Multidimensional solid state NMR of anisotropic interactions in peptides and proteins

Accurate determinations of chemical shift anisotropy (CSA) tensors are valuable for NMR of biological systems. In this review we describe recent developments in CSA measurement techniques and applications, particularly in the context of peptides and proteins. These techniques include goniometeric measurements of single crystals, slow magic-angle spinning studies of powder samples, and CSA recoupling under moderate to fast MAS. Experimental CSA data can be analyzed by comparison with ab initio calculations for structure determination and refinement. This approach has particularly high potential for aliphatic (13)C analysis, especially Calpha tensors which are directly related to structure. Carbonyl and (15)N CSA tensors demonstrate a more complex dependence upon hydrogen bonding and electrostatics, in addition to conformational dependence. The improved understanding of these tensors and the ability to measure them quantitatively provide additional opportunities for structure determination, as well as insights into dynamics.     

Structural revision of peribysins C and D

Structural revision of the cell-adhesion inhibitory eremophilane sesquiterpenoid peribysins C and D is reported. A CAST/CNMR system is utilized in the reinvestigation of ¹³C NMR chemical shift values and structures, and geometric analyses with molecular and quantum mechanics calculations, and revalidation of NMR data support the revised structures.     

Quantum chemistry investigation of electronic structure and NMR spectral characteristics for fluorides of dialkylamidosulfoxylic acids and related compounds

The parent (H₂N? S? F) and N,N‐dialkyl‐substituted fluorides of amidosulfoxylic acid (R₂N? S? F, R?Me or R₂N?Morph) as well as the related compounds X? S? F (X?CH₃, OH, F, SiH₃, PH₂, SH, Cl) have been investigated with quantum chemical calculations at the ab initio (MP2) level of approximation. The geometries, electronic structures, molecular orbital (MO) energies and NMR chemical shift values have been calculated to evaluate the role and extent of the polarization and delocalization effects in forming of the high‐field fluorine NMR resonances within the series of interest. The δF magnitudes for all investigated fluorides of amidosulfoxylic acid as well as the δN value calculated for Me₂N? S? F are in the good agreement with the ¹⁹F and ¹⁴N NMR chemical shift values measured experimentally. For the parent compounds, H₂N? S? F and H₂N? SO₂? F, the orientation of principal axes of the magnetic shielding tensors and the corresponding principal σ_ii values along these axes have been qualitatively interpreted basing on the analysis of the MO interactions in the presence of the rotating magnetic field. Copyright © 2009 John Wiley & Sons, Ltd.     

Determinations of 15N chemical shift anisotropy magnitudes in a uniformly 15N,13C-labeled microcrystalline protein by three-dimensional magic-angle spinning nuclear magnetic resonance spectroscopy

Amide 15N chemical shift anisotropy (CSA) tensors provide quantitative insight into protein structure and dynamics. Experimental determinations of 15N CSA tensors in biologically relevant molecules have typically been performed by NMR relaxation studies in solution, goniometric analysis of single-crystal spectra, or slow magic-angle spinning (MAS) NMR experiments of microcrystalline samples. Here we present measurements of 15N CSA tensor magnitudes in a protein of known structure by three-dimensional MAS solid-state NMR. Isotropic 15N, 13C alpha, and 13C' chemical shifts in two dimensions resolve site-specific backbone amide recoupled CSA line shapes in the third dimension. Application of the experiments to the 56-residue beta1 immunoglobulin binding domain of protein G (GB1) enabled 91 independent determinations of 15N tensors at 51 of the 55 backbone amide sites, for which 15N-13C alpha and/or 15N-13C' cross-peaks were resolved in the two-dimensional experiment. For 37 15N signals, both intra- and interresidue correlations were resolved, enabling direct comparison of two experimental data sets to enhance measurement precision. Systematic variations between beta-sheet and alpha-helix residues are observed; the average value for the anisotropy parameter, delta (delta = delta(zz) - delta(iso)), for alpha-helical residues is 6 ppm greater than that for the beta-sheet residues. The results show a variation in delta of 15N amide backbone sites between -77 and -115 ppm, with an average value of -103.5 ppm. Some sites (e.g., G41) display smaller anisotropy due to backbone dynamics. In contrast, we observe an unusually large 15N tensor for K50, a residue that has an atypical, positive value for the backbone phi torsion angle. To our knowledge, this is the most complete experimental analysis of 15N CSA magnitude to date in a solid protein. The availability of previous high-resolution crystal and solution NMR structures, as well as detailed solid-state NMR studies, will enhance the value of these measurements as a benchmark for the development of ab initio calculations of amide 15N shielding tensor magnitudes.     

