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

Abstract

Ascorbate peroxidase (APX) 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 (H2O2) under various stresses. In this study, computational characterization and homology analysis of APX protein from waterlogging tolerant (ICPL 84023) and sensitive (ICP 7035) pigeon pea genotypes were carried out resulting in 100% homology with Glycine max 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 APX enzyme was then tested to dock with H2O2along 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 APX for scavenging reactive oxygen species (ROS) production making this genotype more tolerant. The important binding residues in the ICPL 84023-H2O2complex (SER1, THR4, GLU23, and GLY13) have shown less fluctuation than the ICP 7035-H2O2 complex (SER1, THR4, and GLU23). Overall, our results showed that amino acid residue glycine in ICPL 84023 APX gene has a high binding affinity with H2O2 which could be a key factor associated with waterlogging stress tolerance in pigeon pea.