been due to both improvements in NMR hardware and methodology. This review will focus on mainly methodology improvements, particularly in pulse sequences, acquisition and processing methods which are particularly relevant to natural product research, with lesser discussion of hardware improvements.

Study of near-symmetric cyclodextrins by compressed sensing 2D NMR

The compressed sensing NMR (CS-NMR) is an approach to processing of nonuniformly sampled NMR data. Its idea is to introduce minimal l(p) -norm (0 < p ≤ 1) constraint to a penalty function used in a reconstruction algorithm. Here, we demonstrate that 2D CS-NMR spectra allow the full spectral assignment of near-symmetric β-cyclodextrin derivatives (mono-modified at the C6 position). The application of CS-NMR ensures experimental time saving and the resolution improvement, necessary because of very low chemical shift dispersion. In the overnight experimental time, the set of properly resolved 2D NMR spectra required for the unambiguous assignment of mono(6-deoxy-6-(1-1,2,3-triazo-4-yl)-1-propane-3-O-(phenyl)) β-cyclodextrin was obtained. The highly resolved HSQC spectrum was reconstructed from 5.12% of the data. Moreover, reconstructed 2D HSQC-TOCSY spectrum yielded information about the correlations within one sugar unit, and 2D HSQC-NOESY technique allowed the sequential assignment of the glucosidic units.

Resolving structural isomers of monosaccharide methyl glycosides using drift tube and traveling wave ion mobility mass spectrometry

Monosaccharide structural isomers including sixteen methyl-D-glycopyranosides and four methyl-N-acetylhexosamines were subjected to ion mobility measurements by electrospray ion mobility mass spectrometry. Two ion mobility-MS systems were employed: atmospheric pressure drift tube ion mobility time-of-flight mass spectrometry and a Synapt G2 HDMS system which incorporates a low pressure traveling wave ion mobility separator. All the compounds were investigated as [M + Na](+) ions in the positive mode. A majority of the monosaccharide structural isomers exhibited different mobility drift times in either system, depending on differences in their anomeric and stereochemical configurations. In general, drift time patterns (relative drift times of isomers) matched between the two instruments. Higher resolving power was observed using the atmospheric pressure drift tube. Collision cross section values of monosaccharide structural isomers were directly calculated from the atmospheric pressure ion mobility experiments, and a collision cross section calibration curve was made for the traveling wave ion mobility instrument. Overall, it was demonstrated that ion mobility-mass spectrometry using either drift tube or traveling wave ion mobility is a valuable technique for resolving subtle variations in stereochemistry among the sodium adducts of monosaccharide methyl glycosides.

Differentiation of the stereochemistry and anomeric configuration for 1-3 linked disaccharides via tandem mass spectrometry and 18O-labeling

Collision-induced dissociation (CID) of deprotonated hexose-containing disaccharides (m/z 341) with 1-2, 1-4, and 1-6 linkages yields product ions at m/z 221, which have been identified as glycosyl-glycolaldehyde anions. From disaccharides with these linkages, CID of m/z 221 ions produces distinct fragmentation patterns that enable the stereochemistries and anomeric configurations of the non-reducing sugar units to be determined. However, only trace quantities of m/z 221 ions can be generated for 1-3 linkages in Paul or linear ion traps, preventing further CID analysis. Here we demonstrate that high intensities of m/z 221 ions can be built up in the linear ion trap (Q3) from beam-type CID of a series of 1-3 linked disaccharides conducted on a triple quadrupole/linear ion trap mass spectrometer. (18)O-labeling at the carbonyl position of the reducing sugar allowed mass-discrimination of the "sidedness" of dissociation events to either side of the glycosidic linkage. Under relatively low energy beam-type CID and ion trap CID, an m/z 223 product ion containing (18)O predominated. It was a structural isomer that fragmented quite differently than the glycosyl-glycolaldehydes and did not provide structural information about the non-reducing sugar. Under higher collision energy beam-type CID conditions, the formation of m/z 221 ions, which have the glycosyl-glycolaldehyde structures, were favored. Characteristic fragmentation patterns were observed for each m/z 221 ion from higher energy beam-type CID of 1-3 linked disaccharides and the stereochemistry of the non-reducing sugar, together with the anomeric configuration, were successfully identified both with and without (18)O-labeling of the reducing sugar carbonyl group.

