Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings.

Despite the importance of molecular dynamics for biological activity, most approaches to protein structure determination, whether based on crystallographic or solution studies, propose three-dimensional atomic representations of a single configuration that take no account of conformational fluctuation. Non-averaged anisotropic NMR interactions, such as residual dipolar couplings, that become measurable under conditions of weak alignment, provide sensitive probes of both molecular structure and dynamics. Residual dipolar couplings are becoming increasingly powerful for the study of proteins in solution. In this minireview we present their use for the simultaneous determination of protein structure and dynamics.     

The structure of acrolein in a liquid crystal phase

The (1)H NMR spectrum of a sample of acrolein dissolved in the nematic liquid crystal phase I52 has been analysed to yield 18 dipolar couplings between all the magnetic nuclei in the molecule; moreover, the (13)C and (13)C{(1)H} NMR spectra of a sample of acrolein in CDCl(3) were recorded and analysed to determine the indirect J(ij) couplings. The data were used to obtain the relative positions of the carbon and hydrogen atoms, assuming that these are independent of the conformations generated by rotation around the C--C bond through an angle phi, and to obtain a probability distribution P(phi). It has been found that in the liquid phase, the distribution is a maximum at the trans form whereas the abundance of the cis form is significantly smaller compared with that found by microwave spectroscopy or high level quantum mechanical calculations. Such calculations produced also a suitable force field needed to develop suitable strategies for vibrational correction procedure in the case of flexible molecules.     

Molecular Conformations of Shape Anisometrically Variant Mesogens in Liquid Crystalline Phase Studied by 13C NMR Spectroscopy

Mesogens that vary in shape anisometry have been investigated by ¹³C solid-state NMR in the liquid crystalline phase to inspect the conformations. The molecules examined comprise of (i) rod-like mesogen with three-phenyl ring core and terminal hexyloxy chains, (ii) three-ring core linked to the fourth phenyl ring via a spacer, and (iii) trimesic acid connected to three side arms core units through a spacer. The order parameter (S_zz) values for the phenyl rings of the rod-like mesogen are 0.65–0.68, while the mesogen with a three-ring core linked to a phenyl ring via spacer showed dissimilarity. Consequently, for the core unit phenyl rings, S_zz is ~0.70, and the terminal phenyl ring showed a low value of 0.12. For the trimesic acid based mesogen, the S_zz value for the side arm phenyl rings is ~0.53, and for the central phenyl ring, a very low value of 0.11 is witnessed. By considering the ordering of the rod-like mesogen as a yardstick and employing the ratios of S_zz values of the phenyl rings, the average conformations of other mesogens are arrived. Accordingly, for the trimesic acid based mesogen, a tripod-like conformation instead of λ shape is proposed in the liquid crystalline phase.     

NMR spectroscopy investigation of the cooperative nature of the internal rotational motions in acetophenone.

The proton NMR spectrum of the doubly enriched acetophenone-carbonyl,methyl-13C2 isotopomer dissolved in a liquid-crystalline solvent (LXNMR) was analyzed to yield a data set of 19 dipolar couplings. The presence of so many couplings, and in particular the dependence of some of them on the acetyl carbons enabled the investigation of the structure of the acetyl moiety and of possible cooperative motions about the aryl-carbonyl and carbonyl-methyl bonds. Methodological aspects, and approximations relating to the application of the vibrational correction procedure in the presence of large-amplitude torsional motions, are discussed. Results show that it is possible to discriminate between a continuous and a discrete conformer distribution about the angle phi(1) but not among a few proposed continuous shapes of U(iso)({phi}). In this study, the use of dipolar couplings with a non-negligible contribution from the indirect spin-spin coupling tensor J, (D(C8C9) in our case), for structural determination is extended from rigid to flexible molecules. The 1/2J(aniso)(C8C9) contribution was derived theoretically using the density functional theory linear response (DFT-LR) first-principles calculation of the J(C8C9) spin-spin coupling tensor.     