Theoretical and experimental 13C and 15N NMR investigation of guanylhydrazones in solution

Experimental and theoretical ¹⁵N and ¹³C NMR data for the three nitrobenzaldehyde guanylhydrazones are reported. The theoretical data were obtained using sequential molecular dynamics/quantum mechanics methodology for the calculation of flexible molecules in a condensed phase, followed by the use of the GIAO/DFT method with the 6–311G** basis set. The experimental ¹⁵N chemical shifts for the guanylhydrazones are compared with the calculated shifts. Copyright © 2003 John Wiley & Sons, Ltd.     

Natural Abundance 15N NMR by Dynamic Nuclear Polarization: Fast Analysis of Binding Sites of a Novel Amine‐Carboxyl‐Linked Immobilized Dirhodium Catalyst

A novel heterogeneous dirhodium catalyst has been synthesized. This stable catalyst is constructed from dirhodium acetate dimer (Rh₂(OAc)₄) units, which are covalently linked to amine‐ and carboxyl‐bifunctionalized mesoporous silica (SBA‐15?NH₂?COOH). It shows good efficiency in catalyzing the cyclopropanation reaction of styrene and ethyl diazoacetate (EDA) forming cis‐ and trans‐1‐ethoxycarbonyl‐2‐phenylcyclopropane. To characterize the structure of this catalyst and to confirm the successful immobilization, heteronuclear solid‐state NMR experiments have been performed. The high application potential of dynamic nuclear polarization (DNP) NMR for the analysis of binding sites in this novel catalyst is demonstrated. Signal‐enhanced ¹³C CP MAS and ¹⁵N CP MAS techniques have been employed to detect different carboxyl and amine binding sites in natural abundance on a fast time scale. The interpretation of the experimental chemical shift values for different binding sites has been corroborated by quantum chemical calculations on dirhodium model complexes.     

N7‐ and N9‐substituted purine derivatives: a 15N NMR study

The ¹⁵N NMR chemical shifts of N⁷‐ and N⁹‐substituted purine derivatives were investigated systematically at the natural abundance level of the ¹⁵N isotope. The NMR chemical shifts were determined and assigned using GSQMBC, GHMBC, GHMQC and GHSQC experiments in solution. ¹⁵N cross‐polarization magic angle spinning data were recorded for selected compounds in order to study the principal values of the ¹⁵N chemical shifts. Geometric parameters obtained by using RHF/6–31G** and single‐crystal x‐ray structural analysis were used to calculate the chemical‐shielding constants (GIAO and IGLO) which were then used to assign the nitrogen resonances observed in the solid‐state NMR spectra and to determine the orientation of the principal components of the shift tensors. Copyright © 2002 John Wiley & Sons, Ltd.     

Solid-state NMR and quantum chemical investigations of 13Calpha shielding tensor magnitudes and orientations in peptides: determining phi and psi torsion angles

We report the experimental determination of the (13)C(alpha) chemical shift tensors of Ala, Leu, Val, Phe, and Met in a number of polycrystalline peptides with known X-ray or de novo solid-state NMR structures. The 700 Hz dipolar coupling between (13)C(alpha) and its directly bonded (14)N permits extraction of both the magnitude and the orientation of the shielding tensor with respect to the C(alpha)-N bond vector. The chemical shift anisotropy (CSA) is recoupled under magic-angle spinning using the SUPER technique (Liu et al., J. Magn. Reson. 2002, 155, 15-28) to yield quasi-static chemical shift powder patterns. The tensor orientation is extracted from the (13)C-(14)N dipolar modulation of the powder line shapes. The magnitudes and orientations of the experimental (13)C(alpha) chemical shift tensors are found to be in good accord with those predicted from quantum chemical calculations. Using these principal values and orientations, supplemented with previously measured tensor orientations from (13)C-(15)N and (13)C-(1)H dipolar experiments, we are able to predict the (phi, psi, chi(1)) angles of Ala and Val within 5.8 degrees of the crystallographic values. This opens up a route to accurate determination of torsion angles in proteins based on shielding tensor magnitude and orientation information using labeled compounds, as well as the structure elucidation of noncrystalline organic compounds using natural abundance (13)C NMR techniques.     

