1H-13C selective NOE studies of the decapeptide gramicidin S

Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation

The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR. The efficiency of magnetization transfer by the NOE depends on the molecular rotational correlation time, whose value depends on solution viscosity. The magnitude of the NOE between ¹H nuclei varies from +50% when molecular tumbling is fast to -100% when it is slow, the latter case corresponding to the spin diffusion limit. In an intermediate tumbling regime, the NOE may be vanishingly small. Increasing the viscosity of the solution increases the motional correlation time, and as a result, otherwise unobservable NOEs may be revealed and brought close to the spin diffusion limit. The goal of this review is to report the resolution of structural problems that benefited from the manipulation of the negative NOE by means of viscous solvents, including examples of molecular structure determination, conformation elucidation and mixture analysis (the ViscY method).

Solution structure of folic acid. Molecular mechanics and NMR investigation

The structure of folic acid in solution was investigated by nuclear magnetic resonance (NMR) and theoretical calculations. Dynamical information and geometrical constraints were obtained by carbon-13 relaxation study, homo-nuclear NOESY spectra and hetero-nuclear 1H-13C NOE experiments. This set of experimental data was used for the molecular mechanics and molecular dynamic calculations. The accuracy of the final structure was established by the R(NMR) factor, which was calculated comparing the experimental NOESY cross-peaks intensities and the corresponding values simulated by using the complete relaxation matrix analysis (CORMA) approach.

Stereochemistry of protected ornithine side chains of gramicidin S derivatives: X-ray crystal structure of the bis-Boc-tetra-N-methyl derivative of gramicidin S

An X-ray crystallographic analysis of the bis-Ndelta-Boc-tetra-Nalpha-methyl derivative of gramicidin S, cyclo(-Val-MeOrn(Boc)-Leu-d-MePhe-Pro-)2, was undertaken successfully (R-factor = 0.088). As expected, the main chain adopts an antiparallel pleated beta-sheet conformation, but the pleated sheet is slightly twisted, and the sense of twisting is opposite to that found in the reported crystal structures of the gramicidin S-urea complex and the bis-Ndelta-(trichloroacetyl) and bis-Ndelta-(m-bromobenzoyl) derivatives of gramicidin S. In agreement with the observed resistance toward N-methylation, the urethane NH groups of the protected Orn side chains are hydrogen bonded to the carbonyl groups of the d-Phe residues. However, the side-chain-main-chain hydrogen bonding is in the i --> i - 3 mode, although hydrogen bonding in the i --> i + 2 mode was deduced from a 1H NMR study of protected gramicidin S derivatives and was actually found in the crystal structures of the diacylated gramicidin S.

Conformational features of charged dibucaine in solution as investigated by 13C- and 1H-NMR

Conformational features of charged dibucaine in [2H6]DMSO were elucidated by measuring 13C and 1H spin-lattice relaxation rates and 1H-(1H) and 13C-(1H) nuclear Overhauser effects. The reorientational correlation time of the aromatic moiety was evaluated at 0.16 ns at room temperature and side chains were observed to display segmental motion. Relevant distances were calculated by isolating dipolar interaction terms of 1H-1H or 13C-1H pairs. The 'preferred' conformation in solution was shown to present several analogies, but also some differences, with the structures obtained by solid state experiments, energy calculations and LIS data.

Properties of synthetic analogs of gramicidin S containing L-serine or L-glutamic acid residue in place of L-ornithine residue

In order to investigate the biological role of the delta-amino groups of the Orn residue in gramicidin S, the four analogs, [Ser2]-, [Ser2.2']-, [Glu2]- and [Glu2.2']-gramicidin S were synthesized by a solution method. Except for the last one, these analogs show antibiotic activity to a certain extent against gram-positive micro-organisms, but the activites are weaker than that of gramicidin S. These results indicate that the delta-amino group of the Orn residue is quite important for exhibiting of the activity of gramicidin S, but is not essential to the activity. NMR and CD studies of these analogs indicate that these analogs possess four intramolecular hydrogen bonds between the Val and Leu residues similar to those of GS, and the removal or diminution of the delta-amino group of ornithine residues give the considerable influence to the dihedral angle of NxH-CxH of D-Phe residues and consequently affect the type II' beta-turn structure of the cyclic peptides.

A variable target intensity-restrained global optimization (VARTIGO) procedure for determining three-dimensional structures of polypeptides from NOESY data: application to gramicidin-S

A global optimization method for intensity-restrained structure refinement, based on variable target function (VTF) analysis, is illustrated using experimental data on a model peptide, gramicidin-S (GS) dissolved in DMSO. The method (referred to as VARTIGO for variable target intensity-restrained global optimization) involves minimization of a target function in which the range of NOE contacts is gradually increased in successive cycles of optimization in dihedral angle space. Several different starting conformations (including all-trans) have been tested to establish the validity of the method. Not all optimizations were successful, but these were readily identifiable from their large NOE R-factors. We also show that it is possible to simultaneously optimize the rotational correlation time along with the dihedral angles. The structural features of GS thus obtained from the successful optimizations are in excellent agreement with the available experimental data. A comparison is made with structures generated from an intensity-restrained single target function (STF) analysis. The results on GS suggest that VARTIGO refinement is capable of yielding better quality structures. Our work also underscores the need for a simultaneous analysis of different NOE R-factors in judging the quality of optimized structures. The NOESY data on GS in DMSO appear to provide evidence for the presence of two orientations for the ornithine side chain, in fast exchange. The NOESY spectra for this case were analyzed using a relaxation rate matrix which is a weighted average of the relaxation rate matrices for the individual conformations.

Nuclear magnetic resonance investigations of calcium antagonist drugs. II: Conformational and dynamic features of verapamil in [2H6]DMSO

Conformational features of verapamil in [2H6]DMSO have been delineated by measuring 13C and 1H NMR parameters. Spin-lattice relaxation rates were interpreted within the frame of an extended alkane chain with segmental motions hampered by the aromatic substituents at both ends. The effective correlation times were all evaluated in the range 0.16-0.22 ns at 293 K. The aromatic rings were found to lie somewhat out-of-plane with the alkane chain. The NMR data were used to construct a Dreiding model of the most probable spatial arrangement and a molecular modeling system was utilized to represent the "preferred" conformation of verapamil in solution.

Structural and dynamical characterization of piroxicam by 1H- and 13C-NMR relaxation studies

Carbon spin-lattice relaxation rates of an anti-inflammatory drug, piroxicam, have been measured. These results have been used in determining the reorientational rates of the proton carbon vectors. An analysis of internal motions within the pyridinyl moiety of piroxicam was carried out. Selective proton-carbon nuclear Overhauser effect (NOE) measurements were made in order to determine the solution structure of piroxicam. The effect of indirect NOE arising from exchangeable protons has been analyzed and considered.

The mechanisms of interaction between furanochromones and DNA. A heteronuclear Overhauser effect study on the khellin-thymidine model system

The furanochromones khellin and visnagin have been characterised by 1H and 13C mono- and bidimensional NMR spectroscopies. Their strong affinity with DNA was experimentally confirmed by the complete disappearance of the furano-chromones' NMR signals upon additions of DNA. An intermolecular interaction between furanochromones and the thymidyl moieties of DNA, stabilized by the formation of a hydrogen bond between the thymidyl NH hydrogen and the C = O group of khellin or visnagin, is here proposed. This is suggested by the strong donor-acceptor behavior of these two molecular moieties, as pointed out by a selective 1H-13C Overhauser effect study of the khellin-thymidine model system.