Total Correlation Spectroscopy Spectra Research Articles

Total Correlation Spectroscopy across All NMR-Active Nuclei by Mixing at Zero Field

Multidimensional nuclear magnetic resonance (NMR) is based on a combination of well-established building blocks for polarization transfer. These blocks are used to design correlation experiments through one or a few chemical bonds or through space. Here, we introduce a building block that enables polarization transfer across all NMR-active nuclei in a coupled network of spins: isotropic mixing at zero and ultralow field (ZULF). Exploiting mixing under ZULF-NMR conditions, heteronuclear TOtal Correlation SpectroscopY (TOCSY) experiments were developed to highlight coupled spin networks. We demonstrate 1H-13C and 1H-15N correlations in ZULF-TOCSY spectra of labeled amino acids, which allow one to obtain cross-peaks among all heteronuclei belonging to the same coupled network, even when the direct interaction between them is negligible. We also demonstrate the potential of ZULF-TOCSY to analyze complex mixtures on a growth medium of isotope-labeled biomolecules. ZULF-TOCSY enables the quick identification of individual compounds in the mixture by their coupled spin networks. The ZULF-TOCSY method will lead to the development of a new toolbox of experiments to analyze complex mixtures by NMR.

Absolute Minimal Sampling of Homonuclear 2D NMR TOCSY Spectra for High-Throughput Applications of Complex Mixtures.

Modern applications of 2D NMR spectroscopy to diagnostic screening, metabolomics, quality control, and other high-throughput applications are often limited by the time-consuming sampling requirements along the indirect time domain t1 . 2D total correlation spectroscopy (TOCSY) provides unique spin connectivity information for the analysis of a large number of compounds in complex mixtures, but standard methods typically require >100 t1 increments for an accurate spectral reconstruction, rendering these experiments ineffective for high-throughput applications. For a complex metabolite mixture it is demonstrated that absolute minimal sampling (AMS), based on direct fitting of resonance frequencies and amplitudes in the time domain, yields an accurate spectral reconstruction of TOCSY spectra using as few as 16 t1 points. This permits the rapid collection of homonuclear 2D NMR experiments at high resolution with measurement times that previously were only the realm of 1D experiments.

Absolute Minimal Sampling of Homonuclear 2D NMR TOCSY Spectra for High‐Throughput Applications of Complex Mixtures

AbstractModern applications of 2D NMR spectroscopy to diagnostic screening, metabolomics, quality control, and other high‐throughput applications are often limited by the time‐consuming sampling requirements along the indirect time domain t1. 2D total correlation spectroscopy (TOCSY) provides unique spin connectivity information for the analysis of a large number of compounds in complex mixtures, but standard methods typically require >100 t1 increments for an accurate spectral reconstruction, rendering these experiments ineffective for high‐throughput applications. For a complex metabolite mixture it is demonstrated that absolute minimal sampling (AMS), based on direct fitting of resonance frequencies and amplitudes in the time domain, yields an accurate spectral reconstruction of TOCSY spectra using as few as 16 t1 points. This permits the rapid collection of homonuclear 2D NMR experiments at high resolution with measurement times that previously were only the realm of 1D experiments.

Maximal clique method for the automated analysis of NMR TOCSY spectra of complex mixtures.

Characterization of the chemical components of complex mixtures in solution is important in many areas of biochemistry and chemical biology, including metabolomics. The use of 2D NMR total correlation spectroscopy (TOCSY) experiments has proven very useful for the identification of known metabolites as well as for the characterization of metabolites that are unknown by taking advantage of the good resolution and high sensitivity of this homonuclear experiment. Due to the complexity of the resulting spectra, automation is critical to facilitate and speed-up their analysis and enable high-throughput applications. To better meet these emerging needs, an automated spin-system identification algorithm of TOCSY spectra is introduced that represents the cross-peaks and their connectivities as a mathematical graph, for which all subgraphs are determined that are maximal cliques. Each maximal clique can be assigned to an individual spin system thereby providing a robust deconvolution of the original spectrum for the easy extraction of critical spin system information. The approach is demonstrated for a complex metabolite mixture consisting of 20 compounds and for E. coli cell lysate.

