Separating Structure and Dynamics in CSA/DD Cross-Correlated Relaxation: A Case Study on Trehalose and Ubiquitin

We present two new sensitivity enhanced gradient NMR experiments for measuring interference effects between chemical shift anisotropy (CSA) and dipolar coupling interactions in a scalar coupled two-spin system in both the laboratory and rotating frames. We apply these methods for quantitative measurement of longitudinal and transverse cross-correlation rates involving interference of ¹³C CSA and ¹³C–¹H dipolar coupling in a disaccharide, α,α- -trehalose, at natural abundance of ¹³C as well as interference of amide ¹⁵N CSA and ¹⁵N–¹H dipolar coupling in uniformly ¹⁵N-labeled ubiquitin. We demonstrate that the standard heteronuclear T₁, T₂, and steady-state NOE autocorrelation experiments augmented by cross-correlation measurements provide sufficient experimental data to quantitatively separate the structural and dynamic contributions to these relaxation rates when the simplifying assumptions of isotropic overall tumbling and an axially symmetric chemical shift tensor are valid.     

Characterization of 15N chemical shift tensors via 15N-13C REDOR and 1N-1H dipolar-shift CPMAS NMR spectroscopy

As part of our studies on the characterization of 15N chemical shift anisotropy (CSA) via magic angle spinning (MAS) NMR spectroscopy, we have investigated via numerical simulations the sensitivity of two different REDOR experimental protocols to the angles defining the orientation of the 15N-13C' bond vector in the principal axis system of the 15N CSA tensor of the amide nitrogen in a peptide bond. Additionally, employing polycrystalline samples of 15N and 13C', 15N-labeled acetanilide, we have obtained, in a first study of this type, the orientation of the 15N CSA tensor in the molecular frame by orienting the tensor with respect to the 15N-3C' and 15N-1H dipolar vectors via 15N-13C' REDOR and 15N-1H dipolar-shift MAS experiments, respectively.     

Separating structure and dynamics in CSA/DD cross-correlated relaxation: a case study on trehalose and ubiquitin

We present two new sensitivity enhanced gradient NMR experiments for measuring interference effects between chemical shift anisotropy (CSA) and dipolar coupling interactions in a scalar coupled two-spin system in both the laboratory and rotating frames. We apply these methods for quantitative measurement of longitudinal and transverse cross-correlation rates involving interference of (13)C CSA and (13)C-(1)H dipolar coupling in a disaccharide, alpha,alpha-D-trehalose, at natural abundance of (13)C as well as interference of amide (15)N CSA and (15)N-(1)H dipolar coupling in uniformly (15)N-labeled ubiquitin. We demonstrate that the standard heteronuclear T(1), T(2), and steady-state NOE autocorrelation experiments augmented by cross-correlation measurements provide sufficient experimental data to quantitatively separate the structural and dynamic contributions to these relaxation rates when the simplifying assumptions of isotropic overall tumbling and an axially symmetric chemical shift tensor are valid.     

The roles of homonuclear line narrowing and the1H amide chemical shift tensor in structure determination of proteins by solid-state NMR spectroscopy

The seminal contributions of Ulrich Haeberlen to homonuclear line narrowing and the determination of¹H chemical shift tensors are crucial for protein structure determination by solid-state nuclear magnetic resonance spectroscopy. The¹H chemical shift is particularly important in spectra obtained on oriented samples of membrane proteins as a mechanism for providing dispersion among resonances that are not resolved with the¹H-¹⁵N dipolar coupling and¹⁵N chemical shift frequencies. This is demonstrated with three-dimensional experiments on uniformly¹⁵N-labeled samples of Magainin antibiotic peptide and the protein Vpu from HIV-1 in oriented lipid bilayers. These experiments enable resonances in two-dimensional¹H-¹⁵N dipolar coupling/¹⁵N chemical shift planes separated by¹H chemical shift frequencies to be resolved and analyzed. These three-dimensional spectra are compared to one-dimensional spectra of full-length Vpu, the cytoplasmic domain of Vpu, and Magainin, as well as to two-dimensional spectra of fd coat protein and Colicin El polypeptide. The¹H amide chemical shift tensor provides valuable structural information, and this is demonstrated with its contributions to orientational restrictions to one of the in-plane helical residues of Magainin.     

