Motional properties in the structure of GlcNAc(beta 1,3)Gal(beta)OMe studied by NMR spectroscopy and molecular modeling

Conformational flexibilities of the GlcNAc(beta 1,3)Gal(beta)OMe are investigated through NMR spectroscopy and molecular modeling. Adiabatic energy map generated with a dielectric constant of 50 contains three local minima. All of the molecular dynamics simulations on three local minimum energy structures show fluctuations between two low energy structures, N2 at phi=80 degrees and phi=60 degrees and N3 at phi=60 degrees and phi=-40 degrees. We have presented adequate evidences to state that GlcNAc(beta 1,3)Gal(beta)OMe exists in two conformationally discrete forms. Two state model of N2 and N3 conformers with a population ratio of 40:60 is used to calculate the effective cross relaxation rate and reproduces the experimental nOes very well. Molecular dynamics simulation in conjunction with two state model proves successfully the dynamic equilibrium existed in GlcNAc(beta 1,3)Gal(beta)OMe and can be considered as a powerful method to analyze the motional properties in the structure of carbohydrate. This observation also cautions against the indiscriminate use of a rigid model to analyze NMR data.