Determination of Internucleotide JHN Couplings by the Modified 2D JNN-Correlated [N, H] TROSY

Recent developments in the direct observation of J couplings across hydrogen bonds in proteins and nucleic acids provide additional information for structure and function studies of these molecules by NMR spectroscopy. A J_NN-correlated [¹⁵N, ¹H] TROSY experiment proposed by Pervushin et al. (Proc. Natl. Acad. Sci. USA 95, 14147–14151, 1998) can be applied to measure ^hJ_HN in smaller nucleic acids in an E.COSY manner. However, it cannot be effectively applied to large nucleic acids, such as tRNA^Trp, since one of the peaks corresponding to a fast relaxing component will be too weak to be observed in the spectra of large molecules. In this Communication, we proposed a modified J_NN-correlated [¹⁵N, ¹H] TROSY experiment which enables direct measurement of ^hJ_HN in large nucleic acids.     

Suppression of Diagonal Peaks in TROSY-Type H NMR NOESY Spectra of N-Labeled Proteins

A novel method for suppression of diagonal peaks in the amide region of NOESY NMR spectra of ¹⁵N-labeled proteins is presented. The method is particularly useful for larger proteins at high magnetic fields where interference between dipolar and chemical shift anisotropy relaxation mechanisms results in large TROSY effects, i.e., large differences in ¹H^N linewidths depending on the spin state of attached ¹⁵N nuclei. In this limit the new TROSY NOESY method does not compromise sensitivity. It is demonstrated using a perdeuterated ¹⁵N-labeled protein sample, Neural Cell Adhesion Molecule 213–308 (NCAM) from rat, in H₂O at 800 MHz.     

More line narrowing in TROSY by decoupling of long-range couplings: shift correlation and JNC′ coupling constant measurements

Since the introduction of RDCs in high-resolution NMR studies of macromolecules, there is a growing interest in the development of accurate, and sensitive methods for determining coupling constants. Most methods for extracting these couplings are based on the measurement of the splitting between multiplet components in J-coupled spectra. However, these methods are often unreliable since undesired multiple-bond couplings can considerably broaden the multiplet components and consequently make accurate determination of their position difficult. To demonstrate one approach to this problem, G-BIRD^(r) decoupled TROSY sequences are proposed for the measurement of ¹J_NH and ¹J_NC′ coupling constants. Resolved or unresolved splittings due to remote protons are removed by a G-BIRD^(r) module employed during t₁ and as a result, spectra with narrow, well-resolved peaks are obtained from which heteronuclear one-bond couplings can be accurately measured. Moreover, introduction of a spin-state-selective α/β-filter in the TROSY sequence allows the separation of the ¹J_NC′ doublet components into two subspectra which contain the same number of peaks as the regular TROSY spectrum. The ¹J_NC′ couplings are obtained from the displacement between the corresponding peaks in the subspectra.     

Optimization of Three-Dimensional TROSY-Type HCCH NMR Correlation of Aromatic H–C Groups in Proteins

Improved methods for three-dimensional TROSY-Type HCCH correlation involving protons of negligible CSA are presented. The TROSY approach differs from the conventional approach of heteronuclear decoupling in evolution and detection periods by not mixing fast and slowly relaxing coherences and usually suppressing the former. Pervushin et al. (J. Am. Chem. Soc. 120, 6394–6400 (1998)) have proposed a 3D TROSY-type HCCH experiment where the TROSY approach is applied only in one of the ¹³C dimensions. A new pulse sequence applying the TROSY approach in both indirect dimensions is advantageous when the TROSY effect of the carbons is large or when a relatively high resolution is required. For lower resolutions or moderate TROSY effects we show that it is possible to combine the best of both worlds, namely to suppress heteronuclear couplings without mixing fast and slowly relaxing coherences while at the same time superimpose the two components and thus have both contribute to the detected signal. That is possible using the novel technique of Spin-State-Selective Time-Proportional Phase Incrementation (S³ TPPI). The new 3D S³ TPPI TROSY HCCH method is demonstrated on a ¹³C,¹⁵N-labeled protein sample, RAP 18–112 (N-terminal domain of α₂-macroglobulin receptor associated protein), at 750 MHz and average sensitivity enhancements of 10% are obtained for the cross peaks in comparison to methods based on conventional decoupling on one of the carbons or on TROSY on both carbons.     