Measurement of Cross Correlation between Dipolar Coupling and Chemical Shift Anisotropy in the Spin Relaxation ofC,N-Labeled Proteins

We present a simple method for extracting interference effects between chemical shift anisotropy (CSA) and dipolar coupling from spin relaxation measurements in macromolecules, and we apply this method to extracting cross-correlation rates involving interference of amide¹⁵N CSA and¹⁵N–¹H dipolar coupling and interference of carbonyl¹³C′ CSA and¹⁵N–¹³C′ dipolar coupling, in a small protein. A theoretical basis for the interpretation of these rates is presented. While it proves difficult to quantitatively separate the structural and dynamic contributions to these cross-correlation rates in the presence of anisotropic overall tumbling and a nonaxially symmetric chemical shift tensor, some useful qualitative correlations of data with protein structure can be seen when simplifying assumptions are made.     

Fluorine-19 Solid-State NMR Magic-Angle-Turning Experiments Using Multiple-Pulse Homonuclear Decoupling

For compounds giving “crowded” 1-dimensional magic-angle-spinning spectra, information about the local atomic environment in the form of the chemical shift anisotropy (CSA) is sacrificed for high resolution of the less informative isotropic chemical shift. Magic-angle-turning (MAT) NMR pulse sequences preserve the CSA information by correlating it to the isotropic chemical shift in a 2-dimensional experiment. For low natural abundance nuclei such as ¹³C and ¹⁵N and under ¹H heteronuclear dipolar decoupling conditions, the dominant NMR interaction is the chemical shift. For abundant nuclei such as ¹H, ¹⁹F, and ³¹P, the homonuclear dipolar interaction becomes a significant contribution to the observed linewidth in both F₁ and F₂ dimensions. We incorporate MREV8 homonuclear multiple-pulse decoupling sequences into the MAT experiment to give a multiple-pulse MAT (MP-MAT) experiment in which the homonuclear dipolar interaction is suppressed while maintaining the chemical shift information. Extensive use of computer simulation using GAMMA has guided the pulse sequence development. In particular, we show how the MREV8 pulses can be incorporated into a quadrature-detected sequence such as MAT. The MP-MAT technique is demonstrated for a model two-site system containing a mixture of silver trifluoroacetate and calcium difluoride. The resolution in the isotropic evolution dimension is improved by faster sample spinning, shorter MREV8 cycle times in the evolution dimension, and modifications of the MAT component of the pulse sequence.     

A 15N NMR Study of Some Imidazolidine-2,4-Dichalcogen Derivatives

The ¹⁵N NMR chemical shifts and ¹(¹⁵N-¹H) coupling constants of a series of imidazolidine-2,4-dichalcogen (O, S) derivatives are reported.The ¹⁵N NMR chemical shifts show a linear correlatlon wlth the vNH stretchlng vlbratlons. The influence of the substitution of the oxygen at C₂ and/or C₄ with the sulphur, and of the hydrogen at C₅ wlth the methyls and phenyls has been considered. The ¹J(¹⁵N-¹H)'s found In thls serles of molecules agrees well with the expected values.     

天然丰度的N-磷酰化氨基酸的15N NMR 研究

采用¹⁵N-¹H的2D HSQC、HMBC实验方法,测定了天然丰度的N-磷酰化氨基酸样品在溶液中的¹⁵N化学位移δ_N及偶合常数J_N-P,J_N-H. 实验表明：对于¹⁵N天然丰度样品,这是一种快速有效的实验方法. 研究发现：N-酰化后的氨基酸,其δ_N以及与氮原子直接相连的质子¹H的化学位移均发生十分明显的高场位移,而偶合常数¹J_N-P,¹J_N-H的变化与化合物构型相关联 .     

Studies of EPR and ENDOR spectra of14N and15N label bis(2-hydroxyacetophenyl ketoxime)-63Cu(II) and-65Cu(II) complexes in disordered system

The EPR spectra of isotopic label bis(2-hydroxyacetophenyl ketoxime)-Cu(II) [N?Cu-HAP] complexes, such as¹⁴N?⁶³Cu-HAP,¹⁵N?⁶³Cu-HAP and¹⁴N?⁶⁵Cu-HAP in frozen THF solution below 77 K, and their ENDOR spectra in frozen DMSO/EtOH (5∶1) solution below 20 K were studied. The exact values of the components ofg-tensor, of hyperfine tensors of copper isotopes, and of superhyperfine interaction tensors of copper with nuclei of nitrogen isotopes and¹H nuclei, and of the¹⁴N nuclear quadrupolar moment coupling tensor were obtained. The bond parameters α, β, δ, γ and the corresponding energy levels of N?Cu-HAP complexes were calculated by using EPR and ENDOR data. It was shown that the unpaired, electron is delocalized not only to the nearest N atom but also to the H atom, of ligands, which is more far from the Cu ion.     

