In silico analysis of structural complex of HAESA receptor like kinase with PAMP IDA and SERk1 co-receptor

Abstract

Pattern Triggered Immunity (PTI) is actually identified by the activities of pattern recognition receptors (PRRs), which play the most important role in first layer of plant defense mechanism. During aggression of microbes, PRRs immediately bind with the pathogen-associated molecular patterns (PAMPs) and recruit co-receptor protein(s) to activate the defense signal and begin plant's immunity. Although several plant PRRs have been discovered, very few of them have been fully characterized and their functional parameters studied. In this study, the crystallographic structure of HAESA-IDA-SERk1 (PDB ID: 5IYX) complex was simulated for 30 ns in different stages like there were five different combinations of the main crystallographic structure. For every combination 30ns simulated trajectories were analyzed for getting an overview of the interaction and immune response of HAESA towards IDA with the help of co-receptor SERk1. Analyzing the interaction revealed its remarkable resemblance to the other crystallographic structures, which are also a member of the same LRR-RK subfamily (leucine-rich repeat – receptor kinase subfamily XII). Furthermore, it was observed that Tyr56 and Arg67 of IDA contributed significantly to the formation of the HAESA-IDA complex. It can thus be predicted that any change to the PAMP at these positions can be greatly detrimental to the plant, leading to the PRR losing its ability to recognize the PAMP. Moreover, from MM/PBSA analysis it is found that binding energy between HAESA and IDA is more favourable than HAESA and SERk1. -636.824 kJ/mol binding energy is found when co-receptor SERk1 is present inside the complex and during its absence the binding energy between HAESA and IDA goes higher. Again, a notable binding energy between IDA and SERk1 is obtained from this analysis. There are several prominent residues found from HAESA and SERk1, mutation at any of these residues will affect on PTI of Arabidopsis thaliana. Since HAESA has been shown to play a key role in Arabidopsis thaliana plant defense mechanism, its hypothesized binding mechanism with IDA and co-receptor SERk1 will help paint a better understanding of the inceptive stages of PTI.