Modelling the structure of maize starch branching enzyme IIb and effects of serine phosphorylation using bioinformatics
Amylopectin biosynthesis involves several classes of interacting enzymes regulated by post-translational modifications. In 2004, Tetlow et al. identified a multi-enzyme complex, consisting of Starch Synthase I, Starch Synthase IIa, and Starch Branching Enzyme IIb (SBEIIb), involved in amylopectin synthesis. The assembly of this trimer is phosphorylation dependent, with SBEIIb known to be phosphorylated at Serine 286, 297 and 649. Currently, the crystallographic structure of SBEIIb is not known. This project focused on using bioinformatics tools to make predictions about Maize SBEIIb: its structure, effects of serine phosphorylation, putative phosphorylation sites, and corresponding kinases. The SBEIIb structure was identified using homology, ab initio, and threading/fold recognition tools. Across all tools, the core region of the predicted structure agreed, but the N-termius highly varied. Serine 286, 297 and 649 were found to localize on free loops. Phosphorylation was carried out using SYBYL-X 1.3 suite (SYBYL, Tripos Associates, St. Louis, MO), and molecular dynamics simulations were started on GROMACS 4.5.5 software package. Findings from this project widened current understanding about amylopectin biosynthesis.