NMR-Based Metabolic Profiling of Rice Wines by F2-Selective Total Correlation Spectra

In this study, we performed NMR-based metabolic profiling of major rice wines (Japanese sake, Chinese Shaoxing wine, and Korean makgeolli). In the (1)H NMR spectra, the rice wines showed broad resonances in the region of about 7.9-9.0 ppm. These resonances showed many and complex correlations with approximately 0.5-4.5 ppm in the F(2)-selective TOCSY (total correlation spectroscopy) spectra, and these correlations were attributed mainly to peptides. These spectral patterns were characteristic of individual rice wines, and the combination of F(2)-selective TOCSY spectra and principal component analysis enabled us to classify the rice wine species. Furthermore, it also provided information about raw materials, namely, what type of koji (rice koji or wheat koji) was used. These spectra may be useful as a new "fingerprint" for quality control or food authentication.

Hierarchical Alignment and Full Resolution Pattern Recognition of 2D NMR Spectra: Application to Nematode Chemical Ecology

Nuclear magnetic resonance (NMR) is the most widely used nondestructive technique in analytical chemistry. In recent years, it has been applied to metabolic profiling due to its high reproducibility, capacity for relative and absolute quantification, atomic resolution, and ability to detect a broad range of compounds in an untargeted manner. While one-dimensional (1D) 1H NMR experiments are popular in metabolic profiling due to their simplicity and fast acquisition times, two-dimensional (2D) NMR spectra offer increased spectral resolution as well as atomic correlations, which aid in the assignment of known small molecules and the structural elucidation of novel compounds. Given the small number of statistical analysis methods for 2D NMR spectra, we developed a new approach for the analysis, information recovery, and display of 2D NMR spectral data. We present a native 2D peak alignment algorithm we term HATS, for hierarchical alignment of two-dimensional spectra, enabling pattern recognition (PR) using full-resolution spectra. Principle component analysis (PCA) and partial least squares (PLS) regression of full resolution total correlation spectroscopy (TOCSY) spectra greatly aid the assignment and interpretation of statistical pattern recognition results by producing back-scaled loading plots that look like traditional TOCSY spectra but incorporate qualitative and quantitative biological information of the resonances. The HATS-PR methodology is demonstrated here using multiple 2D TOCSY spectra of the exudates from two nematode species: Pristionchus pacificus and Panagrellus redivivus. We show the utility of this integrated approach with the rapid, semiautomated assignment of small molecules differentiating the two species and the identification of spectral regions suggesting the presence of species-specific compounds. These results demonstrate that the combination of 2D NMR spectra with full-resolution statistical analysis provides a platform for chemical and biological studies in cellular biochemistry, metabolomics, and chemical ecology.

One- and two-dimensional NMR studies of methyl acrylate/vinyl acetate/ N-vinyl carbazole terpolymers

Terpolymers of methyl acrylate/vinyl acetate/ N-vinyl carbazole (M/A/C) with different compositions were synthesized by solution polymerization using AIBN as an initiator. Composition of terpolymers was determined from quantitative 13C{ 1H} NMR spectrum. Two-dimensional heteronuclear single quantum correlation (HSQC) and total correlated spectroscopy (TOCSY) were used to assign the methylene and methine carbon resonances by analyzing two and three bond order couplings. Various resonance signals were assigned to different compositional and configurational sequences with the help of one- and two-dimensional NMR spectra. Three and four bond order coupling between carbonyl carbon and other neighboring protons have been investigated with the help of 2D heteronuclear multiple bond correlation (HMBC) spectra. The complex and overlapped 1H NMR spectrum of terpolymer was analyzed completely with the help of 2D HSQC and TOCSY spectra.