Phase-sensitive spectral estimation by the hybrid filter diagonalization method

A more robust way to obtain a high-resolution multidimensional NMR spectrum from limited data sets is described. The Filter Diagonalization Method (FDM) is used to analyze phase-modulated data and cast the spectrum in terms of phase-sensitive Lorentzian "phase-twist" peaks. These spectra are then used to obtain absorption-mode phase-sensitive spectra. In contrast to earlier implementations of multidimensional FDM, the absolute phase of the data need not be known beforehand, and linear phase corrections in each frequency dimension are possible, if they are required. Regularization is employed to improve the conditioning of the linear algebra problems that must be solved to obtain the spectral estimate. While regularization smoothes away noise and small peaks, a hybrid method allows the true noise floor to be correctly represented in the final result. Line shape transformation to a Gaussian-like shape improves the clarity of the spectra, and is achieved by a conventional Lorentzian-to-Gaussian transformation in the time-domain, after inverse Fourier transformation of the FDM spectra. The results obtained highlight the danger of not using proper phase-sensitive line shapes in the spectral estimate. The advantages of the new method for the spectral estimate are the following: (i) the spectrum can be phased by conventional means after it is obtained; (ii) there is a true and accurate noise floor; and (iii) there is some indication of the quality of fit in each local region of the spectrum. The method is illustrated with 2D NMR data for the first time, but is applicable to n-dimensional data without any restriction on the number of time/frequency dimensions.

Increasing the sensitivity of magnetic resonance spectroscopy and imaging

Nuclear magnetic resonance and magnetic resonance imaging are two of the most important techniques in analytical chemistry and noninvasive medical imaging, respectively. They share a common physical basis, one aspect of which is a low intrinsic sensitivity relative to complementary techniques. Encouragingly, recent advances in physics, chemistry, engineering, and data processing have enabled significant increases in sensitivity, as measured by both increased signal-to-noise and reduced data acquisition times, allowing previously unattainable data to be acquired and also new types of experiments to be designed.

Filter diagonalization using a "sensitivity-enhanced basis": improved performance for noisy NMR spectra

The Filter Diagonalization Method (FDM) has been used to process NMR data in liquids and can be advantageous when the spectrum is sparse enough, the lines are sharp and Lorentzian, raw sensitivity is adequate, and the measured time-domain data is short, so that the Fourier Transform spectrum exhibits distorted line shapes. Noise can adversely impact resolution and/or frequency accuracy in FDM spectral estimates. Paradoxically, more complete data can lead to worse FDM spectra if there is appreciable noise. However, by modifying the numerical method, the FDM noise performance improves significantly, without apparently losing any of the existing advantages. The two key modifications are to adjust the FDM basis functions so that matrix elements computed from them have less noise contribution on average, and to regularize each dimension of a multidimensional spectrum independently. The modifications can be recommended for general-purpose use in the case of somewhat noisy, incomplete data.

Iterative algorithm of discrete Fourier transform for processing randomly sampled NMR data sets

Spectra obtained by application of multidimensional Fourier Transformation (MFT) to sparsely sampled nD NMR signals are usually corrupted due to missing data. In the present paper this phenomenon is investigated on simulations and experiments. An effective iterative algorithm for artifact suppression for sparse on-grid NMR data sets is discussed in detail. It includes automated peak recognition based on statistical methods. The results enable one to study NMR spectra of high dynamic range of peak intensities preserving benefits of random sampling, namely the superior resolution in indirectly measured dimensions. Experimental examples include 3D (15)N- and (13)C-edited NOESY-HSQC spectra of human ubiquitin.