Measurement of one and two bond N–C couplings in large proteins by TROSY-based J-modulation experiments

Residual dipolar couplings (RDCs) between NC′ and NC^α atoms in polypeptide backbones of proteins contain information on the orientation of bond vectors that is complementary to that contained in NH RDCs. The ¹J_NC^α and ²J_NC^α scalar couplings between these atoms also display a Karplus relation with the backbone torsion angles and report on secondary structure. However, these N–C couplings tend to be small and they are frequently unresolvable in frequency domain spectra having the broad lines characteristic of large proteins. Here a TROSY-based J-modulated approach for the measurement of small ¹⁵N–¹³C couplings in large proteins is described. The cross-correlation interference effects inherent in TROSY methods improve resolution and signal to noise ratios for large proteins, and the use of J-modulation to encode couplings eliminates the need to remove frequency distortions from overlapping peaks during data analysis. The utility of the method is demonstrated by measurement of ¹J_NC′, ¹J_NC^α, and ²J_NC^α scalar couplings and ¹D_NC′ and ¹D_NC^α residual dipolar couplings for the myristoylated yeast ARF1·GTPγs protein bound to small lipid bicelles, a system with an effective molecule weight of 70 kDa.     

The 2D {P} Spin-Echo-Difference Constant-Time [C, H]-HMQC Experiment for Simultaneous Determination of JH3′P and JC4′P in C-Labeled Nucleic Acids and Their Protein Complexes

A two-dimensional {³¹P} spin-echo-difference constant-time [¹³C, ¹H]-HMQC experiment (2D {³¹P}-sedct-[¹³C, ¹H]-HMQC) is introduced for measurements of ³J_C4′P and ³J_H3′P scalar couplings in large ¹³C-labeled nucleic acids and in DNA–protein complexes. This experiment makes use of the fact that ¹H–¹³C multiple-quantum coherences in macromolecules relax more slowly than the corresponding ¹³C single-quantum coherences. ³J_C4′P and ³J_H3′P are related via Karplus-type functions with the phosphodiester torsion angles β and ε, respectively, and their experimental assessment therefore contributes to further improved quality of NMR solution structures. Data are presented for a uniformly ¹³C, ¹⁵N-labeled 14-base-pair DNA duplex, both free in solution and in a 17-kDa protein–DNA complex.     

Density Matrix Simulations of the Effects of J Coupling in Spin Echo and Fast Spin Echo Imaging

A computer simulation has been used to calculate the effects of J coupling on the amplitudes of echoes produced by CPMG sequences. The program computes the evolution of the density matrix for different pulse intervals and can predict the signals obtainable from spin systems of any size and complexity. Results from the simulation confirm the prediction that a decrease in the effects of J coupling is largely responsible for the bright fat signal seen in fast spin echo imaging at high pulse rates. The effects of J coupling on CPMG echotrains are examined for A3B2 and A3B2C2 spin systems over a wide range of J coupling and chemical shift values and pulse spacings. The effects of J coupling on the point spread function obtained with fast spin echo imaging are also discussed.     

Spin-State-Selective TPPI: A New Method for Suppression of Heteronuclear Coupling Constants in Multidimensional NMR Experiments

A novel multidimensional NMR pulse sequence tool, spin-state-selective time-proportional phase incrementation (S(3) TPPI), is introduced. It amounts to application of different TPPIs on the two components of doublets so that their frequencies can be manipulated independently. The chief application is for suppression of large heteronuclear one-bond coupling constants in indirect dimensions of multidimensional experiments without interchanging the two transverse magnetization components of doublets as conventional decoupling does, which is advantageous when they relax at different rates such as by partial compensation of dipolar and CSA relaxation contributions. For experimental confirmation we use a sample of (15)N-labeled neural cell adhesion molecule modules 1 and 2, a protein with a molecular weight of about 20 kDa. The new tool is general and can be combined with many multidimensional NMR experiments for proteins.     