Toward direct determination of conformations of protein building units from multidimensional NMR experiments I. A theoretical case study of For‐Gly‐NH2 and For‐L‐Ala‐NH2

NMR chemical shielding anisotropy tensors have been computed, employing several basis sets and the GIAO‐RHF and GIAO‐MP2 formalisms of electronic structure theory, for all the atoms of the five and nine typical backbone conformers of For‐Gly‐NH₂ and For‐L ‐Ala‐NH₂, respectively. Multidimensional chemical shift plots, as a function of the respective backbone fold, have been generated for both peptide models. On the 2D ¹H^NH‐¹⁵N^NH and ¹⁵N^NH‐¹³C^α plots the most notable feature is that at all levels of theory studied the backbone conformers cluster in different regions. Computed chemical shifts, as well as their averages, have been compared to relevant experimental values taken from the BioMagnetic Resonance Bank (BMRB). At the highest levels of theory, for all nuclei but the amide protons, deviations between statistically averaged theoretical and experimental shifts are as low as 1–3%. These results indicate that chemical shift information from selected multiple‐pulse NMR experiments (e.g., 2D‐HSQC and 3D‐HNCA) could directly be employed to extract folding information for polypeptides and proteins. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 882–900, 2000     

13C and 15N NMR spectra of high‐energy polyazidocyanopyridines

¹³C and ¹⁵N NMR spectra of high‐energy 2,4,6‐triazidopyridine‐3,5‐dicarbonitrile, 2,3,5,6‐tetraazidopyridine‐4‐carbonitrile and 3,4,5,6‐tetraazidopyridine‐2‐carbonitrile are reported. The assignment of signals in the spectra was performed on the basis of density functional theory calculations. The molecular geometries were optimized using the M06‐2X functional with the 6‐311+G(d,p) basis set. The magnetic shielding tensors were calculated by the gauge‐independent atomic orbital method with the Tao–Perdew–Staroverov–Scuseria hybrid functional known as TPSSh. In all the calculations, a polarizable continuum model was used to simulate solvent effects. This approach provided accurate predictions of the ¹³C and ¹⁵N chemical shifts for all the three compounds despite complications arising due to non‐coplanar arrangement of the azido groups in the molecules. It was found that the ¹⁵N chemical shifts of the N_α atoms in the azido groups of 2,4,6‐triazidopyridines correlate with the ¹³C chemical shifts of the carbon atoms attached to these azido groups. Copyright © 2016 John Wiley & Sons, Ltd.     

The diethyl dithiophosphate complex of tetraphenylantimony(V) and its solvated form, [Sb(C6H5)4{S2P(OC2H5)2}] · 1/2 C6H6: Synthesis, crystal structure, and 13C, 31P CP/MAS NMR study. an example of monodentate coordination of dithio ligands

The O,O′-diethyl dithiophosphate complex of tetraphenylantimony(V) [Sb(C₆H₅)₄{S₂P(OC₂H₅)₂}] (I) and its benzene-solvated form I · 1/2C₆H₆ (II) were synthesized and studied by high-resolution solid-state ¹³C and ³¹P NMR (MAS NMR). The diethyl dithiophosphate (Dtph) groups in I and II were quantitatively characterized by the ³¹P chemical shift anisotropy (δ_aniso), the asymmetry parameter (η), and the principal values of chemical shift tensors (δ _xx , δ _yy , δ _zz ). The calculation of the anisotropy parameters included construction of χ² statistic diagrams from full ³¹P MAS NMR spectra. In both complexes, the Dtph groups were found to have mainly axially symmetric ³¹P chemical shift tensors (for δ _zz < δ _xx ≈ δ _yy ) with similar anisotropy parameters (δ_aniso and η), which is due to their identical S-monodentate function. According to X-ray diffraction data, II has a trigonal bipyramidal (TBP) molecular structure with Smonodentate coordination of Dtph in the TBP axial position and outer-sphere position of the benzene molecule. The desorption of the outer-sphere benzene solvent molecules from structure II, which was noted in MAS NMR experiment, passes through the formation of three intermediate solvated forms with benzene content n < 1/2.     

