Epibrassinolide binding affinity to tomato receptor-like kinase SLLYK12 using molecular docking and dynamics simulations

Abstract

LysM receptor-like kinases (LysM-RLKs) in plants are plant-specific receptor-like kinases (RLKs) that are essential in recognizing microbial signals and initiating responses. These receptor signalling can activate different plant responses leading either to establish symbiosis with symbiotic microorganisms or to launch defence responses against microbial pathogens. Due to their crucial role in symbiosis and in governing defence responses against invading pathogens, LysM-RLKs have the potential to be used as a biological target for the sustainable management of plant diseases. . In this study, a library of phytochemicals including phenolics, flavonoids and phytohormones were screened against the tomato LysM-RLK ‘SlLYK12’ using molecular docking and molecular dynamics (MD) simulations. The initial SlLYK12 models were created with the Alphafold, I-TASSER, SWISS-MODEL, and trRosetta online tools. The models ranked ‘1’ were selected from all four modelling servers for initial quality analysis as it is the ‘Model 1’ that shows the best quality/criteria scores devised by the modelling servers. Further quality analysis of the selected models from each modelling server was performed by online quality structure assessment tools available on the Saves server and the model proposed by trRosetta was deemed of good quality. Based on the molecular docking performed using Autodock Vina software, 24-epibrassinolide had best docking scores of -9.3 Kcal mol-1 as compared to Galbacin (-8.7 Kcal mol-1), Quercetin (-8.3 Kcal mol-1), and Traumatin 7-Oxotyphasterol (-8.2 Kcal mol-1) The best conformation of 24-epibrassinolide with the best docking score was further subjected to molecular dynamics using AMBER 99 force field using md_run.mcr script of YASARA software. The MD simulation was performed for 60 ns with constant pressure and temperature during the simulation. Water molecules (0.997 g/mL density) were added with 0.9% NaCl salt to mimic physiological conditions. MD analysis revealed that after 30 ns the equilibrium was achieved, the complex remained reasonably stable, and the RMSD fluctuations were found to be within a range of 1.2–1.8 A. The systems showed RMSF within a range of 0.3–7.6 A. Accordingly, this study provided a strong basis for the exogenous use of the 24-epibrassinolide for an e establishment of defence responses or root endosymbiosis in plants.