Solvent effect on the stability of isomaltose conformers

Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling

Explicit-solvent molecular dynamics (MD) simulations of the 11 glucose-based disaccharides in water at 300K and 1bar are reported. The simulations were carried out with the GROMOS 45A4 force-field and the sampling along the glycosidic dihedral angles phi and psi was artificially enhanced using the local elevation umbrella sampling (LEUS) method. The trajectories are analyzed in terms of free-energy maps, stable and metastable conformational states (relative free energies and estimated transition timescales), intramolecular H-bonds, single molecule configurational entropies, and agreement with experimental data. All disaccharides considered are found to be characterized either by a single stable (overwhelmingly populated) state ((1-->n)-linked disaccharides with n=1, 2, 3, or 4) or by two stable (comparably populated and differing in the third glycosidic dihedral angle omega ; gg or gt) states with a low interconversion barrier ((1-->6)-linked disaccharides). Metastable (anti-phi or anti-psi) states are also identified with relative free energies in the range of 8-22 kJ mol(-1). The 11 compounds can be classified into four families: (i) the alpha(1-->1)alpha-linked disaccharide trehalose (axial-axial linkage) presents no metastable state, the lowest configurational entropy, and no intramolecular H-bonds; (ii) the four alpha(1-->n)-linked disaccharides (n=1, 2, 3, or 4; axial-equatorial linkage) present one metastable (anti-psi) state, an intermediate configurational entropy, and two alternative intramolecular H-bonds; (iii) the four beta(1-->n)-linked disaccharides (n=1, 2, 3, or 4; equatorial-equatorial linkage) present two metastable (anti-phi and anti-psi) states, an intermediate configurational entropy, and one intramolecular H-bond; (iv) the two (1-->6)-linked disaccharides (additional glycosidic dihedral angle) present no (isomaltose) or a pair of (gentiobiose) metastable (anti-phi) states, the highest configurational entropy, and no intramolecular H-bonds. The observed conformational preferences appear to be dictated by four main driving forces (ring conformational preferences, exo-anomeric effect, steric constraints, and possible presence of a third glycosidic dihedral angle), leaving a secondary role to intramolecular H-bonding and specific solvation effects. In spite of the weak conformational driving force attributed to solvent-exposed H-bonds in water (highly polar protic solvent), intramolecular H-bonds may still have a significant influence on the physico-chemical properties of the disaccharide by decreasing its hydrophilicity. Along with previous work, the results also complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups, glycosidic dihedral angleomega in (1-->6)-linked disaccharides), approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi). The calculated average values of the glycosidic torsional angles agree well with the available experimental data, providing validation for the force-field and simulation methodology employed.

Theoretical Study of the Relative Stability of Rotational Conformers of α and β-d-Glucopyranose in Gas Phase and Aqueous Solution

The alpha-beta anomer energy difference and the stability of 10 rotamers of counterclockwise D-glucopyranose were studied in vacuo and in aqueous solution at the B3LYP/6-31+G(d,p) level. To obtain the solute charge distribution and the solvent structure around it, we used the averaged solvent electrostatic potential from molecular dynamics method, ASEP/MD, which alternates molecular dynamics and quantum mechanics calculations in an iterative procedure. The main characteristics of the anomeric equilibrium, both in vacuo and in solution, are well reproduced. The relative stability of the different anomers is related to the availability of the free pairs of electrons in the anomeric oxygen to interact with the water molecules. The influence of solvation in the conformer equilibrium is also analyzed.

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.

