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

Anshika Tyagi; Sandhya Sharma; Harsha Srivastava; Nagendra Kumar Singh; Kishor Gaikwad

doi:10.7717/peerj.10888

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

PeerJ. 2021 May 12:9:e10888. doi: 10.7717/peerj.10888. eCollection 2021.

Authors

Anshika Tyagi¹, Sandhya Sharma¹, Harsha Srivastava¹, Nagendra Kumar Singh¹, Kishor Gaikwad¹

Affiliation

¹ ICAR- National Institute for Plant Biotechnology, New Delhi, India.

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.

Keywords: Ascorbate peroxidase; Docking; Molecular modeling; Pigeon pea; Simulation; Waterlogging tolerance.

Grants and funding

This work was financially supported by the DBT-RA Program in Biotechnology and Life Sciences. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.