Simulations of 129Xe NMR chemical shift of atomic xenon dissolved in liquid benzene

The isotropic ¹²⁹Xe NMR chemical shift of atomic Xe dissolved in liquid benzene was simulated by combining classical molecular dynamics and quantum chemical calculations of ¹²⁹Xe nuclear magnetic shielding. Snapshots from the molecular dynamics trajectory of xenon atom in a periodic box of benzene molecules were used for the quantum chemical calculations of isotropic ¹²⁹Xe chemical shift using nonrelativistic density functional theory as well as relativistic Breit?CPauli perturbation corrections. Thus, the correlation and relativistic effects as well as the temperature and dynamics effects could be included in the calculations. Theoretical results are in a very good agreement with the experimental data. The most of the experimentally observed isotropic ¹²⁹Xe shift was recovered in the nonrelativistic dynamical region, while the relativistic effects explain of about 8% of the total ¹²⁹Xe chemical shift.     

Crystallographic and Dynamic Aspects of Solid‐State NMR Calibration Compounds: Towards ab Initio NMR Crystallography

The excellent results of dispersion‐corrected density functional theory (DFT‐D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT‐D calculations is a target, especially for the field of molecular NMR crystallography. Four ¹³C ss‐NMR calibration compounds are investigated by single‐crystal X‐ray diffraction, molecular dynamics and DFT‐D calculations. The crystal structure of 3‐methylglutaric acid is reported. The rotator phases of adamantane and hexamethylbenzene at room temperature are successfully reproduced in the molecular dynamics simulations. The calculated ¹³C chemical shifts of these compounds are in excellent agreement with experiment, with a root‐mean‐square deviation of 2.0 ppm. It is confirmed that a combination of classical molecular dynamics and DFT‐D chemical shift calculation improves the accuracy of calculated chemical shifts.     

15N NMR chemical shifts in solid NH+4 salts

¹⁵N NMR CP/MAS spectra of solid NH⁺₄ salts show substantial chemical shift differences. Ab initio calculations indicate that changes in NH⁺₄ geometry and anion environment can account for the range of shifts.     

13C chemical shielding tensor orientations in a phosphoenolpyruvate moiety from 13C rotational-resonance MAS NMR lineshapes

The absolute orientations of the three ¹³C chemical shielding tensors in the phosphoenolpyruvate (PEP) moiety in a PEP-model compound with known crystal structure are reported. The study uses a fully ¹³C-enriched polycrystalline sample of triammonium phosphoenolpyruvate monohydrate, (NH₄)₃(PEP)⋅H₂O, and ¹³C MAS NMR experiments fulfilling various different ¹³C rotational-resonance conditions. The absolute ¹³C chemical shielding tensor orientations are derived by iterative fitting, employing numerically exact simulations, of various rotational-resonance ¹³C MAS NMR lineshapes of the three-¹³C-spin system in fully ¹³C-enriched (NH₄)₃(PEP)⋅H₂O. The implications of the results of this study for future, biochemically oriented solid-state NMR studies on the PEP moiety are outlined.     

Structure and protonation of some indolizine derivatives studied by ab initio MO calculations

Some gauge invariant atomic orbitals-coupled-perturbed Hartree-Fock (GIAO-CPHF) calculations were performed for seven indolizine derivatives and their monoprotonated forms. Chemical shift, molecular geometry, and charge distribution data are reported for each molecule. The calculations support the results of nuclear magnetic resonance (NMR) spectroscopy measurements showing that protonation occurs preferentially at N1. The good agreement between the calculated and observed ¹³C and ¹⁵N chemical shifts show that such calculations can be used for chemical shift assignment purposes. Cation structures and probable sites for electrophilic reaction or second protonation are also discussed.     

NMR “Crystallography” for Uniformly (13C, 15N)-Labeled Oriented Membrane Proteins

In oriented-sample (OS) solid-state NMR of membrane proteins, the angular-dependent dipolar couplings and chemical shifts provide a direct input for structure calculations. However, so far only ¹H–¹⁵N dipolar couplings and ¹⁵N chemical shifts have been routinely assessed in oriented ¹⁵N-labeled samples. The main obstacle for extending this technique to membrane proteins of arbitrary topology has remained in the lack of additional experimental restraints. We have developed a new experimental triple-resonance NMR technique, which was applied to uniformly doubly (¹⁵N, ¹³C)-labeled Pf1 coat protein in magnetically aligned DMPC/DHPC bicelles. The previously inaccessible ¹H_α–¹³C_α dipolar couplings have been measured, which make it possible to determine the torsion angles between the peptide planes without assuming α-helical structure a priori. The fitting of three angular restraints per peptide plane and filtering by Rosetta scoring functions has yielded a consensus α-helical transmembrane structure for Pf1 protein.     

