A conformational dynamics study of α-L-Rhap-(1-2)[α-L-Rhap-(1→3)1-α-L-Rhap-OMe in solution by NMR experiments and molecular simulations

The conformational preference of alpha-L-Rhap-(1 -> 2)[alpha-L-Rhap-(1 -> 3)]-alpha-L-Rhap-OMe in solution has been studied by NMR spectroscopy using one-dimensional H-1,H-1 T-ROESY experiments and measurement of trans-glycosidic (3)J(C),(H) coupling constants. Molecular dynamics (MD) simulations with a CHARMM22 type of force field modified for carbohydrates were performed with water as the explicit solvent. The homonuclear cross-relaxation rates, interpreted as effective proton-proton distances, were compared to those obtained from simulation. Via a Karplus torsional relationship, (3)J(C),(H) values were calculated from simulation and compared to experimental data. Good agreement was observed between experimental data and the MD simulation, except for one inter-residue T-ROE between protons in the terminal sugar residues. The results show that the trisaccharide exhibits substantial conformational flexibility, in particular along the psi glycosidic torsion angles. Notably, for these torsions, a high degree of correlation (77%) was observed in the MD simulation revealing either psi(+)(2) psi(+)(3) or psi(-)(2)psi(-)(3) states. The simulations also showed that non-exoanomeric conformations were present at the phi torsion angles, but to a limited extent, with the phi(3) state populated to a larger extent than the phi(2) state. Further NMR analysis of the trisaccharide by translational diffusion measurements and (CT1)-C-13 relaxation experiments quantified global reorientation using an anisotropic model together with interpretation of the internal dynamics via the model-free approach. Fitting of the dynamically averaged states to experimental data showed that the psi(+)(2) psi(+)(3) state is present to similar to 49%, psi(-)(2) psi(-)(3) to similar to 39%, and phi(3) (non-exo) to similar to 12%. Finally, using a dynamic and population-averaged model, H-1,H-1 T-ROE buildup curves were calculated using a full relaxation matrix approach and were found to be in excellent agreement with experimental data, in particular for the above inter-residue proton-proton interaction between the terminal residues.