Pin1 Catalyzes Conformational Changes of Thr-187 in p27Kip1 and Mediates Its Stability through a Polyubiquitination Process

The cis-trans peptidylprolyl isomerase Pin1 plays a critical role in regulating a subset of phosphoproteins by catalyzing conformational changes on the phosphorylated Ser/Thr-Pro motifs. The phosphorylation-directed ubiquitination is one of the major mechanisms to regulate the abundance of p27(Kip1). In this study, we demonstrate that Pin1 catalyzes the cis-trans conformational changes of p27(Kip1) and further mediates its stability through the polyubiquitination mechanism. Our results show that the phosphorylated Thr-187-Pro motif in p27(Kip1) is a key Pin1-binding site. In addition, NMR analyses show that this phosphorylated Thr-187-Pro site undergoes conformational change catalyzed by Pin1. Moreover, in Pin1 knock-out mouse embryonic fibroblasts, p27(Kip1) has a shorter lifetime and displays a higher degree of polyubiquitination than in Pin1 wild-type mouse embryonic fibroblasts, suggesting that Pin1 plays a critical role in regulating p27(Kip1) degradation. Additionally, Pin1 dramatically reduces the interaction between p27(Kip1) and Cks1, possibly via isomerizing the cis-trans conformation of p27(Kip1). Our study thus reveals a novel regulatory mechanism for p27(Kip1) stability and sheds new light on the biological function of Pin1 as a general regulator of protein stability.

MetaboMiner – semi-automated identification of metabolites from 2D NMR spectra of complex biofluids

BackgroundOne-dimensional (1D) 1H nuclear magnetic resonance (NMR) spectroscopy is widely used in metabolomic studies involving biofluids and tissue extracts. There are several software packages that support compound identification and quantification via 1D 1H NMR by spectral fitting techniques. Because 1D 1H NMR spectra are characterized by extensive peak overlap or spectral congestion, two-dimensional (2D) NMR, with its increased spectral resolution, could potentially improve and even automate compound identification or quantification. However, the lack of dedicated software for this purpose significantly restricts the application of 2D NMR methods to most metabolomic studies.ResultsWe describe a standalone graphics software tool, called MetaboMiner, which can be used to automatically or semi-automatically identify metabolites in complex biofluids from 2D NMR spectra. MetaboMiner is able to handle both 1H-1H total correlation spectroscopy (TOCSY) and 1H-13C heteronuclear single quantum correlation (HSQC) data. It identifies compounds by comparing 2D spectral patterns in the NMR spectrum of the biofluid mixture with specially constructed libraries containing reference spectra of ~500 pure compounds. Tests using a variety of synthetic and real spectra of compound mixtures showed that MetaboMiner is able to identify >80% of detectable metabolites from good quality NMR spectra.ConclusionMetaboMiner is a freely available, easy-to-use, NMR-based metabolomics tool that facilitates automatic peak processing, rapid compound identification, and facile spectrum annotation from either 2D TOCSY or HSQC spectra. Using comprehensive reference libraries coupled with robust algorithms for peak matching and compound identification, the program greatly simplifies the process of metabolite identification in complex 2D NMR spectra.

Poly(acrylonitrile‐co‐methyl methacrylate‐co‐methyl acrylate): Synthesis and stereosequence distribution analysis by 2D NMR

AbstractTerpolymers of acrylonitrile (A), methyl methacrylate (B), and methyl acrylate (M) were synthesized under optimized atom transfer radical polymerization conditions using 2‐bromopropionitrile as an initiator and CuBr/dinonyl bipyridine as a catalyst. Variation of the feed composition led to terpolymers with different compositions. Composition of synthesized terpolymers were calculated from quantitative 13C{1H} NMR spectra. Number average molecular weight and polydispersity index were determined by gel permeation chromatography. The overlapping and broad signals of the terpolymers were assigned completely to various compositional and configurational sequences by correlation of one‐dimensional 1H, 13C{1H}, and distortionless enhancement by polarization transfer and two‐dimensional heteronuclear single quantum coherence (HSQC) and total correlation spectroscopy (TOCSY). 2D HSQC NMR study shows one to one correlation between carbon and proton signals, while 2D TOCSY spectra were used to confirm 1, 2 bond geminal couplings between nonequivalent protons of same methylene group. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 25–37, 2009