Selective heteronuclear Hartmann-Hahn: a multiple-pulse sequence for selective magnetization transfer in the structural elucidation of "isotagged" oligosaccharides

A new selective heteronuclear Hartmann-Hahn (SHEHAHA) multiple-pulse mixing sequence is proposed for the solution structure elucidation of milligram amounts of peracetylated oligosaccharides in which the acetyl groups are enriched in carbon-13, so-called "isotags". SHEHAHA accomplishes exclusive in-phase magnetization transfer between the isotag carbonyl (13)C and the proximal proton on the sugar ring. Relayed transfer around the sugar rings by proton-proton TOCSY is suppressed, while the heteronuclear transfer from the labeled carbonyl carbon to the proximal ring proton is maintained. The sequence is broadband in the sense that all acetyl groups simultaneously give good signal transfer to their respective nearest proton neighbors. The (1)H-detected spectra have decent sensitivity and excellent resolution, giving patterns that unambiguously identify common structural subunits in human glycans. Peracetylated maltitol is shown as a test case of the method. Lineshapes are pure absorption, allowing facile measurement of vicinal proton-proton couplings. Linkage points can be deduced, and the 2D correlation spectra may be useful for more ambitious prediction algorithms and machine identification by a spectral database.

Coupled decomposition of four-dimensional NOESY spectra

Four-dimensional (4D) NOESY spectra provide unambiguous distance information at a resolution that cannot be achieved in fewer dimensions and thus increase the quality of biomolecular structure determination substantially. Since the degree of chemical shift degeneracy increases with protein size, the use of 4D NOESY spectra is particularly important for large proteins. The potential high resolution in 4D spectra cannot be achieved in a reasonable time with conventional acquisition routines that sample the Nyquist grid uniformly. It can, however, be obtained with nonuniform sampling of the data grid, but optimal processing of such data has not yet been established. Here we describe a processing method for a pair of sparsely sampled 4D NOESY spectra, a methyl-methyl and an amide-methyl NOESY, recorded on a perdeuterated protein with protonated isoleucine, leucine, and valine methyl groups. The coupled multidimensional decomposition (Co-MDD) of these two spectra together with a 2D template spectrum results in a substantial increase in sensitivity, evidenced by 50-100% additional cross peaks, when compared to alternative processing schemes. At the same time, Co-MDD allows the use of low sparse levels of 10-15% of the full data grid for NOESY spectra. For the 283-residue integral human membrane protein VDAC-1, which has a rotational correlation time of about 70 ns in detergent micelles, the two 4D Co-MDD NOESYs yielded a total of 366 NOEs, resulting in 139 unambiguous upper limit distance constraints for the structure calculation.

Enhanced spectral resolution by high-dimensional NMR using the filter diagonalization method and "hidden" dimensions

High-dimensional (HD) NMR spectra have poorer digital resolution than low-dimensional (LD) spectra, for a fixed amount of experiment time. This has led to "reduced-dimensionality" strategies, in which several LD projections of the HD NMR spectrum are acquired, each with higher digital resolution; an approximate HD spectrum is then inferred by some means. We propose a strategy that moves in the opposite direction, by adding more time dimensions to increase the information content of the data set, even if only a very sparse time grid is used in each dimension. The full HD time-domain data can be analyzed by the filter diagonalization method (FDM), yielding very narrow resonances along all of the frequency axes, even those with sparse sampling. Integrating over the added dimensions of HD FDM NMR spectra reconstitutes LD spectra with enhanced resolution, often more quickly than direct acquisition of the LD spectrum with a larger number of grid points in each of the fewer dimensions. If the extra-dimensions do not appear in the final spectrum, and are used solely to boost information content, we propose the moniker hidden-dimension NMR. This work shows that HD peaks have unmistakable frequency signatures that can be detected as single HD objects by an appropriate algorithm, even though their patterns would be tricky for a human operator to visualize or recognize, and even if digital resolution in an HD FT spectrum is very coarse compared with natural line widths.

