A conformational study of the xyloglucan oligomer, XXXG, by NMR spectroscopy and molecular modeling.

A structural study of the XXXG xyloglucan heptasaccharide (X = alpha-D-Xylp(1 --> 6)-beta-D-Glcp and G = beta-D-Glcp) isolated from apple fruit has been undertaken with nmr and molecular mechanics methods. Quantitative 400 MHz nmr data including nuclear Overhauser effect spectroscopy (NOESY) volumes were recorded at both 6 and 20 degrees C. In spite of severe overlapping of resonances, it was possible to estimate summed NOEs for the majority of the anomeric and glucosyl methylene protons. An ensemble-average population of preferred geometries has been established with the CICADA conformational searching algorithm associated with the MM3 force field. Comparison of the theoretical data obtained by back-calculation of the NOESY volumes from the ensemble-average distance matrix program and motional models based on the Stokes-Einstein-Debye relation satisfactorily reproduce the experimental data. Conformational averaging about the mainchain glycosidic linkages includes both the syn and anti conformers and a minor gauche-gauche population is highly probable. The theoretical data overestimate the syn preference of the Glc(c) --> Glc(b) linkage as well as the Glc(c) GT rotamer population. Finally, both the motional models and the conformational search indicate a fairly rigid backbone and greater flexiblity for the xylose side chains.

Conformational analysis of disaccharides using molecular dynamics and NMR methods.

The internal dynamics of four disaccharides, a galacturonic acid dimer, beta-ethyl-lactoside, sucralose and arabinobiose, have been studied using molecular dynamics and nuclear magnetic resonance methods. Theoretical motion models, which include order parameters and correlation times for internal motions, were extracted from dynamics trajectories in vacuo. In parallel, theoretical NOESY volumes were calculated from averaged distance matrices using 'model-free' spectral densities. These data were least-squares fitted to the normalized experimental NOESY volumes using the order parameters and internal motion correlation times as adjustable parameters. The resulting 'experimental' motional models were in good agreement with the theoretical ones with the exception of the galacturonic acid dimer which was best described by the rigid molecule approximation.

Thermodynamic and structural properties of r(ACC) as revealed by ultraviolet electronic absorption, circular dichroism, 1H-NMR spectroscopy and Monte Carlo simulations.

UV absorption, circular dichroism (CD) and 1H NMR, associated with Monte Carlo (MC) molecular structure simulations have been applied to the study of the trinucleoside diphosphate: r(ACC). The MC study which has been conducted as a function of temperature, is based on random variations of the nucleotide conformational angles, i.e. phosphodiester chain torsional angles and sugar pucker pseudorotational angles. All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker. Six different initial structures have been selected in order to explore the molecular conformational space as completely as possible. This simulation procedure led to distinct families of equilibrium conformations at 283, 298 and 318 K. The thermodynamical parameters such as variations in entropy, enthalpy and also melting temperature (delta SX0, delta HX0 and Tm) of the stacking (X) equilibrium were obtained from UV absorption and circular dichroism (CD) spectra recorded over a 80K temperature range. Chemical shifts (delta), vicinal coupling constants (3Jk,l), and cross-relaxation rate (sigma k,l) of trimers were measured at 400.13 MHz over a range of concentrations (2-13 mM) and temperatures (283-333K). Least-squares fitting of the experimental chemical shifts to simple models of association (A) and stacking equilibria allowed separation of the variations in the delta values (delta delta X and delta delta A) due to either phenomenon. The three NMR data sets (delta delta X, 3Jk,l, and sigma k,l) were then evaluated for the minima conformers obtained with the MC stimulations. Theoretical values of delta delta X were estimated using the results of an ab initio study while the coupling constant data were simulated with Karplus-type equations. Finally, the relaxation data were simulated from the distance matrices using treatment for cases of both slow conformational exchange accompanied by rapid small-amplitude fluctuations about the minima structures. A consistent picture of the large amplitude deformations (torsional angle variation) of these trimers has emerged from the present study. Optimized conformational blends at 283,296 and 318K were obtained by least-squares fitting of the experimental data to the theoretical ones, while considering the populations as adjustable parameters. As it would be expected, the right-handed helical conformation (A-RNA type) is found to be the major stacked species, in the temperature range of 283 to 318K. Limited evidence for bulged structures has been obtained, whereas novel reverse-stacked and half-stacked conformers also presented theoretical data compatible with the NMR observables of aqueous r(ACC).