Non-negative matrix factorization of two-dimensional NMR spectra: Application to complex mixture analysis

A central problem in the emerging field of metabolomics is how to identify the compounds comprising a chemical mixture of biological origin. NMR spectroscopy can greatly assist in this identification process, by means of multi-dimensional correlation spectroscopy, particularly total correlation spectroscopy (TOCSY). This Communication demonstrates how non-negative matrix factorization (NMF) provides an efficient means of data reduction and clustering of TOCSY spectra for the identification of unique traces representing the NMR spectra of individual compounds. The method is applied to a metabolic mixture whose compounds could be unambiguously identified by peak matching of NMF components against the BMRB metabolomics database.

Evidence for Domain-specific Recognition of SK and Kv Channels by MTX and HsTx1 Scorpion Toxins

Maurotoxin (MTX) and HsTx1 are two scorpion toxins belonging to the alpha-KTx6 structural family. These 34-residue toxins, cross-linked by four disulfide bridges, share 59% sequence identity and fold along the classical alpha/beta scaffold. Despite these structural similarities, they fully differ in their pharmacological profiles. MTX is highly active on small (SK) and intermediate (IK) conductance Ca(2+)-activated (K(+)) channels and on voltage-gated Kv1.2 channel, whereas HsTx1 potently blocks voltage-gated Kv1.1 and Kv1.3 channels only. Here, we designed and chemically produced MTX-HsTx1, a chimera of both toxins that contains the N-terminal helical region of MTX (sequence 1-16) and the C-terminal beta-sheet region of HsTx1 (sequence 17-34). The three-dimensional structure of the peptide in solution was solved by (1)H NMR. MTX-HsTx1 displays the activity of MTX on SK channel, whereas it exhibits the pharmacological profile of HsTx1 on Kv1.1, Kv1.2, Kv1.3, and IK channels. These data demonstrate that the helical region of MTX exerts a key role in SK channel recognition, whereas the beta-sheet region of HsTx1 is crucial for activity on all other channel types tested.

Microstructure analysis of poly(styrene‐co‐vinylidene chloride) copolymers by NMR spectroscopy

Poly(styrene-co-vinylidene chloride) (S/V) copolymers were prepared by free-radical photopolymerization using uranyl nitrate as an initiator. The microstructure of the copolymer S/V was investigated by 1H- and 13C{1H}-NMR, 1H–13C-heteronuclear shift quantum correlation (HSQC) NMR, and homonuclear total correlated spectroscopy (TOCSY). The 1H-NMR spectra of the copolymers is complex due to overlapping resonance signals of the various triad configurations. Assignments were made up to the triad and tetrad levels for the methylene and methine regions using two-dimensional HSQC experiments. A 13C-distortionless enhancement by polarization transfer (DEPT) spectrum was used to differentiate between the carbon resonance signals of methine and the methylene units. The geminal couplings in the methylene protons and vicinal coupling between the methine and methylene protons were detected from the TOCSY spectra. Monte Carlo simulations were used to investigate the effect of the degree of polymerization on the triad fractions. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 79: 544–554, 2001

Lipid oxidation in blood plasma of patients with neurological disorders

Nuclear magnetic resonance (NMR) spectra of blood plasma lipids from lyophilized plasma samples from patients with neurological disorders stored for several weeks in an evacuated exsiccator show characteristic differences compared to freshly lyophilized plasma samples. The main differences concern the unsaturated fatty acids, e.g., the extent of unsaturation and their structural composition. The total amount of double bond signals of unsaturated fatty acids are noticeably reduced in intensity and new signals arise from conjugated double bonds. These signals can be assigned to keto-octadecadienoic acid (KODE) or hydroxy-octadecadienoic acid (HODE). The proton and carbon NMR chemical shifts and their structural assignment to the main molecular components are given. Whereas the KODE and HODE signals occur only as storage artifacts in the spectra, we have found small amounts of 9,11-octadecadienoic acid also in fresh blood plasma of controls. Its concentration is about 60 μM. In two-dimensional H,H total correlation spectroscopy spectra also a very low amount (6–7 μM) of 13-HODE can be detected.