Application of the forward linear prediction on high-resolution NMR spectra in inhomogeneous fields

In homogeneous fields, the advantages of forward linear prediction (LP) for processing 2D NMR data sets have long been recognized. In this paper, the forward LP method was employed to obtain high-resolution NMR spectra in inhomogeneous fields. Intermolecular multiple-quantum coherence (iMQC) signals are caused by intermolecular dipolar interactions and can be used to obtain 1D high-resolution NMR spectra from the 2D iMQC spectra acquired in inhomogeneous fields. However, when the 2D spectra are acquired with insufficient increments to save experimental time, wiggles around strong peaks and bad resolution will occur. Extending the data set by forward LP in the indirect dimension is a good way to improve spectral resolution. Compared to normal discrete Fourier transform, the forward LP method can shorten experimental time by a factor of four or more at the same level of sensitivity and resolution.

Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data

The necessity to acquire large multidimensional datasets, a basis for assignment of NMR resonances, results in long data acquisition times during which substantial degradation of a protein sample might occur. Here we propose a method applicable for such a protein for automatic assignment of backbone resonances by direct inspection of multidimensional NMR spectra. In order to establish an optimal balance between completeness of resonance assignment and losses of cross-peaks due to dynamic processes/degradation of protein, assignment of backbone resonances is set as a stirring criterion for dynamically controlled targeted nonlinear NMR data acquisition. The result is demonstrated with the 12 kDa (13)C,(15) N-labeled apo-form of heme chaperone protein CcmE, where hydrolytic cleavage of 29 C-terminal amino acids is detected. For this protein, 90 and 98% of manually assignable resonances are automatically assigned within 10 and 40 h of nonlinear sampling of five 3D NMR spectra, respectively, instead of 600 h needed to complete the full time domain grid. In addition, resonances stemming from degradation products are identified. This study indicates that automatic resonance assignment might serve as a guiding criterion for optimal run-time allocation of NMR resources in applications to proteins prone to degradation.

High-resolution pyrimidine- and ribose-specific 4D HCCH-COSY spectra of RNA using the filter diagonalization method

The NMR spectra of nucleic acids suffer from severe peak overlap, which complicates resonance assignments. 4D NMR experiments can overcome much of the degeneracy in 2D and 3D spectra; however, the linear increase in acquisition time with each new dimension makes it impractical to acquire high-resolution 4D spectra using standard Fourier transform (FT) techniques. The filter diagonalization method (FDM) is a numerically efficient algorithm that fits the entire multi-dimensional time-domain data to a set of multi-dimensional oscillators. Selective 4D constant-time HCCH-COSY experiments that correlate the H5-C5-C6-H6 base spin systems of pyrimidines or the H1'-C1'-C2'-H2' spin systems of ribose sugars were acquired on the (13)C-labeled iron responsive element (IRE) RNA. FDM-processing of these 4D experiments recorded with only 8 complex points in the indirect dimensions showed superior spectral resolution than FT-processed spectra. Practical aspects of obtaining optimal FDM-processed spectra are discussed. The results here demonstrate that FDM-processing can be used to obtain high-resolution 4D spectra on a medium sized RNA in a fraction of the acquisition time normally required for high-resolution, high-dimensional spectra.

920 MHz ultra-high field NMR approaches to structural glycobiology

Although NMR spectroscopy has great potential to provide us with detailed structural information on oligosaccharides and glycoconjugates, the carbohydrate NMR analyses have been hampered by the severe spectral overlapping and the insufficiency of the conformational restraints. Recently, ultra-high field NMR spectrometers have become available for applications to structural analyses of biological macromolecules. Here we demonstrate that ultra-high fields offer not only increases in sensitivity and chemical shift dispersion but also potential benefits for providing unique information on chemical exchange and relaxation, by displaying NMR spectral data of oligosaccharide, glycoprotein, and glycolipid systems recorded at a 21.6 T magnetic field (corresponding to 920 MHz (1)H observation frequency). The ultra-high field NMR spectroscopy combined with sugar library and stable-isotope labeling approaches will open new horizons in structural glycobiology.

