Plant Stress (Mar 2024)
Homology modeling and protein-protein interaction studies of GAPDH from Helopeltis theivora and chitinase from Pseudomonas fluorescens to control infection in tea [Camellia sinensis (L.) O. Kuntze] plants
Abstract
Tea [Camellia sinensis (L.) O. Kuntze] is an important crop cultivated in all over the world. The main problem in tea cultivation is the attack by a bug called Helopeltis theivora. Many different strategies, such as the use of pesticides and insecticides, have been developed to prevent pest attacks on tea crops. However, most pesticides and insecticides are also hazardous to the environment. Therefore, biopesticides can be used as alternatives to chemical pesticides to prevent pest attacks on crops. Chitinase is an important biopesticide owing to its ability to prevent pest growth. Hence, this enzyme could be used to target H. theivora by attacking C. sinensis. The present study involved in silico docking and binding analysis of a chitinase from Pseudomonas fluorescens MP-13 with glyceraldehyde 3-phosphate dehydrogenase (GAPDH) from H. theivora. The secondary structures of chitinase and GAPDH were determined using SOPMA, and their three-dimensional structures were modeled using the Swiss model and validated using PROCHECK and Ramachandran plots. Chitinase and GAPDH were docked using HADDOCK docking software. Docking studies governed a HADDOCK docking score of -125.8, which showed good binding between the two proteins. The amino acid residues involved in binding were analyzed using PDBSum and the final docked structure was visualized using PyMol. Furthermore, in molecular dynamics studies, the binding region between chitinase and GAPDH residues was intact and stable, and did not detach throughout the simulation duration. It is clearly evidenced that chitinase from P. fluorescens and GAPDH from H. theivora interacted well with each other, thereby improves the chitinase's ability to target H. theivora and hence, chitinase can be used as a potent biopesticide. However, a detailed molecular functional and experimental studies are mandates to confirm the role of P. fluorescens in regulation of H. theivora.