Cation Binding Induced Changes inN CSA in a Membrane-Bound Polypeptide

Cation binding to the monovalent cation selective channel, gramicidin A, is shown to induce changes in the dipolar and chemical shift observables from uniformly aligned samples. While these changes could be the result of structural or dynamic changes, they are shown to be primarily induced by through-bond polarizability effects when cations are solvated by the carbonyl oxygens of the peptide backbone. Upon cation binding partial charges are changed throughout the peptide plane, inducing large changes in the¹³C₁chemical shifts, smaller changes in the¹⁵N chemical shifts, and even smaller effects for the¹⁵N–¹³C₁and¹⁵N–²H dipolar interactions. These conclusions are substantiated by characterizing the¹⁵N chemical shift tensors in the presence and absence of cations in fast-frozen lipid bilayer preparations of gramicidin A.     

Molecular-orientation analysis based on alignment-induced TROSY chemical shift changes

We present a new NMR technique for determining the alignment tensor of a weakly aligned protein using only alignment-induced ¹⁵N transverse relaxation optimized spectroscopy (TROSY) chemical shift changes. Alignment-induced TROSY chemical shift changes reflect the combined contributions from two different anisotropic spin interactions including the residual dipolar couplings (RDCs) and the residual chemical shift anisotropy effects (RCSAs). We show here that these two residual anisotropic spin interactions’ values, encoded in the TROSY chemical shift changes, can be used to determine a weakly aligned protein’s alignment tensor. To prove the significance of this method, we show that our TROSY-based analysis gives the consistent alignment angles with those determined using RDCs for ¹⁵N-labeled ubiquitin (8.6 kDa) in an aligned medium, within an uncertainty range estimated by considering experimental and structural noises, being 5° at most. Because our approach requires a pre-determined ¹⁵N CSA tensor value, we also estimated the uncertainties associated with the resultant alignment tensor values caused by variation in ¹⁵N CSA tensors. In spite of the significant variations in literature-reported ¹⁵N CSA tensors, they gave consistent orientation angles within an uncertainty range. These results ensure that our TROSY-based approach is a useful alternative to the RDC-based method to determine the alignment angles especially for large proteins in a weakly aligned state.     

A Study of Dipolar Interactions and Dynamic Processes of Water Molecules in Tendon byH andH Homonuclear and Heteronuclear Multiple-Quantum-Filtered NMR Spectroscopy

The effect of proton exchange on the measurement of¹H–¹H,¹H–²H, and²H–²H residual dipolar interactions in water molecules in bovine Achilles tendons was investigated using double-quantum-filtered (DQF) NMR and new pulse sequences based on heteronuclear and homonuclear multiple-quantum filtering (MQF). Derivation of theoretical expressions for these techniques allowed evaluation of the¹H–¹H and¹H–²H residual dipolar interactions and the proton exchange rate at a temperature of 24°C and above, where no dipolar splitting is evident. The values obtained for these parameters at 24°C were 300 and 50 Hz and 3000 s⁻¹, respectively. The results for the residual dipolar interactions were verified by repeating the above measurements at a temperature of 1.5°C, where the spectra of the H₂O molecules were well resolved, so that the¹H–¹H dipolar interaction could be determined directly from the observed splitting. Analysis of the MQF experiments at 1.5°C, where the proton exchange was in the intermediate regime for the¹H–²H dipolar interaction, confirmed the result obtained at 24°C for this interaction. A strong dependence of the intensities of the MQF signals on the proton exchange rate, in the intermediate and the fast exchange regimes, was observed and theoretically interpreted. This leads to the conclusion that the MQF techniques are mostly useful for tissues where the residual dipolar interaction is not significantly smaller than the proton exchange rate. Dependence of the relaxation times and signal intensities of the MQF experiments on the orientation of the tendon with respect to the magnetic field was observed and analyzed. One of the results of the theoretical analysis is that, in the fast exchange regime, the signal decay rates in the MQF experiments as well as in the spin echo or CPMG pulse sequences (T₂) depend on the orientation as the square of the second-rank Legendre polynomial.     