Structure of Tuberoinfundibular Peptide of 39 Residues

Structure of Tuberoinfundibular Peptide of 39 Residues

Folding and structural characterization of highly disulfide-bonded beetle antifreeze protein produced in bacteria.

The hyperactive antifreeze protein from the beetle, Tenebrio molitor, is an 8.5-kDa, threonine-rich protein containing 16 Cys residues, all of which are involved in disulfide bonds. When produced by Escherichia coli, the protein accumulated in the supernatant in an inactive, unfolded state. Its correct folding required days or weeks of oxidation at 22 or 4 degrees C, respectively, and its purification included the removal of imperfectly folded forms by reversed-phase HPLC. NMR spectroscopy was used to assess the degree of folding of each preparation. One-dimensional (1)H and two-dimensional (1)H total correlation spectroscopy spectra were particularly helpful in establishing the characteristics of the fully folded antifreeze in comparison to less well-folded forms. The recombinant antifreeze had no free -SH groups and was rapidly and completely inactivated by 10 mM DTT. It had a thermal hysteresis activity of 2.5 degrees C at a concentration of 1 mg/ml, whereas fish antifreeze proteins typically show a thermal hysteresis of approximately 1.0 degrees C at 10-20 mg/ml. The circular dichroism spectra of the beetle antifreeze had a superficial resemblance to those of alpha-helical proteins, but deconvolution of the spectra indicated the absence of alpha-helix and the presence of beta-structure and coil. NMR analysis and secondary structure predictions agree with the CD data and are consistent with a beta-helix model proposed for the antifreeze on the basis of its 12-amino-acid repeating structure and presumptive disulfide bond arrangement.

Microstructure analysis of poly(styrene-co-vinylidene chloride) copolymers by NMR spectroscopy

Poly(styrene-co-vinylidene chloride) (S/V) copolymers were prepared by free-radical photopolymerization using uranyl nitrate as an initiator. The microstructure of the copolymer S/V was investigated by 1H- and 13C{1H}-NMR, 1H–13C-heteronuclear shift quantum correlation (HSQC) NMR, and homonuclear total correlated spectroscopy (TOCSY). The 1H-NMR spectra of the copolymers is complex due to overlapping resonance signals of the various triad configurations. Assignments were made up to the triad and tetrad levels for the methylene and methine regions using two-dimensional HSQC experiments. A 13C-distortionless enhancement by polarization transfer (DEPT) spectrum was used to differentiate between the carbon resonance signals of methine and the methylene units. The geminal couplings in the methylene protons and vicinal coupling between the methine and methylene protons were detected from the TOCSY spectra. Monte Carlo simulations were used to investigate the effect of the degree of polymerization on the triad fractions. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 79: 544–554, 2001

Structure of the IGF-binding domain of the insulin-like growth factor-binding protein-5 (IGFBP-5): implications for IGF and IGF-I receptor interactions.