The F NMR spectrum of bis-trifluoromethylmercury Hg(CF3)2 in the nematic phase: DAISY — a novel program system for the analysis and simulation of NMR spectra

The ¹⁹F NMR spectrum of bis-trifluoromethylmercury in the nematic phase has been analysed using the DAISY program system. The scalar and the dipolar coupling constants have been obtained.     

Multiple quantum NMR spectra of toluene and p‐bromotoluene partially aligned in a nematic phase

¹H multiple quantum (MQ) NMR spectra of toluene and p‐bromotoluene, partially aligned in a liquid crystalline solvent, were acquired using gradient‐assisted methods. The MQ spectra were analysed to give the dipolar couplings (D_ij) and these were used to determine the molecular shape and average orientation of the of the spin systems. Copyright © 2003 John Wiley & Sons, Ltd.     

Banana-shaped molecules peculiarly oriented in a magnetic field: (2)H NMR spectroscopy and quantum mechanical calculations.

The orientational properties of the banana-shaped liquid crystal 4-chloro-1,3-phenylenebis{4-[4'-(10-undecenyloxy)]benzoyloxy} benzoate (ClPbis11BB) are reported in the nematic phase under the effect of an external magnetic field. A new hypothesis, which states that the central ring of the aromatic core is oriented perpendicularly to the external magnetic field, is proposed. In support of this hypothesis, a series of studies based on (2)H NMR spectroscopy, both in the bulk and in solution, are discussed. (2)H NMR measurements on three selectively deuterium-labelled isotopomers are presented, together with DFT results from B3LYP/cc-pvDz calculations performed on the aromatic core. The rather flat shape of the investigated intramolecular energy surface allows for several different conformations to be populated, the computed magnetic susceptibilities of which are consistent with the proposed hypothesis of peculiar orientation of banana-shaped molecules. Moreover, the orientation of the magnetic susceptibility tensor is shown to be strongly dependent on the internal conformation of the banana-shaped molecules.     

Solution- and bound-state conformational study of N,N',N"-triacetyl chitotriose and other analogous potential inhibitors of hevamine: application of trNOESY and STD NMR spectroscopy

The solution-state conformations of N,N',N"-triacetyl chitotriose (1) and other potential chitinase inhibitors 2-4 were studied using a combination of NMR spectroscopy (NOESY) and molecular mechanics calculations. Determination solely of the global energy minimum conformation was found to be insufficient for an agreement with the NMR results. An appropriate consistency between the NMR experimental data and theoretical calculations was only reached by assessing the structures as population-weighted average conformers based on Boltzmann distributions derived from the calculated relative energies. Analogies, but also particular differences, between the synthetic compounds 2-4 and the naturally-occurring N,N',N"-triacetyl chitotriose were found. Furthermore, the conformation of compounds 1 and 2 when bound to hevamine was also studied using transferred NOESY experiments and the binding process was found to impart a level of conformational restriction on the ligands. The preferred conformation as determined for 1 in the bound state to hevamine belonged to one of the conformational families found for the compound when free in solution, although full characterisation of the bound-state conformations was impeded due to severe signal overlap. Saturation transfer difference NMR experiments were also employed to analyse the binding epitopes of the bound compounds. We thus determined that it is mainly the acetyl amido groups of the trisaccharide and the heterocyclic moiety which are in close contact with hevamine.     

Determination of natural abundance 15N-1H and 13C-1H dipolar couplings of molecules in a strongly orienting media using two-dimensional inverse experiments

NMR spectra of molecules oriented in liquid crystals provide homo- and heteronuclear dipolar couplings and thereby the geometry of the molecules. Several inequivalent dilute spins such as 13C and 15N coupled to protons form different coupled spin systems in their natural abundance and appear as satellites in the proton spectra. Identification of transitions belonging to each spin system is essential to determine heteronuclear dipolar couplings, which is a formidable task. In the present study, using 15N-1H and 13C-1H HSQC, and HMQC experiments we have selectively detected spectra of each rare spin coupled to protons. The 15N-1H and 13C-1H dipolar couplings have been determined in the natural abundance of 13C and 15N for the molecules pyrazine, pyrimidine and pyridazine oriented in a thermotropic liquid crystal.     

