Exploring the structure of single amylose chains using molecular dynamics

Amylose is a polymeric chain consisting of glucose molecules bound through α-1,4 glycosidic linkages. Amylose can assume a variety of conformations in water – the structure and dynamics of which are of primary interest in this research. Despite well-defined secondary structures of amylose chains in experimental studies, the structures obtained through MD simulations lack such well-defined conformations (ie. helical structures). Presented are results from all-atom MD simulations of single amylose chains (V-amylose) in water. From these simulations, criteria for helix-like structures is developed and the prevalence of these structures is explored. Dynamics such as bond flipping and other structural changes and their effects on helices are also discussed.