Structure determination in "shiftless" solid state NMR of oriented protein samples

An efficient formalism for calculating protein structures from oriented-sample NMR data in the torsion-angle space is presented. Angular anisotropies of the NMR observables are treated by utilizing an irreducible spherical basis of rotations. An intermediate rotational transformation is introduced that greatly speeds up structural fitting by rendering the dependence on the torsion angles Φ and Ψ in a purely diagonal form. Back-calculation of the simulated solid-state NMR spectra of protein G involving 15N chemical shift anisotropy (CSA), and 1H-15N and 1Hα-13Cα dipolar couplings was performed by taking into account non-planarity of the peptide linkages and experimental uncertainty. Even a relatively small (to within 1 ppm) random variation in the CSA values arising from uncertainties in the tensor parameters yields the RMSD's of the back-calculated structures of more than 10 ?. Therefore, the 15N CSA has been substituted with heteronuclear dipolar couplings which are derived from the highly conserved bond lengths and bond angles associated with the amino-acid covalent geometry. Using the additional 13Cα-15N and 13C'-15N dipolar couplings makes it possible to calculate protein structures entirely from "shiftless" solid-state NMR data. With the simulated "experimental" uncertainty of 15 Hz for protein G and 120 Hz for a helical hairpin derived from bacteriorhodopsin, back-calculation of the synthetic dipolar NMR spectra yielded a converged set of solutions. The use of distance restraints dramatically improves structural convergence even if larger experimental uncertainties are assumed.     

Quantitative Investigation of Dipole–CSA Cross-Correlated Relaxation by ZQ/DQ Spectroscopy

A zero-quantum/double-quantum HNCO(H) constant time experiment is presented for the quantitative evaluation of dipole–CSA cross-correlated relaxation involving the¹H^N,¹⁵N, and¹³C′ nuclei of the peptide plane. A simple procedure that allows the extraction of cross-correlated relaxation rate constants from intensity ratios of well-resolved doublet components along ω₁is described. The experiment is demonstrated on fully¹³C,¹⁵N-labeled ubiquitin.     

Accurate 13-C and 15-N molecular crystal chemical shielding tensors from fragment-based electronic structure theory

Standard nuclear magnetic resonance (NMR) spectroscopy experiments measure isotropic chemical shifts, but measuring the chemical shielding anisotropy (CSA) tensor can provide additional insights into solid state chemical structures. Interpreting the principal components of these tensors is facilitated by first-principles chemical shielding tensor predictions. Here, the ability to predict molecular crystal CSA tensor components for ¹³C and ¹⁵N nuclei with fragment-based electronic structure techniques is explored. Similar to what has been found previously for isotropic chemical shifts, the benchmarking demonstrates that fragment-based techniques can accurately reproduce CSA tensor components. The use of hybrid density functionals like PBE0 or B3LYP provide higher accuracy than generalized gradient approximation functionals like PBE. Unlike for planewave density functional techniques, hybrid density functionals can be employed routinely with modest computational cost in fragment approaches. Finally, good consistency between the regression parameters used to map either isotropic shieldings or CSA tensor components is demonstrated, providing further evidence for the quality of the models and highlighting that models trained for isotropic shifts can also be applied to CSA tensor components.     

13C and 15N spectral editing inside histidine imidazole ring through solid-state NMR spectroscopy

Histidine usually exists in three different forms (including biprotonated species, neutral τ and π tautomers) at physiological pH in biological systems. The different protonation and tautomerization states of histidine can be characteristically determined by ¹³C and ¹⁵N chemical shifts of imidazole ring. In this work, solid-state NMR techniques were developed for spectral editing of ¹³C and ¹⁵N sites in histidine imidazole ring, which provides a benchmark to distinguish the existing forms of histidine. The selections of ¹³C_γ, ¹³C_δ2, ¹⁵N_δ1, and ¹⁵N_ε2 sites were successfully achieved based on one-bond homo- and hetero-nuclear dipole interactions. Moreover, it was demonstrated that ¹H, ¹³C, and ¹⁵ chemical shifts were roughly linearly correlated with the corresponding atomic charge in histidine imidazole ring by theoretical calculations. Accordingly, the ¹H, ¹³C and ¹⁵N chemical shifts variation in different protonation and tautomerization states could be ascribed to the atomic charge change due to proton transfer in biological process.     