The dependence of glucan conformational dynamics on linkage position and stereochemistry

The 13C NMR T1 relaxation times for the (1-->4)-linked maltooligomers (Mi) and the (1-->6)-linked isomaltooligomers (IMi) with i = 2, 4, 6, and 8 were measured in aqueous solution at 22 and 65 degrees C at a concentration (3%) low enough to have removed concentration-dependent effects on the measured T1 values. Separate T1 values were measured for each carbon in the residue at the reducing end of the oligosaccharide, in the residue at the non-reducing end, and in the interior, i.e., non-terminal, residue(s). Analogous data for the corresponding high polymers show that at 22 degrees C the relaxation times for the carbons of the interior residues of the oligomers have converged to their high chain length asymptotes at about i = 10. This observation suggests that at room temperature polymeric motions in the frequency domain effective for 13C NMR relaxation at a magnetic field strength of 11.7 T have a "wavelength" of the order of 10 residues. The relaxation times characterizing the two ends of the chain are different, with longer T1 values for the carbons of the reducing end than for those of the non-reducing end. Carbons of alpha-anomeric residues at the reducing end have shorter relaxation times than those of the corresponding beta-anomeric reducing sugars. Carbons of the interior residues have T1 values shorter than the carbons of either type of terminal residue. For oligomers of a given dp there is no T1 difference between oligomers of the Mi and IMi series at room temperature. This observation is seemingly at odds with the great differences in the inherent conformational freedom of the (1-->4)- and (1-->6)-linkages. At elevated temperatures the orientational relaxation behavior of the two series of oligomers measured by 13C T1 values show interesting differences, and in the case of the Mi series, structure develops in the chain length dependence of the T1 values.

Relaxed-residue conformational mapping of the three linkage bonds of isomaltose and gentiobiose with MM3 (92)

Isoenergy surfaces were calculated for the alpha- and beta-anomers of isomaltose and gentiobiose, based on 46,656 conformers for each disaccharide. Low-energy regions exist for each of the three staggered positions about the C-5'-C-6' bonds, and known crystal structures lie in two of these regions. As expected, the molecular partition function showed greater flexibility for these three-bond-linked disaccharides than for comparable two-bond-linked structures. A model miniature crystal of gentiobiose accounts for most of the remaining structural differences between the modeled isolated molecule and the crystal structure. Based on models of isolated molecules of isomaltose and gentiobiose, the predicted Boltzmann-weighted nmr coupling constants were satisfactory, as were predicted optical rotations for gentiobiose.

Flexibility in a tetrasaccharide fragment from the high mannose type of N-linked oligosaccharides

An analysis has been carried out of the three-dimensional structure of a tetrasaccharide, Man(alpha 1-3)Man(alpha 1-6)Man(beta 1-4)GlcN Ac beta 1-OCD3, which is a fragment from the high mannose type of N-linked oligosaccharides. Although earlier work had suggested that this fragment might adopt a stable three-dimensional structure, both n.m.r. and conformational energy calculations support the existence of an ensemble of structures. The conformational entropy calculated from the ensemble and the distribution of distances between the terminal Man(alpha 1-3) and GlcN Ac residues, however, suggests that a significant fraction of the ensemble has the two terminal residues in close proximity.

One-bond carbon-proton coupling constants: angular dependence in alpha-linked oligosaccharides

An investigation is presented of the angular dependence of 1JC,H in model compounds related to alpha-linked oligosaccharides. Values calculated by FPT formulation in the semi-empirical INDO method for models of (1----1)-, (1----2)-, (1----3)-, and (1----4)-linked disaccharides were compared, and the effect of the orientation of HO-2 was elucidated. The angular dependence of 1JC,H on the glycosidic dihedral angles phi H and psi H was characterised in the form 1JC,H = A cos 2 phi + B cos phi + C sin 2 phi + D sin phi + E. The 1JC,H values, measured by DEPT methods for C-1-H-1 and C-X'-H-X' in various rigid carbohydrates, were used to adjust the calculated angular dependences and to determine solvent effects. Based on the abundance of the conformers for maltose and isomaltose, the thermodynamically averaged 1JC,H values have been calculated. The results obtained (less than 1JC-1,H-1 greater than 169.9, less than 1JC-4',H-4' greater than 147.7 Hz for methyl beta-maltoside and less than 1JC-1,H-1 greater than 169.8 Hz for methyl beta-isomaltoside) agree with the experimental values of 172.4, 147.7, and 170.3 Hz, respectively.