Lineshapes and artifacts in Multidimensional Fourier Transform of arbitrary sampled NMR data sets

The comprehensive description of Multidimensional Fourier Transform applied to arbitrary sampled NMR data is presented. Lineshapes and signal-to-artifact ratio are discussed in detail with regard to time domain sampling scheme and applied data weighting. It is demonstrated that transformation method with simple summation instead of numerical integration is most useful for significantly undersampled experiments. Additionally, the optimized random sampling schedule which enables significant improvement of obtained spectra is proposed. The new procedure of cleaning spectra is presented, it is based on predictability of artifacts pattern when sampling scheme and amplitude of intense signals are known. The results enable observation of high dynamic range spectra as for example heteronuclear edited NOESY. We show the application of new approach to the 3D (15)N-edited NOESY-HSQC spectrum acquired for (13)C, (15)N labeled ubiquitin sample with random time domain sampling.

The Stereochemical Dependence of Unimolecular Dissociation of Monosaccharide-Glycolaldehyde Anions in the Gas Phase: A Basis for Assignment of the Stereochemistry and Anomeric Configuration of Monosaccharides in Oligosaccharides by Mass Spectrometry via a Key Discriminatory Product Ion of Disaccharide Fragmentation, m/z 221

Mass spectrometry of hexose-containing disaccharides often yields product ions of m/z 221 in the negative ion mode. Using a Paul trap, isolation and collision-induced dissociation of the m/z 221 anions yielded mass spectra that easily differentiated their stereochemistry and anomeric configuration, for all 16 stereochemical variants. The ions were shown to be glycopyranosyl-glycolaldehydes through chemical synthesis of their standards. The stereochemistry dramatically affected fragmentation which was dependent on four relative stereochemical arrangements: (1) the relationship between the hydroxyl group at position 2 and the anomeric configuration, (2) a cis relationship of the anomeric position and positions 2 and 3 (1,2,3-cis), (3) a 1,2 trans-2,3 cis relationship, and (4) the relationship between the hydroxyl group at position 4 and the anomeric configuration. After labeling the reducing carbonyl oxygen of a series of disaccharides with 18O to mass-discriminate between their monosaccharide components, it was demonstrated that m/z 221 anions are comprised of an intact nonreducing sugar glycosidically linked to a 2-carbon aglycon derived from the reducing sugar, irrespective of the linkage position between monosaccharides. This enabled the location of the intact sugar to be assigned to the nonreducing side of a glycosidic linkage. Detailed studies of experimental factors necessary for reproducibility demonstrated that the unique mass spectrum for each m/z 221 anion could be obtained from month-to-month through the use of an internal energy-input calibrant ion that ensured reproducible energy deposition into the ions. The counterparts to these ions for the 2-acetamido-2-deoxyhexoses were m/z 262 anions, and the anomeric configuration and stereochemistry of these anions could also be reproducibly discriminated for N-acetylglucosamine and N-acetylgalactosamine. The fragmentation patterns of m/z 221 anions provide a firm reproducible basis for assignment of sugar stereochemistries in the gas phase.

Three-dimensional NMR Spectroscopy of organic molecules by random sampling of evolution time space and multidimensional Fourier transformation

In this communication we present the application of a new method, which enables one to acquire 3D NMR spectra in a reasonable time and preserves high resolution in indirectly detected domains. The new method is based on random distribution of time domain data points followed by Quaternion FT with respect to two time variables in one step. The experimental examples include three-dimensional spectra of strychnine in CDCl3, TOCSY-HSQC, COSY-HMBC, and the new technique proposed here: heteronuclear single quantum multiple bond correlation (HSQMBC). The obtained spectra are compared to those recorded at the same time employing the conventional acquisition scheme. We show that high-quality 3D spectra of organic compounds can be obtained in reasonable experimental time and that they are of great interest in cases when direct analysis of 2D spectra is difficult.

Random sampling of evolution time space and Fourier transform processing

Application of Fourier Transform for processing 3D NMR spectra with random sampling of evolution time space is presented. The 2D FT is calculated for pairs of frequencies, instead of conventional sequence of one-dimensional transforms. Signal to noise ratios and linewidths for different random distributions were investigated by simulations and experiments. The experimental examples include 3D HNCA, HNCACB and (15)N-edited NOESY-HSQC spectra of (13)C (15)N labeled ubiquitin sample. Obtained results revealed general applicability of proposed method and the significant improvement of resolution in comparison with conventional spectra recorded in the same time.