Differential Line Broadening in the Presence of Quadrupolar–CSA Interference

The formalism for calculating the lineshape of a spin 1/2J-coupled to a high-spin nucleus undergoing quadrupolar and chemical shift anisotropy (CSA) relaxations is derived in the case where the tensors of both interactions are noncoincident and nonaxial. The expressions show that the CSA–quadrupolar interference term which is responsible for the asymmetry of lines involves a term depending on tensorial parameters. The effect of this term on the lineshapes is discussed with respect to three cases, namely coincident–axially symmetric, noncoincident–axially symmetric, and general noncoincident quadrupolar and CSA tensors. These cases are considered in the analysis of the lineshape of the¹H-decoupled spectra of the³¹P nucleusJ-coupled to the⁵⁹Co nucleus encountered in the tetrahedral cluster HFeCo₃(CO)₁₁PPh₂H.     

Iterative Lineshape Fitting of MAS NMR Spectra: A Tool to Investigate HomonuclearJCoupling in Isolated Spin Pairs

Possibilities and limitations of iterative lineshape fitting procedures of MAS NMR spectra of isolated homonuclear spin pairs, aiming at determination of magnitudes and orientations of the various interaction tensors, are explored. Requirements regarding experimental MAS NMR spectra as well as simulation and fitting procedures are discussed. Our examples chosen are the isolated³¹P spin pairs in solid Na₄P₂O₇· 10H₂O, (1), and Cd(NO₃)₂· 2PPh₃, (2). In both cases the two³¹P chemical shielding tensors in the molecular unit are related byC₂symmetry, and determination of the orientations of these two tensors in the molecular frame is possible. In addition, aspects of homonuclearJcoupling will be addressed. For 1, both magnitude and sign of²J_iso(³¹P,³¹P) (J_iso= −19.5 ± 2.5 Hz) are obtained; for 2, (J_iso= +139 ± 3 Hz) anisotropy ofJwith an orientation of theJ-coupling tensor collinear, or nearly collinear, with the dipolar coupling tensor can be excluded, while absence or presence of anisotropy ofJwith any other relative orientation of theJ-coupling tensor cannot be determined.     

1H detected 1H,15N correlation spectroscopy in rotating solids

We describe new correlation experiments suitable for determining long-range 1H-1H distances in 2H,15N-labeled peptides and proteins. The approach uses perdeuteration together with back substitution of exchangeable protons during sample preparation as a means of attenuating the strong 1H-1H dipolar couplings that broaden 1H magic angle spinning (MAS) spectra of solids. In the approach described here, we retain 100% of the 1H sensitivity by labeling and detecting all exchangeable sites. This is in contrast to homonuclear multiple pulse decoupling sequences that are applied during detection and that compromise sensitivity because of the requirement of sampling between pulses. As a result 1H detection provides a gain in sensitivity of >5 compared to the 15N detected version of the experiment (at a MAS frequency of 13.5kHz). The pulse schemes make use of the favorable dispersion of the amide 15Ns resonances in the protein backbone. The experiments are demonstrated on a sample of the uniformly 2H,15N-labeled dipeptide N-Ac-Val-Leu-OH and are analogous to the solution-state suite of HSQC-NOESY experiments. In this compound the 1H amide linewidths at 750MHz vary from approximately 0.67 ppm at omega(r)/2pi approximately 5kHz to approximately 0.20 ppm at omega(r)/2pi approximately 30kHz, indicating that useful resolution is available in the 1H spectrum via this approach. Since the experiments circumvent the problem of dipolar truncation in the 1H-1H spin system, they should make it possible to measure long-range distances in a uniformly labeled environment. Thus, we expect the experiments to be useful in constraining the global fold of a protein.     

Two- and Three-Dimensional H/C PISEMA Experiments and Their Application to Backbone and Side Chain Sites of Amino Acids and Peptides

Two-dimensional ¹H/¹³C polarization inversion spin exchange at the magic angle experiments were applied to single crystal samples of amino acids to demonstrate their potential utility on oriented samples of peptides and proteins. High resolution is achieved and structural information obtained on backbone and side chain sites from these spectra. A triple-resonance experiment that correlates the ¹H–¹³C_α dipolar coupling frequency with the chemical shift frequencies of the α-carbon, as well as the directly bonded amide ¹⁵N site, is also demonstrated. In this experiment the large ¹H–¹³C_α heteronuclear dipolar interaction provides an independent frequency dimension that significantly improves the resolution among overlapping ¹³C resonances of oriented polypeptides, while simultaneously providing measurements of the ¹³C_α chemical shift, ¹H–¹³C dipolar coupling, and ¹⁵N chemical shift frequencies and angular restraints for backbone structure determination.