In silico characterization and homology modeling of cytosolic gene predicts novel glycine residue modulating waterlogging stress response in pigeon pea.

Ascorbate peroxidase () is a member of the family of heme-containing peroxidases having a similar structure with Cytochrome c peroxidase (CCP) that effectively scavenge cytosolic and chloroplastic hydrogen peroxide (HO) under various stresses. In this study, computational characterization and homology analysis of protein from waterlogging tolerant (ICPL 84023) and sensitive (ICP 7035) pigeon pea genotypes were carried out resulting in 100% homology with in case of former and 99% in later genotypes respectively with 97.39% alignment coverage among each other. The model structure was further refined by various tools like PROCHECK, ProSA, and Verify3D. The planned model of the enzyme was then tested to dock with HOalong with molecular dynamics (MD) simulation analysis. The docked complex of ICPL 84023 showed the best G-score (23.39 kcal/mol) in comparison to ICP 7035 (16.74 kcal/mol) depicting the higher production of for scavenging reactive oxygen species (ROS) production making this genotype more tolerant. The important binding residues in the ICPL 84023-HOcomplex (SER1, THR4, GLU23, and GLY13) have shown less fluctuation than the ICP 7035-HO complex (SER1, THR4, and GLU23). Overall, our results showed that amino acid residue glycine in ICPL 84023 gene has a high binding affinity with HO which could be a key factor associated with waterlogging stress tolerance in pigeon pea.