Solid‐state NMR studies of 1,3‐imidazolidine‐2‐selenone and some related compounds

Solid‐state cross‐polarization magic angle spinning ¹³C, ⁷⁷Se and ¹⁵N NMR spectra were recorded for 1,3‐imidazolidine‐2‐selenone, its N‐substituted derivatives and some related compounds. The spinning sideband manifold intensities were used to obtain principal values of ¹³C and ⁷⁷Se chemical shift tensors. Large selenium chemical shift anisotropies were observed for these selenones. Copyright © 2003 John Wiley & Sons, Ltd.     

Polymorphism of N,N'-diacetylbiuret studied by solid-state 13C and 15N NMR spectroscopy, DFT calculations, and X-ray diffraction

The molecular configuration and crystal structure of solid polycrystalline N,N′′‐diacetylbiuret (DAB), a potential nitrogen‐rich fertilizer, have been analyzed by a combination of solid‐ and liquid‐state NMR spectroscopy, X‐ray diffraction, and DFT calculations. Initially a pure NMR study (“NMR crystallography”) was performed as available single crystals of DAB were not suitable for X‐ray diffraction. Solid‐state ¹³C NMR spectra revealed the unexpected existence of two polymorphic modifications (α‐ and β‐DAB) obtained from different chemical procedures. Several NMR techniques were applied for a thorough characterization of the molecular system, revealing chemical shift anisotropy (CSA) tensors of selected nuclei in the solid state, chemical shifts in the liquid state, and molecular dynamics in the solid state. Dynamic NMR spectroscopy of DAB in solution revealed exchange between two different configurations, which raised the question, is there a correlation between the two different configurations found in solution and the two polymorphic modifications found in the solid state? By using this knowledge, a new crystallization protocol was devised which led to the growth of single crystals suitable for X‐ray diffraction. The X‐ray data showed that the same symmetric configuration is present in both polymorphic modifications, but the packing patterns in the crystals are different. In both cases hydrogen bonds lead to the formation of planes of DAB molecules. Additional symmetry elements, a two‐fold screw in the case of α‐DAB and a c‐glide plane in the case of β‐DAB, lead to a more symmetric (α‐DAB) or asymmetric (β‐DAB) intermolecular hydrogen‐bonding pattern for each molecule.     

Interaction of Cd and Zn with biologically important ligands characterized using solid-state NMR and ab initio calculations

For the first time, coordination geometry and structure of metal binding sites in biologically relevant systems are studied using chemical shift parameters obtained from solid-state NMR experiments and quantum chemical calculations. It is also the first extensive report looking at metal-imidazole interaction in the solid state. The principal values of the (113)Cd chemical shift anisotropy (CSA) tensor in crystalline cadmium histidinate and two different cadmium formates (hydrate and anhydrate) were experimentally measured to understand the effect of coordination number and geometry on (113)Cd CSA. Further, (13)C and (15)N chemical shifts have also been experimentally determined to examine the influence of cadmium on the chemical shifts of (15)N and (13)C nuclei present near the metal site in the cadmium-histidine complex. These values were then compared with the chemical shift values obtained from the isostructural bis(histidinato)zinc(II) complex as well as from the unbound histidine. The results show that the isotropic chemical shift values of the carboxyl carbons shift downfield and those of amino and imidazolic nitrogens shift upfield in the metal (Zn,Cd)-histidine complexes relative to the values of the unbound histidine sample. These shifts are in correspondence with the anticipated values based on the crystal structure. Ab initio calculations on the cadmium histidinate molecule show good agreement with the (113)Cd CSA tensors determined from solid-state NMR experiments on powder samples. (15)N chemical shifts for other model complexes, namely, zinc glycinate and zinc hexaimidazole chloride, are also considered to comprehend the effect of zinc binding on (15)N chemical shifts.