Multiple-Quantum J-Resolved NMR Spectroscopy (MQ-JRES): Measurement of Multiple-Quantum Relaxation Rates and Relative Signs of Spin Coupling Constants

The technique of multiple-quantum J-resolved NMR spectroscopy (MQ-JRES) is introduced and applied to the spin system SI₃–M (such as in the example given here, the ¹³CH₃–¹²CH in alanine). The SI₃ spin system was excited to its highest quantum state (8S_yI_xI_yI_y), which consists of four coherences: quadruple quantum of (3I + S), double quantum of (3I − S), double quantum of (I + S), and zero quantum of (I − S). In the MQ spectrum generated from the projection onto the F₁ dimension, the resonances of the different multiple-quantum coherences are resolved by their coupling constants to the remote spin (M). The absorptive lineshapes in both F₁ and F₂ dimensions enable accurate measurements of transverse relaxation rates, and both amplitude and relative signs of the long-range coupling constants are to be derived from either frequency or time domain data. The selective detection of MQ-JRES spectra of the individual MQ coherences using either phase cycling or pulsed field gradients is presented.     

The First in Vivo Observation of C–N Coupling in Mammalian Brain

[5-¹³C,¹⁵N]Glutamine, with ¹J(¹³C–¹⁵N) of 16 Hz, was observed in vivo in the brain of spontaneously breathing rats by ¹³C MRS at 4.7 T. The brain [5-¹³C]glutamine peak consisted of the doublet from [5-¹³C,¹⁵N]glutamine and the center [5-¹³C,¹⁴N]glutamine peak, resulting in an apparent triplet with a separation of 8 Hz. The time course of formation of brain [5-¹³C,¹⁵N]glutamine was monitored in vivo with a time resolution of 20–35 min. This [5-¹³C,¹⁵N]glutamine was formed by glial uptake of released neurotransmitter [5-¹³C]glutamate and its reaction with ¹⁵NH₃ catalyzed by the glia-specific glutamine synthetase. The neurotransmitter glutamate C5 was selectively¹³C-enriched by intravenous [2,5-¹³C]glucose infusion to ¹³C-label whole-brain glutamate C5, followed by [¹²C]glucose infusion to chase ¹³C from the small and rapidly turning-over glial glutamate pool, leaving ¹³C mainly in the neurotransmitter [5-¹³C]glutamate pool, which is sequestered in vesicles until release. Hence, the observed [5-¹³C,¹⁵N]glutamine arises from a coupling between ¹³C of neuronal origin and ¹⁵N of glial origin. Measurement of the rate of brain [5-¹³C,¹⁵N]glutamine formation provides a novel noninvasive method of studying the kinetics of neurotransmitter uptake into glia in vivo, a process that is crucial for protecting the brain from glutamate excitotoxicity.     

Energy transfer between Sm and Er in orthophosphate YPO4

The energy transfer between Sm³⁺ and Er³⁺ ions in yttrium orthophosphate is studied. This choice of ions is based on the possibility of quantum cutting processes and the host material is selected according to the position of the 5d bands of the Sm³⁺ ion. The Sm³⁺ and Er³⁺ doped and Sm³⁺, Er³⁺ co-doped YPO₄ have been synthesized. Spectroscopic studies were done in the ultraviolet and vacuum ultraviolet ranges. The energy transfer between Sm³⁺ and Er³⁺ is very efficient but it does not lead to Er³⁺ visible emission. Whatever the excitation wavelength, the emission of co-doped samples mainly occurs in the infrared range.     

In Vivo3D LocalizedC Spectroscopy Using Modified INEPT and DEPT

The 3D localized¹³C spectroscopy methods LINEPT and LODEPT, which are modifications of INEPT and DEPT, are proposed. As long as a¹³C inversion pulse (180-degree pulse) is applied at 1/(4J) before the proton echo time in LINEPT and a¹³C excitation pulse (90-degree pulse) is applied at 1/(2J) before the proton echo time in LODEPT, the proton echo time can be set to any value longer than 1/(2J) in LINEPT and longer than 1/Jin LODEPT. As a result, the proton and the¹³C pulses can be applied separately and these proton pulses can be made slice-selective pulses. These localization features of LINEPT and LODEPT were evaluated using a phantom consisting of a cylinder filled with ethanol placed inside another cylinder filled with oil, and localized ethanol spectra could be obtained.In vivo3D localized¹³C spectra from the brain of a monkey could be obtained using decoupled LINEPT, and glutamate C-4 appeared directly after the administration of glucose C-1, followed by the appearance of glutamate C-2, C-3 and glutamine C-2, C-3, C-4.     

