Computational Analysis Reveals that Dual Point Mutation in Rice SBEIIb Leads to Decrease in Starch Binding Affinity

Abstract

Aim: To check the effect of mutation on the binding affinity of Starch branching enzyme II with maltopentaose substrate. Place and Duration of Study: Department of Bioinformatics, Centre for Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, between May 2022 and July 2022. Methodology: The wild type rice SBEIIb and mutated rice SBEIIb protein were modelled using SWISS MODEL and subjected to PROCHECK for validation of the modelled protein. These protein structures were docked with ligand maltopentaose using Auto dock vina of PyRx software. The docked structures were visualized in BIOVIA Discovery studio. Results: There was a decrease in binding affinity after mutating the protein at 2 of the maltopentaose binding sites (Y178A & F234A). The binding energy of wild type rice SBEIIb protein was -7.5kcal mol-1 whereas after mutation it decreased to -5.8 kcal mol-1. The number of hydrogen bonds also decreased from 8 to 4 respectively. Conclusion: Double mutation of binding site residues resulted in binding affinity as well as interactions.  In silico analysis prior to wet lab experiments lead to rational choice of mutations that may lead to the production of rice grains with reduced amylopectin content.