Approach for the simulation and modeling of flexible rings:: Application to the α-D-arabinofuranoside ring, a key constituent of polysaccharides from Mycobacterium tuberculosis

A number of lower organisms (bacteria, fungi, and parasites) produce glycoconjugates that contain furanose rings. Of particular interest to our group are cell wall polysaccharicles from mycobacteria, including the human pathogen, Mycobacterium tuberculosis, which contain a large number of arabinofuranose resides. As part of a larger project on the conformational analysis of these molecules, we report here molecular dynamics simulations on methyl alpha-D-arabinofuranoside (1) using the AMBER force field and the GLYCAM carbohydrate parameter set. We initially studied the ability of this method to predict rotamer populations about the hydroxymethyl group (C4 - C5) bond. Importantly, we show that simulation times of up to 200 ns are required in order to obtain convergence of the rotamer populations for this ring system. We also propose a new charge derivation approach that accounts for the flexibility of the furanoside ring by taking an average of the charges from a large number of conformers across the psuedorotational itinerary. The approach yields rotamer populations that are in good agreement with available NMR data and, in addition, provides insight into the nature of the puckering angle and amplitude in 1.