Natural abundance deuterium NMR spectroscopy in polypeptide liquid crystals as a new and incisive means for the enantiodifferentiation of chiral hydrocarbons

Polymeric chiral liquid-crystalline solvents based on homopolypeptides are of interest with the view to discriminate between enantiomeric pairs of chiral hydrocarbons using proton-decoupled deuterium one- and two-dimensional NMR spectroscopy at natural abundance level. This method offers the major advantage that neither chemical modification nor isotopic labelling of the solutes to be studied is required. Chiral differentiation between optical isomers is observed through a difference in residual deuterium quadrupolar splittings. The spectroscopic separations and the S/N ratio from the spectra are usually large enough to measure the enantiomeric excess with an accuracy varying between 5 to 10 %. This analytical approach is successfully applied to a large collection of chiral, rigid or flexible unsaturated as well as saturated hydrocarbons, including cases of axial chirality, atropoisomerism, and moieties existing as a mixture of enantiomers interconverting by ring inversion. Using the results reported in literature, a systematic comparison with other analytical strategies (NMR, GC, HPLC, VCD) is made and discussed. Also, a tentative proposal to rationalise the various results in terms of chiral differentiation and enantioselective shape recognition is presented. We show that this original tool provides an attractive and incisive alternative to the existing analytical techniques for studying nonfunctionalised chiral materials.     

Heteronuclear dipolar decoupling in liquid‐crystal NMR using supercycled SWf‐TPPM sequences

Heteronuclear dipolar decoupling is an essential requirement for extracting structural information from the ¹³C NMR spectra of liquid crystals. Efficient schemes for heteronuclear dipolar decoupling in such systems are formulated here by supercycling SW_f‐TPPM, a sequence introduced recently for this purpose in rotating solids. These sequences are compared with two other commonly used decoupling schemes in liquid‐crystal NMR, SPINAL‐64 and SW_f‐TPPM, by analyzing the intensities of various resonances in the proton decoupled ¹³C spectrum of the liquid‐crystal 4‐n‐pentyl‐4′‐cyanobiphenyl (5CB). The effectiveness of the decoupling programs with respect to experimental parameters such as RF field strength, decoupler offset frequency and phase angle is also presented. Copyright © 2010 John Wiley & Sons, Ltd.     

Multiple refocusing in NMR spectroscopy: compensation of pulse imperfections by scalar couplings.

When applying multiple refocusing pulses to characterize the cross-correlated relaxation of heteronuclear multiple quantum coherence 2NxHx in biomolecules, the unavoidable effects of pulse imperfections are compensated by the scalar couplings between nitrogen atoms and protons. The experiment, which is useful as a tool for studying slow internal dynamics of biomolecules, greatly benefits from this compensation. The underlying effect is a manifestation of an interchange between three noncommuting components of the density operator. One perturbing Hamiltonian is counteracted by another, which leads to a nearly complete suppression of the perturbation. The effect proves to be an example of a hitherto unknown phenomenon in NMR spectroscopy.     

Unexpected conformational properties of 1-trifluoromethyl-1-silacyclohexane, C5H10SiHCF3: gas electron diffraction, low-temperature NMR spectropic studies, and quantum chemical calculations

