In-silico prediction of surface residue clusters for enzyme-substrate specificity

One of the most remarkable properties of enzyme-substrate binding is the high substrate specificity among homologous enzymes. Identification of regions in enzymes that play an important role in substrate recognition presents an opportunity to understand their basic molecular mechanisms. Current methods are limited to identifying conserved residues, ignoring potential contributions of non-conserved residues. Our method overcomes this limitation. In case studies, we investigated several highly homologous enzymatic protein pairs such as guanylyl vs. adenylyl cyclases and lactate vs. malate dehydrogenases, and applied our method on plant and cyano-bacterial RuBisCos. We identified several critical mono-residue and multi-residue clusters that were consistent with experimental results. Some of the identified clusters, primarily the mono-residue ones, represent residues that are directly involved in enzyme-substrate interactions. Others, mostly the multi-residue ones, represent residues vital for domain-domain and regulator-enzyme interactions, indicating their complementary roles in specificity determination.