Dipolar spectral densities from off-resonance 1H NMR relaxation measurements

Cadmium-glutathione solution structures provide new insights into heavy metal detoxification

Cadmium is a heavy metal and a pollutant that can be found in large quantities in the environment from industrial waste. Its toxicity for living organisms could arise from its ability to alter thiol-containing cellular components. Glutathione is an abundant tripeptide (γ-Glu-Cys-Gly) that is described as the first line of defence against cadmium in many cell types. NMR experiments for structure and dynamics determination, molecular simulations, competition reactions for metal chelation by different metabolites (γ-Glu-Cys-Gly, α-Glu-Cys-Gly and γ-Glu-Cys) combined with biochemical and genetics experiments have been performed to propose a full description of bio-inorganic reactions occurring in the early steps of cadmium detoxification processes. Our results give unambiguous information about the spontaneous formation, under physiological conditions, of the Cd(GS)(2) complex, about the nature of ligands involved in cadmium chelation by glutathione, and provide insights on the structures of Cd(GS)(2) complexes in solution at different pH. We also show that γ-Glu-Cys, the precursor of glutathione, forms a stable complex with cadmium, but biological studies of the first steps of cadmium detoxification reveal that this complex does not seem to be relevant for this purpose.

Pharmacophore mapping via cross-relaxation during adiabatic fast passage

A novel NMR method is demonstrated for the investigation of protein ligand interactions. In this approach an adiabatic fast passage pulse, i.e. a long, weak pulse with a linear frequency sweep, is used to probe (1)H-(1)H NOEs. During the adiabatic fast passage the effective rotating-frame NOE is a weighted average of transverse and longitudinal cross-relaxation contributions that can be tuned by pulse power and frequency sweep rate. It is demonstrated that the occurrence of spin diffusion processes leads to sizable deviations from the theoretical relationship between effective relaxation rate and effective tilt angle in the spin lock frame and can be used to probe protein-ligand binding. This methodology comprises high sensitivity and ease of implementation. The feasibility of this technique is demonstrated with two protein complexes, vanillic acid bound to the quail lipocalin Q83 and NAD(+) and AMP binding to alcohol dehydrogenase (ADH).

Dilute liquid crystals used to enhance residual dipolar couplings may alter conformational equilibrium in oligosaccharides

The solution structures of a trisaccharide and a pentasaccharide containing the Lewis(x) motif were determined by two independent approaches using either dipolar cross-relaxation (NOE) or residual dipolar coupling (RDC) data. For the latter, one-bond 13C[bond](1)H RDC enhanced by two different mineral liquid crystals were used alone. Home-written programs were employed firstly for measuring accurately the coupling constants in the direct dimension of non-decoupled HSQC experiments, secondly for transforming each RDC data set into geometrical restraints. In this second program, the complete molecular structure was expressed in a unique frame where the alignment tensor is diagonal. Assuming that the pyranose rings are rigid, their relative orientation is defined by optimizing the glycosidic torsion angles. For the trisaccharide, a good agreement was observed between the results of both approaches (NOE and RDC). In contrast, for the pentasaccharide, strong discrepancies appeared, which seem to result from interactions between the pentasaccharide and the mesogens, affecting conformational equilibrium. This observation is of importance, as it reveals that using simultaneously NOE and RDC can be hazardous as the former represent 99% of the molecules free in solution, whereas the latter correspond to less than 1% of the structure bound to the mesogen.

Complexation between tert-butyl ketones and beta-cyclodextrin. Structural study by NMR and MD simulations

A structural study (NMR and MD) of the complexation between tert-butyl ketones and beta-cyclodextrin has been performed. A priority order for the alkyl and phenyl groups composing the ketones has been determined based on association constants: Ph- > C(6)H(11)- = t-Bu- > Bu-, Pr-, Me-. Geometries for the complexes are proposed based on NOE values and on the MD simulations. Bimodal complexation occurs in all the compounds studied.

Quantitative measurement of longitudinal and transverse cross-relaxation rates: an application to the analysis of the internal dynamics of ranalexin in water and trifluoroethanol

We describe a quantitative processing method which gives access to the longitudinal and transverse cross-relaxation rates from off-resonance ROESY intensities. This method takes advantage of the dependence of the off-resonance ROESY experiments at any mixing time and any spin-lock angle θ on two relaxation matrices, the longitudinal and the transverse ones. This allows one to take into account multistep magnetization transfers even if the measurements are performed only at one or two mixing times. The ratio of the longitudinal to transverse cross-relaxation rates can then be used as a local indicator of the internal dynamics, without assuming a structure or a model of motion. After validation of this processing method by numerical simulations, it is applied to the analysis of the dynamics of the peptide ranalexin dissolved in pure water and in water/TFE.

Tilt angle dependence of cross-relaxation in off-resonance ROESY

We present an efficient experimental method to evaluate whether the effective cross-relaxation rate between a pair of spins vanishes when applying an off-resonance spin-lock field. It is shown that the cross-relaxation rate can be made to vanish even when the two spins concerned resonate at different offsets and experience significantly different tilt angles of their respective spin-lock fields. This is verified experimentally using a sample of 15N-labeled human ubiquitin, through selective excitation of chosen amide protons. The results are relevant for the quantitative interpretation of off-resonance ROESY experiments.

NMR study of a Lewis(X) pentasaccharide derivative: solution structure and interaction with cations

The structure and conformation of the synthetic pentasaccharide Gal(beta 1-4){Fuc(alpha 1-3)}GlcNAc(beta 1-3)Gal(beta 1-4)Glc-beta OMe of the Lewis(X) family has been determined by NMR spectroscopy in dimethyl sulfoxide and methanol. In these solvents, the binding constants with calcium have been evaluated as 9.5 and 29.6 M-1, respectively. Study of the interaction sites has been achieved through the use of paramagnetic divalent cations and distance triangulation methods. Two regions have been found, the first one in the vicinity of the fucose unit, the second one closer to the lactose part.