The molecular structure of axial and equatorial conformers of 1-trifluoromethyl-1-silacyclohexane, (C5H10SiHCF3), as well as the thermodynamic equilibrium between these species was investigated by means of gas electron diffraction (GED), dynamic nuclear magnetic resonance (DNMR) spectroscopy, and quantum chemical calculations (B3LYP, MP2, and CBS-QB3). According to GED, the compound exists as a mixture of two Cs symmetry conformers possessing the chair conformation of the six-membered ring and differing in the axial or equatorial position of the CF3 group (axial=58(12) mol%/equatorial=42(12) mol%) at T=293 K. This result is in a good agreement with the theoretical prediction. This is, however, in sharp contrast to the conformational properties of the cyclohexane analogue. The main structural feature for both conformers is the unusually long exocyclic bond length Si--C 1.934(10) A. A low-temperature 19F NMR experiment results in an axial/equatorial ratio of 17(2) mol%:83(2) mol% at 113 K and a DeltaG (not equal) of 5.5(2) kcal mol-1. CBS-QB3 calculations in the gas-phase and solvation effect calculations using the PCM(B3LYP/6-311G*) and IPCM(B3LYP/6-311G*) models were applied to estimate the axial/equatorial ratio in the 100-300 K temperature range, which showed excellent agreement with the experimental results. The minimum energy pathways for the chair-to-chair inversion of trifluoromethylsilacyclohexane and methylsilacyclohexane were also calculated using the STQN(Path) method.     

NMR Spectroscopic Characterization of the C-Mannose Conformation in a Thrombospondin Repeat Using a Selective Labeling Approach

Despite the great interest in glycoproteins, structural information reporting on conformation and dynamics of the sugar moieties are limited. We present a new biochemical method to express proteins with glycans that are selectively labeled with NMR-active nuclei. We report on the incorporation of ¹³C-labeled mannose in the C-mannosylated UNC-5 thrombospondin repeat. The conformational landscape of the C-mannose sugar puckers attached to tryptophan residues of UNC-5 is characterized by interconversion between the canonical ¹C₄ state and the B₀₃ / ¹S₃ state. This flexibility may be essential for protein folding and stabilization. We foresee that this versatile tool to produce proteins with selectively labeled C-mannose can be applied and adjusted to other systems and modifications and potentially paves a way to advance glycoprotein research by unravelling the dynamical and conformational properties of glycan structures and their interactions.     

Analysis of the 13C NMR spectra of molecules, chiral by isotopic substitution, dissolved in a chiral oriented environment: towards the absolute assignment of the pro-R/pro-S character of enantiotopic ligands in prochiral molecules

We examined and discuss the proton- and deuterium-decoupled carbon-13 1D spectrum of a molecule, chiral by virtue of the isotopic substitution, dissolved in a chiral oriented medium which simultaneously exhibits chiral discrimination, enantiomeric enrichment and isotope effect. Using the 1-deutero-(2',3',4',5',6'-pentadeuterophenyl)phenylmethanol orientationally ordered in a chiral nematic liquid crystal as illustrative example, we point out three important features. First, we demonstrate that the absolute assignment of the pro-R/pro-S character may be derived from the absolute configuration of the isotopically chiral analogue. Second, we report evidence that isotopic effect on (13)C chemical shift anisotropy is negligible in a weakly orienting solvent. Third, we definitely establish that the molecular orientation of prochiral C(s) symmetry molecules and their parent compounds that are chiral by virtue of the isotopic substitution is the same.     

The tautomerism of Omeprazole in solution: a 1H and 13C NMR study

The tautomerism of 5(6)-methoxy-2-([(4-methoxy-3,5-dimethyl-2-pyridinyl)methyl] sulfinyl)-1H-benzimidazole (omeprazole) was determined in solution, K(T) = 0.59 in THF at 195 K, in favor of the 6-methoxy tautomer. The assignment of the signals was made by comparison with its two N-methyl derivatives in acetone-d6 and through theoretical calculations of the absolute shieldings (GIAO/DFT/6-311++G**).     

Towards the automatic analysis of NMR spectra: part 6. Confirmation of chemical structure employing both 1H and 13C NMR spectra

A method of comparing predicted and experimental chemical shifts was used to confirm or refute postulated structures. 1H NMR spectra returned all true positives with a false positive rate of 4%. When an analogous procedure was adopted for 13C NMR spectra, the false positive rate dropped to 1%, whereas the more practical HSQC data yielded a false positive rate of 2%. If the HSQC results were combined with 1H results, a false positive rate of 1% resulted, 4 times more accurate than 1H alone.