The conformational analysis of methyl beta-xylobioside: effect of choice of potential functions.

In order to determine the effect of the choice of potential function used in the conformational analysis of a carbohydrate, the NMR spectrum of methyl beta-xylobioside [beta-D-Xyl-(1-->4)-beta-D-Xyl-(1-->O)-Me] was interpreted using calculated J13C-H coupling constants and nuclear Overhauser effects for protons across the anomeric linkage. Conformational flexibility was described by calculating average phi and psi angles, and estimating their standard deviations. ECEPP2, ECEPP83, and HSEA potentials were used in the first series of calculations. The calculated coupling constants and nuclear Overhauser effects were averaged over the Boltzmann distribution of conformations of the disaccharide in which the entire phi, psi space was scanned in ten-degree steps while retaining fixed bond distances and angles in the remainder of the molecule. In the second series of calculations, MM2, MM2CARB, and PCILO parameters were used to calculate conformational energies. Conformational optimization was done. The effect of temperature and solvent on the calculated coupling constants was negligible. Calculated properties from conformations whose energies were based on the ECEPP parameters gave the best agreement with experiment. Exploration of the conformational space in breadth rather than on a detailed level of full optimization appears to be a preferable course of action.

Nuclear Overhauser effects and the flexibility of saccharides: methyl beta-xylobioside.

The behavior of methyl beta-xylobioside has been analysed by 1H-n.m.r. spectroscopy for solutions in water and methanol in the range - 15 degrees to 85 degrees. Experimental n.O.e. values did not change with temperature and solvent in contrast to the inter-glycosidic 3JC,H values. Experimental n.O.e. data accorded with the values calculated from time-averaged cross-relaxation terms. The tumbling times were determined from relaxation data and were in the sub-ns range.

Monte Carlo calculations on the conformations of models for the glycopeptide linkage of glycoproteins.

In order to search for probable conformations of the peptide, the amino acid side chain, and the carbohydrate linkage in glycoproteins, conformational energy surfaces of glycopeptide model compounds were studied by Monte Carlo methods using the Metropolis algorithm. The potential energies were composed of empirical energy functions which include nonbonded interactions, electrostatics, hydrogen bonding, and torsional energies specified by parameters which have been used for peptides. Calculations were performed on 1-N-acetyl-2-acetamido-beta-D-glucopyranosyl amine and the glycosylated dipeptide N-acetyl-delta-N-(2-acetamido-beta-D-glucopyranosyl)-L-asparaginyl-N'-methyl amide as models for N-glycosylated peptides and on methyl-2-acetamido-alpha-D-galactopyranoside as well as the glycosylated dipeptides N-acetyl-gamma-O-(2-acetamido-alpha-D-galactopyranosyl)-L-threonyl-N'-methyl amide and its seryl analog as models for O-glycosylated glycoproteins. The probable conformations of these compounds were analyzed by single-angle probability tables and by two-dimensional conformation density maps projected from the Markov chains which contained up to six independently varied conformational dihedral angles. The presence of high barriers to rotation required the use of search strategies which resulted in a rather low acceptance rate for new conformations in the Metropolis algorithm in order to avoid trapping of the Markov chain in local energy minima. This problem contributed to the failure of these calculations to attain complete convergence to the thermodynamic limit for the glycosylated dipeptide models in which six dihedral angles were independently varied. Analysis of the results shows that the conformational space available to the highly crowded axial glycosides of the alpha-O-GalNAc type is much more restricted than that for the N-asparaginyl glycopeptides. The most probable conformation for the O-glycosylated peptides is is a beta-turn while N-glycosylated peptides may be either in a beta-turn or an extended conformation.