In silico Discovery of Substrate Specificity of Soluble Starch Synthases via Secondary Structure Features

The enzyme isoforms in starch biosynthesis pathway generally are believed to have a lot of influences on starch qualities and quantities. Understanding the relationships between enzyme isoforms and properties of starch is therefore of economical importance in the applications of starch in many industries. However, their precised roles have not been clearly identified by experimental approaches. Thus, we present a novel computational method for classifying and identifying starch enzyme isoforms based on predicted secondary structures. The method can automatically perform unsupervised cluster discovery from the secondary structure of starch biosynthesis enzyme isoforms data input based on their similarity. We applied our method to analyze a set of 36 soluble starch synthase isoforms, and found that the soluble starch synthase isoforms mostly contain structural regions that exhibit similar features in the C-terminal, with the distinctive features in the N-terminal region. The result suggests that the N-terminal variations (difference in both length and homology) in starch synthases may not directly involve in catalytic activity of these enzymes, but instead regulate the binding of glucose substrate to the enzymes. Furthermore, the N-terminus may play a role in targeting starch synthases to specific portions of the starch granule, and interacting with other enzymes in starch biosynthesis mechanism.