Measurement of Small One-Bond Proton–Carbon Residual Dipolar Coupling Constants in Partially Oriented C Natural Abundance Oligosaccharide Samples: Analysis of Heteronuclear JCH-Modulated Spectra with the BIRD Inversion Pulse

Two 2D J-modulated HSQC-based experiments were designed for precise determination of small residual dipolar one-bond carbon–proton coupling constants in ¹³C natural abundance carbohydrates. Crucial to the precision of a few hundredths of Hz achieved by these methods was the use of long modulation intervals and BIRD pulses, which acted as semiselective inversion pulses. The BIRD pulses eliminated effective evolution of all but ¹J_CH couplings, resulting in signal modulation that can be described by simple modulation functions. A thorough analysis of such modulation functions for a typical four-spin carbohydrate spin system was performed for both experiments. The results showed that the evolution of the ¹H–¹H and long-range ¹H–¹³C couplings during the BIRD pulses did not necessitate the introduction of more complicated modulation functions. The effects of pulse imperfections were also inspected. While weakly coupled spin systems can be analyzed by simple fitting of cross peak intensities, in strongly coupled spin systems the evolution of the density matrix needs to be considered in order to analyse data accurately. However, if strong coupling effects are modest the errors in coupling constants determined by the “weak coupling” analysis are of similar magnitudes in oriented and isotropic samples and are partially cancelled during dipolar coupling calculation. Simple criteria have been established as to when the strong coupling treatment needs to be invoked.     

Deuterium Nuclear Spin–Lattice Relaxation Times and Quadrupolar Coupling Constants in Isotopically Labeled Saccharides

¹³C and ²H spin–lattice relaxation times have been determined by inversion recovery in a range of site-specific ¹³C- and ²H-labeled saccharides under identical solution conditions, and the data were used to calculate deuterium nuclear quadrupolar coupling constants (²H NQCC) at specific sites within cyclic and acyclic forms in solution. ¹³C T₁ values ranged from 0.6 to 8.2 s, and ²H T₁ values ranged from 79 to 450 ms, depending on molecular structure (0.4 M sugar in 5 mM EDTA (disodium salt) in ²H₂O-depleted H₂O, pH 4.8, 30°C). In addition to providing new information on ¹³C and ²H relaxation behavior of saccharides in solution, the resulting ²H1 NQCC values reveal a dependency on anomeric configuration within aldopyranose rings, whereas ²H NQCC values at other ring sites appear less sensitive to configuration at C1. In contrast, ²H NQCC values at both anomeric and nonanomeric sites within aldofuranose rings appear to be influenced by anomeric configuration. These experimental observations were confirmed by density functional theory (DFT) calculations of ²H NQCC values in model aldopyranosyl and aldofuranosyl rings.     

Improvement of Spectral Editing in Solids: A Sequence for Obtaining CH + CH2-Only C Spectra

An improved spectral editing method for solids is described which allows one to obtain a set of subspectra in roughly two-thirds the amount of time as our original CPPI editing method for the same signal to noise. This improvement is afforded by a new pulse sequence that is used to acquire a ¹³CH + ¹³CH₂ spectrum which has very little ¹³CH₃ or nonprotonated carbon contamination. By using this new sequence the ¹³CH-only subspectrum is obtained much more efficiently. Criteria for optimizing the signal to noise in the edited subspectra are discussed.     

Structure Elucidation and Assignment of 1H and 13C Spectra of the New Fused Cyclobutane-Naphthofuran Derivative by Two-Dimensional NMR in Different Solvents

One of the major product from the photodimerization of 2-[2-(2-methyl-phenyl)ethenyl)]naphtho[2. 1-b]furan (1) is a new fused cyclobutane-naphthofuran derivative, 6-(2-methylphenyl)-1-[2-(2-methylphenyl)ethenyl]-7-(2-naphtho-[2,1-b]furyl)-3-[2,1]naphtho-2-oxabicyclo[3.2.0]hept-3-ene (2). Its ¹H and ¹³C NMR spectra were fully assigned by the application of COSY, LR COSY, NOESY, APT and HETCOR experiments in deuterated chloroform, acetone and benzene solutions.     

Energy transfers between Sm and Eu in YPO4, LaP5O14 and LaP3O9 phosphates. Potential quantum cutters for red emitting phosphors

This work concerns the studies of energy transfers between Sm³⁺ and Eu³⁺ ions in some phosphates as new luminescent materials emitting in the orange-red color. The choose of ions is based on the possibility of quantum cutting process and the matrices are selected according to the 5d bands position of Sm³⁺ ion. The Sm³⁺ and Eu³⁺ doped YPO₄, LaP₅O₁₄ and LaP₃O₉ are synthesized and spectroscopic studies in ultraviolet and vacuum ultraviolet ranges have been achieved.     

