In silico modelling and molecular interaction of elongation factor receptor with pathogenic elongation factor tu 18

Abstract

Plants depend entirely on innate immunity system to protect them from various pathogenic bacteria, fungi, and viruses. The first layer defense mechanism is named as Pattern-triggered immunity (PTI) system. It is activated by Pathogenassociated molecular pattern (PAMP) of the host plant by Pattern recognition receptor (PRR) with the aid of co-receptor. Elongation factor receptor (EFR), which is also known as PRR, is one of the most recognized receptor used to protect against disease in Brassica species. Although research on transgenic approach and wet labs experiments have been carried out to analyse the EFR model, but the full ectodomain interactions of EFR with PAMP elf18 protein and co-receptor Brassinosteroid Insensitive 1-associated receptor kinases (BAK1) protein through in silico has not been accomplished yet. The purpose of this study was to determine the interaction of EFR protein with elf18 protein through in silico analysis approach. In this study, PRR EFR protein and PAMP elf18 protein was constructed by homology modelling using HHpred Modeller, followed by docking and molecular dynamics (MD) simulation of EFR protein and elf18 protein with co-receptor BAK1 protein (PDB:3UIM) and apo BAK1 (PDB ID:3ULZ) as model for mutant protein using ZDOCK 3.0.2 server and GROMACS 5.0.4 respectively. Finally, superimposition was done between EFR-elf18-BAK1 complex with existed FLS2-flg22-BAK1 crystal structure. Modelling results showed that multiple template modelling (MTM) generated best models compared to single template modelling (STM) due to their best quality of the protein structure obtained by HHpred Modeller generate best validation results of 71.123 ERRAT, 95.67% Verify3D and 92.8% in favoured region of Ramachandran Plot. Docking results showed that the complex interaction of BAK1 protein and elf18 protein binds at the concave surface of Leucine-Rich- Repeat (LRR) EFR, compatible with the existed FLS2 complex binding interactions. For the EFR-elf18-BAK1 (normal) complex, about 20 hydrogen bonds were sustained which is higher compared to EFR-elf18-BAK1 (mutated) complex that only sustained 16 hydrogen bonds, proved that the mutated protein have less interaction after simulation. After 50ns MD Simulation, the results showed that all the docked complexes has significant reduction of H-bonds. For EFR-elf18-BAK1 docked complex, H-bond between EFR protein and BAK1 protein reduced from 45 to 22, and H-bond between elf18 protein and BAK1 protein were reduced from 9 to 0 which caused by the conformational changes of the proteins during simulation. This study helps to understand the Brassica disease in detail and contribute significantly to early event of Pattern Triggered Immunity mechanism of EFR-elf18-BAK1 protein complex.