In-silico study of E169G and F242K double mutations in Leucine-Rich Repeats (LRR) PolyGalacturonase Inhibiting Protein (PGIP) of Gossypium barbadense and associated defense mechanism against plant pathogens

PolyGalacturonase Inhibiting Proteins (PGIPs) play a pivotal role in plant defense against pathogens by inhibiting PolyGalacturonase (PG), an enzyme produced by pathogens to degrade plant cell wall pectin. PGIPs, also known as leucine-rich repeat pathogenesis-related (PR) proteins, activate the host's defense response upon interaction with PG, thereby fortifying the plant against pathogenic attacks. In cotton ( Gossypium barbadense ), the interaction between PGIP and PG is a crucial step in the defense mechanism against major pathogens such as Xanthomonas citri pv. malvacearum and Alternaria macrospora , responsible for bacterial leaf blight and leaf spot diseases, respectively. To unravel the molecular mechanisms underlying these pathogenesis-related proteins, we conducted a comprehensive study involving molecular modeling, protein-protein docking, site-specific double mutation (E169G and F242K), and molecular dynamics simulations. Both wild-type and mutated cotton PGIP were examined in interaction with the PG enzyme from pathogens. Our findings revealed that changes in conformations of double-mutated residues in the active site of PGIP lead to the inhibition of PG binding. The molecular dynamics simulations provide insights into the dynamic behavior and stability of the PGIP-PG complexes, shedding light on the intricate details of the inhibitory and exhibitory mechanism against the fungal and bacterial pathogens respectively. This study not only enhances our understanding of the molecular interactions between PG and PGIP but also presents a potential strategy for developing disease-resistant cotton varieties. By variations in the binding affinities of PG through specific mutations in PGIP, this research offers a promising avenue for the development of cotton plants with enhanced resistance to bacterial leaf blight and leaf spot diseases.