Structure Elucidation of Amide Bonds with Dipolar Chemical Shift NMR Spectroscopy

DFT Calculations of 51V Solid-State NMR Parameters of Vanadium(V) Model Complexes

Two cis-dioxovanadium(V) complexes and three monooxovanadium(V) complexes with different coordination numbers and ligand spheres, serving as model complexes for vanadium haloperoxidases, were studied by 51V solid-state NMR spectroscopy. The most important 51V solid-state NMR parameters (quadrupolar coupling constant C Q , asymmetry of the EFG tensor η Q , isotropic chemical shift δ iso , chemical shift anisotropy δ σ , asymmetry of the CSA tensor η σ and the Euler angles α, β and γ) describing the quadrupolar and chemical shift anisotropy interactions were determined theoretically with DFT methods employing the B3LYP functional and experimentally using genetic fitting algorithms. Calculations of δ iso values were treated with different referencing values of VOCl3 computed with different-sized basis sets using the “counterpoise method”. The calculated C Q values were discussed in terms of the quadrupolar moment Q. Absolute tensor orientations of CSA and EFG tensors were computed by DFT. These orientations were found to correlate to structural features of the model complexes.

(51)V solid-state NMR investigations and DFT studies of model compounds for vanadium haloperoxidases

Three cis-dioxovanadium(V) complexes with similar N-salicylidenehydrazide ligands modeling hydrogen bonding interactions of vanadate relevant for vanadium haloperoxidases are studied by (51)V solid-state NMR spectroscopy. Their parameters describing the quadrupolar and chemical shift anisotropy interactions (quadrupolar coupling constant C(Q), asymmetry of the quadrupolar tensor eta(Q), isotropic chemical shift delta(iso), chemical shift anisotropy delta(sigma), asymmetry of the chemical shift tensor eta(sigma) and the Euler angles alpha, beta and gamma) are determined both experimentally and theoretically using DFT methods. A comparative study of different methods to determine the NMR parameters by numerical simulation of the spectra is presented. Detailed theoretical investigations on the DFT level using various basis sets and structural models show that by useful choice of the methodology, the calculated parameters agree to the experimental ones in a very good manner.

Combined NMR and computational study for azide binding to human manganese superoxide dismutase

Human manganese superoxide dismutase (MnSOD) labeled with 3-fluorotyrosine (Tyf) was complexed with the (15)N-labeled inhibitor azide ([(15)N(3)(-)]). The sample was characterized by solid-state NMR (SSNMR) spectroscopy ((19)F-MAS and (15)N-CPMAS). Employing (19)F-(15)N-REDOR spectroscopy, we determined the distances between the fluorine label in Tyrosine-34 and the three (15)N-nuclei of the azide and the relative orientation of the azide in the binding pocket of the MnSOD. A distance of R(1)=4.85A between the (19)F-label of Tyf34 and the nearest (15)N of the azide and an azide-fluorotyrosine Tyf34 angle of 90 degrees were determined. These geometry data are employed as input for molecular modeling of the location of the inhibitor in the active site of the enzyme. In the computations, several possible binding geometries of the azide near the Mn-complex were assumed. Only when the azide replaces the water ligand at the Mn-complex we obtained a geometry of the azide-Mn-complex, which is consistent with the present NMR data. This indicates that the water molecule ligating to the Mn-complex is removed and the azide is placed at this position. As a consequence the azide forms an H bond with Gln143 instead with Tyf34, in contrast to non-(19)F-labeled MnSOD, where the azide is hydrogen bonded to the hydroxy group of Tyr34.

Polymorphism ofN,N′′-Diacetylbiuret Studied by Solid-State13C and15N 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 (alpha- and beta-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 alpha-DAB and a c-glide plane in the case of beta-DAB, lead to a more symmetric (alpha-DAB) or asymmetric (beta-DAB) intermolecular hydrogen-bonding pattern for each molecule.

Solid state NMR analysis of the dipolar couplings within and between distant CF3-groups in a membrane-bound peptide

Dipolar couplings contain information on internuclear distances as well as orientational constraints. To characterize the structure of the antimicrobial peptide gramicidin S when bound to model membranes, two rigid 4-CF3-phenylglycine labels were attached to the cyclic backbone such that they reflect the behavior of the entire peptide. By solid state 19F NMR we measured the homonuclear dipolar couplings of the two trifluoromethyl-groups in oriented membrane samples. Using the CPMG experiment, both the strong couplings within each CF3-group as well as the weak coupling between the two CF3-groups could be detected. An intra-CF3-group dipolar coupling of 86 Hz and a weak inter-group coupling of 20 Hz were obtained by lineshape simulation of the complex dipolar spectrum. It is thus possible to explore the large distance range provided by 19F-labels and to resolve weak dipolar couplings even in the presence of strong intra-CF3 couplings. We applied this approach to distinguish and assign two epimers of the labeled gramicidin S peptide on the basis of their distinct 19F dipolar coupling patterns.