Binding proteins for insulin-like growth factors (IGFs) IGF-I and IGF-II, known as IGFBPs, control the distribution, function and activity of IGFs in various cell tissues and body fluids. Insulin-like growth factor-binding protein-5 (IGFBP-5) is known to modulate the stimulatory effects of IGFs and is the major IGF-binding protein in bone tissue. We have expressed two N-terminal fragments of IGFBP-5 in Escherichia coli; the first encodes the N-terminal domain of the protein (residues 1-104) and the second, mini-IGFBP-5, comprises residues Ala40 to Ile92. We show that the entire IGFBP-5 protein contains only one high-affinity binding site for IGFs, located in mini-IGFBP-5. The solution structure of mini-IGFBP-5, determined by nuclear magnetic resonance spectroscopy, discloses a rigid, globular structure that consists of a centrally located three-stranded anti-parallel beta-sheet. Its scaffold is stabilized further by two inside packed disulfide bridges. The binding to IGFs, which is in the nanomolar range, involves conserved Leu and Val residues localized in a hydrophobic patch on the surface of the IGFBP-5 protein. Remarkably, the IGF-I receptor binding assays of IGFBP-5 showed that IGFBP-5 inhibits the binding of IGFs to the IGF-I receptor, resulting in reduction of receptor stimulation and autophosphorylation. Compared with the full-length IGFBP-5, the smaller N-terminal fragments were less efficient inhibitors of the IGF-I receptor binding of IGFs.

13C‐labeled oligodeoxyribonucleotides: A solution study of a CCAAT‐containing sequence at the nuclear factor I recognition site of human adenovirus

The solution behavior of the single-stranded CCAAT-containing octamer 1, d(AGCCAATA), that comprises part of the nuclear factor I (NF-I) recognition site at the origin of replication of human adenovirus has been studied by nmr spectroscopy at 500 and 600 MHz. Proton resonance assignments for 1 were aided by selective 13C enrichment at C1' of A1 or A5. High-resolution 13C-1H heteronuclear multiple-bond coherence spectra of the 13C-labeled oligomers permitted the selective detection of furanosyl ring protons within each labeled residue due to short- and long-range 13C-1H couplings to the enriched C1'. The resulting assignments provided firm starting points in the interpretation of double quantum filtered correlated spectra, yielding information supplemented by total correlated spectroscopy (TOCSY) and rotating frame nuclear Overhauser effect spectroscopic data to completely assign the 1H-nmr spectrum of 1 and extract 3JHH values for furanose conformational analysis. Several 13C-1H spin-coupling constants within the 13C-enriched A1 or A5 residues were measured from cross-peak shifts in TOCSY spectra, and their signs determined by inspection of the relative orientations of these shifts. 1H-1H and 13C-1H spin-couplings both indicate a preference (> 75%) for south (C2'-endo) conformations by the furanosyl rings of 1.

Simple Approaches for Estimating Vicinal 1H- 1H Coupling-Constants and for Obtaining Stereospecific Resonance Assignments in Leucine Side Chains

An approach for deriving stereospecific δ-methyl assignments and χ 2 dihedral angle constraints for leucine residues, based on easily recognized patterns of 1H- 1H spin-spin coupling constants and intraresidue nuclear-Overhauser-effect spectroscopy (NOESY) cross-peak intensities, is described. The approach depends on resolved H γ and/or δ-methyl resonances and on initially obtaining stereospecific assignments for H β2 and H β3. As part of the overall strategy, a method is presented for obtaining qualitative or, in favorable cases, semiquantitative estimates of vicinal 1H- 1H coupling constants from peak intensities measured in a short-mixing-time 1H- 1H total correlation spectroscopy (TOCSY) experiment. This method of estimating 1H- 1H spin-spin coupling constants is generally applicable to all side-chain types. The approach is illustrated for several leucine residues within uniformly 15N-labeled and 15N/ 13C-double-labeled isolated light-chain variable domain of the anti-digoxin antibody 26-10. Estimates of 3 J αβ and 3 J βγ coupling constants are derived from a three-dimensional (3D) 13C-edited TOCSY-heteronuclear multiple-quantum coherence (HMQC) spectrum. These data are combined with information from 3D 15N-edited NOESY and 3D 13C-edited NOESY spectra to yield stereospecific H β2, H β3, and δ-methyl assignments, as well as constraints on χ (1) and χ 2 dihedral angles. Although the overall approach is illustrated using 3D 15N-edited and 13C-edited data, it is equally applicable to analysis of two-dimensional 1H- 1H NOESY and TOCSY spectra.