High-resolution four-dimensional carbon-correlated 1H-1H ROESY experiments employing isotags and the filter diagonalization method for effective assignment of glycosidic linkages in oligosaccharides

Four-dimensional nuclear magnetic resonance spectroscopy of oligosaccharides that correlates 1H-1H ROESY cross peaks to two additional 13C frequency dimensions is reported. The 13C frequencies were introduced by derivatization of all free hydroxyl groups with doubly 13C-labeled acetyl isotags. Pulse sequences were optimized for processing with the filter diagonalization method. The extensive overlap typically observed in 2D ROESY 1H-1H planes was alleviated by resolution of ROESY cross peaks in the two added dimensions associated with the carbon frequencies of the isotags. This enabled the interresidue 1H-1H ROESY cross peaks to be unambiguously assigned hence spatially proximate sugar spin systems across glycosidic bonds could be effectively ascertained. An experiment that selectively amplifies interresidue ROESY 1H-1H cross peaks is also reported. It moves the magnetization of an intraresidue proton normally correlated to a sugar H-1 signal orthogonally along the z axis prior to a Tr-ROESY mixing sequence. This virtually eliminates the incoherent intraresidue ROESY transfer, suppresses coherent TOCSY transfer, and markedly enhances the intensity of interresidue ROESY cross peaks.

Two-dimensional Fourier transform of arbitrarily sampled NMR data sets

A new procedure for Fourier transform with respect to more than one time variable simultaneously is proposed for NMR data processing. In the case of two-dimensional transform the spectrum is calculated for pairs of frequencies, instead of conventional sequence of one-dimensional transforms. Therefore, it enables one to Fourier transform arbitrarily sampled time domain and thus allows for analysis of high dimensionality spectra acquired in a short time. The proposed method is not limited to radial sampling, it requires only to fulfill the Nyquist theorem considering two or more time domains at the same time. We show the application of new approach to the 3D HNCO spectrum acquired for protein sample with radial and spiral time domain sampling.

Deterministic and statistical methods for reconstructing multidimensional NMR spectra

Reconstruction of an image from a set of projections is a well-established science, successfully exploited in X-ray tomography and magnetic resonance imaging. This principle has been adapted to generate multidimensional NMR spectra, with the key difference that, instead of continuous density functions, high-resolution NMR spectra comprise discrete features, relatively sparsely distributed in space. For this reason, a reliable reconstruction can be made from a small number of projections. This speeds the measurements by orders of magnitude compared to the traditional methodology, which explores all evolution space on a Cartesian grid, one step at a time. Speed is of crucial importance for structural investigations of biomolecules such as proteins and for the investigation of time-dependent phenomena. Whereas the recording of a suitable set of projections is a straightforward process, the reconstruction stage can be more problematic. Several practical reconstruction schemes are explored. The deterministic methods-additive back-projection and the lowest-value algorithm-derive the multidimensional spectrum directly from the experimental projections. The statistical search methods include iterative least-squares fitting, maximum entropy, and model-fitting schemes based on Bayesian analysis, particularly the reversible-jump Markov chain Monte Carlo procedure. These competing reconstruction schemes are tested on a set of six projections derived from the three-dimensional 700-MHz HNCO spectrum of a 187-residue protein (HasA) and compared in terms of reliability, absence of artifacts, sensitivity to noise, and speed of computation.

The single basis filter diagonalization method: a rapid multidimensional data processing scheme

A new way to apply the filter diagonalization method (FDM) that results in a large increase in the speed of calculation of multidimensional NMR spectra is presented. The speed increase is accompanied by slight differences in spectral lineshapes, although frequency estimates remain essentially identical. For contoured spectra, the method does not result in appreciable differences from the full FDM calculation. Optimal parameter sets for an FDM calculation can be estimated far more rapidly, which makes the FDM more straightforward to employ in practice. The performance of the method versus the full FDM was investigated for both model and experimental signals. The effect of noise on the method was also studied.