Contribution of hydrogen bonding to protein stability estimated from isotope effects

An unresolved issue in structural biology concerns the relative contribution of H bonds to protein stability. We use the small molecules 4-acetamidobenzoic acid and N-acetylanthranilic acid as model compounds to relate the energetic contribution from hydrogen bonds (H bonds) to the deuterium/hydrogen amide isotope effect. N-Acetylanthranilic acid models carbonyl-amide H bonds formed during protein folding; 4-acetamidobenzoic acid models the unfolded state in which the amide H bonds to water. NMR is used to measure shifts in the pK(a) of the ionizable carboxyl group when the amides of the compounds are either protonated or deuterated. From the pK(a) shift, we obtain a quantitative scale factor: SF = partial partial differential(DeltaG(HB))/partial partial differential(RT ln Phi), where DeltaG(HB) is the change in free energy of an H bond upon isotope substitution and Phi is the fractionation factor. Isotope effect data also are reported for a small globular protein, lambda repressor, using the "C(m) experiment". The protein's isotope effect, which reports on the shape of the energy well, is converted to H-bonding free energy by applying the scale factor. We estimate that amide-related H bonds (amide-carbonyl and amide-water) contribute favorably to protein stability by approximately 30-50 kcal/mol in lambda repressor, GCN4 coiled coil, and cytochrome c but unfavorably by approximately 6 kcal/mol in ubiquitin. The results indicate that H-bond strength varies from one protein to another and presumably at different sites within the same protein.

NMR Study of Self-Association of Acetanilide in Chloroform, Acetone, Acetonitrile and Dimethyl Sulphoxide

The self-association of acetanilide through hydrogen bonding between N-H and O=C in the solvents [

Deuterium REDOR: principles and applications for distance measurements

The application of short composite pulse schemes ( and ) to the rotational echo double-resonance (REDOR) spectroscopy of X-2H (X: spin 12, observed) systems with large deuterium quadrupolar interactions has been studied experimentally and theoretically and compared with simple 180 degrees pulse schemes. The basic properties of the composite pulses on the deuterium nuclei have been elucidated, using average Hamiltonian theory, and exact simulations of the experiments have been achieved by stepwise integration of the equation of motion of the density matrix. REDOR experiments were performed on 15N-2H in doubly labeled acetanilide and on 13C-2H in singly 2H-labeled acetanilide. The most efficient REDOR dephasing was observed when composite pulses were used. It is found that the dephasing due to simple 180 degrees deuterium pulses is about a factor of 2 less efficient than the dephasing due to the composite pulse sequences and thus the range of couplings observable by X-2H REDOR is enlarged toward weaker couplings, i.e., larger distances. From these experiments the 2H-15N dipolar coupling between the amino deuteron and the amino nitrogen and the 2H-13C dipolar couplings between the amino deuteron and the alpha and beta carbons have been elucidated and the corresponding distances have been determined. The distance data from REDOR are in good agreement with data from X-ray and neutron diffraction, showing the power of the method. Copyright 1999 Academic Press.

Structural parameters from 19F homonuclear dipolar couplings, obtained by multipulse solid-state NMR on static and oriented systems

Local macromolecular structure can be determined by solid-state NMR measurements of weak dipolar couplings between selectively labeled groups. The nonperturbing use of 2H, 13C, or 15N in biological systems, however, faces drawbacks in terms of a low sensitivity and a comparatively short distance range relative to 1H. To extend these limitations, we illustrate the use of 19F as an alternative NMR probe. The Carr-Purcell-Meiboom-Gill (CPMG) multipulse sequence was adapted here to measure homonuclear dipolar couplings between two fluorine labels in static samples at 470 MHz. Two lipids (4, 4-DMPC-F2, and a difluorinated sterol), which are arranged in liquid crystalline bilayers, serve as models to assess the scope of the technique. In these 19F-background-free biological samples, weak couplings down to 100 Hz could be resolved directly from the splitting of the pure dipolar powder lineshape, and 1H-decoupling was not required. Order parameters were determined for the anisotropic motion of the lipids, consistent with their expected behavior in the membrane. Besides measuring the distance-dependent term of the dipolar coupling in powder samples, we have also used oriented membranes to extract additional angular information from the dipolar anisotropy. The strategy presented here thus has the potential to obtain not only the internuclear distance between two labels, but also their angular orientation in the sample, provided the molecules are aligned as a membrane or a fiber.