In silico evolutionary analysis of plant alpha amylase from monocot to dicot: A plausible explanation for stability and diversity

Alpha-amylase is an essential enzyme in plants that hydrolyses starch into sugars that the growing seedling uses for energy, especially during seed germination. Alpha-amylase also contributes to starch synthesis during seed maturation and in other plant tissues for energy storage and utilisation. In this study, an in silico initiative has been undertaken to characterize the sequences and structures of alpha-amylase in monocot (Oryza sativa subsp. japonica) and dicot (Arabidopsis thaliana) plants. An unavailability structure of dicot alpha-amylase was created through Python homology modelling, along with the structural validations. The results revealed that the sequences of monocot were highly occupied by charged polar and nonpolar amino acids, whereas the dicots mostly increased their uncharged polar amino acids. The alpha-amylase of dicot was more hydrophilic than that of monocot. The instability index and aliphatic index indicate that the alpha-amylase of monocots was more thermostable. The secondary structure assessment of both proteins showed some significant structural differences. The higher formations of different intra-protein interactions significantly increased the stability of monocot alpha-amylase. The molecular dynamics simulations with a run time of 100 ns comparatively disclosed the higher stability, fluctuations, rigidity, and compactness of monocot alpha-amylase. This study will help in understanding how evolution had a marked impact on monocots to dicots. It is also helpful for protein engineering to enzyme synthesis.