Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity

Abstract

The ”effective” dynamics of a biomolecular system can often be described by means of a Markov chain describing ”flipping dynamics” between metastable (geometrical large scale) molecule conformations on ”long” time scales. In this work we present our methods for the identification of metastable conformations by a study of UDP-GlcNAc - a key substrate in sialic acid synthesis. We investigate the system in different environments of increasing complexity (vacuum, water, peptide) by performing force field based molecular dynamic simulations. By applying our analysis techniques to the obtained data we get insights into the conformational dynamics of the system. A comparison of the results reveals interesting environment-dependent properties of UDP-GlcNAc.