Improvement of resolution in solid state NMR spectra with J-decoupling: an analysis of lineshape contributions in uniformly C-enriched amino acids and proteins

In magic angle spinning (MAS) NMR spectra of highly and uniformly 13C,15N-enriched amino acids and proteins, homo-nuclear coupling interactions contribute significantly to the 13C linewidths, particularly for moderate applied magnetic field strengths and sample spinning frequencies. In this work, we attempted to dissect, analyze, and control the contributions of J-coupling and residual homo-nuclear dipolar coupling interactions to the linewidths of uniformly 13C,15N-enriched crystalline alanine; these studies were carried out at 9.4 T using a range of spinning frequencies from 5 to 15 kHz. The anisotropic second-order dipolar shifts and the J-splittings are comparable in their contribution to the linewidths, but behave very differently in terms of experimental protocols for line narrowing. In contrast to the J-coupling interactions, the second-order dipolar broadening cannot be refocused using selective pulses on the passively coupled spin. We carried out experiments to remove or refocus the 13C J-coupling interactions (omega1 J-decoupling) using a selective DANTE pulse in the center of the indirect evolution period. Inversion profiles and bandwidths of selective DANTE pulses acting on transverse magnetization, in the regime of moderate spinning frequencies, were characterized computationally and experimentally. A dramatic improvement in the resolution of the 2D spectrum was achieved when this decoupling protocol was employed.     

C, N CPMAS NMR and GIAO DFT calculations of stereoisomeric oxindole alkaloids from Cat's Claw (Uncaria tomentosa)

Oxindole alkaloids, isolated from the bark of Uncaria tomentosa [Willd. ex Schult.] Rubiaceae, are considered to be responsible for the biological activity of this herb. Five pentacyclic and two tetracyclic alkaloids were studied by solid-state NMR and theoretical GIAO DFT methods. The ¹³C and ¹⁵N CPMAS NMR spectra were recorded for mitraphylline, isomitraphylline, pteropodine (uncarine C), isopteropodine (uncarine E), speciophylline (uncarine D), rhynchophylline and isorhynchophylline. Theoretical GIAO DFT calculations of shielding constants provide arguments for identification of asymmetric centers and proper assignment of NMR spectra. These alkaloids are 7R/7S and 20R/20S stereoisomeric pairs. Based on the ¹³C CP MAS chemical shifts the 7S alkaloids (δ C3 70–71 ppm) can be easily and conveniently distinguished from 7R (δC3 74.5–74.9 ppm), also 20R (δC20 41.3–41.7 ppm) from the 20S (δC20 36.3–38.3 ppm). The epiallo-type isomer (3R, 20S) of speciophylline is characterized by a larger ¹⁵N MAS chemical shift of N4 (64.6 ppm) than the allo-type (3S, 20S) of isopteropodine (δN4 53.3 ppm). ¹⁵N MAS chemical shifts of N1–H in pentacyclic alkaloids are within 131.9–140.4 ppm.     

Detection and Characterization of Boric Acid and Borate Ion Binding to Cytochrome c Using Multiple Quantum Filtered NMR

The application of multiple quantum filtered (MQF) NMR to the identification and characterization of the binding of ligands containing quadrupolar nuclei to proteins is demonstrated. Using relaxation times measured by MQF NMR multiple binding of boric acid and borate ion to ferri and ferrocytochrome c was detected. Borate ion was found to have two different binding sites. One of them was in slow exchange, k_diss = 20 ± 3 s⁻¹ at 5°C and D₂O solution, in agreement with previous findings by ¹H NMR (G. Taler et al., 1998, Inorg. Chim. Acta 273, 388–392). The triple quantum relaxation of the borate in this site was found to be governed by dipolar interaction corresponding to an average B–H distance of 2.06 ± 0.07 Å. Other, fast exchanging sites for borate and boric acid could be detected only by MQF NMR. The binding equilibrium constants at these sites at pH 9.7 were found to be 1800 ± 200 M⁻¹ and 2.6 ± 1.5 M⁻¹ for the borate ion and boric acid, respectively. Thus, detection of binding by MQF NMR proved to be sensitive to fast exchanging ligands as well as to very weak binding that could not be detected using conventional methods.