Protein-protein molecular recognition in plant disease modulated by metastable state frequencies : the AvrptoB-Pto system

Abstract

Plant pathogens secrete effector proteins that interact with host immune receptors, often exploiting conformational plasticity to evade recognition. Understanding such dynamic processes is crucial for designing durable resistance strategies. The conformational landscape of the AvrPtoB effector protein in complex with tomato Pto kinase was investigated, combining Molecular Dynamics (MD), biased MD, and protein–protein docking. Clustering of MD trajectories identified three metastable states of AvrPtoB, which were subjected to docking against Pto. Redocking of the crystallographic complex served as reference. Among the three metastates, metastate 2 achieved a superior docking score, surpassing the crystallographic reference, while metastates 1 and 3 displayed less favorable energies. Notably, metastate 2 was also the most populated state (52.2% of conformations), reinforcing its biological relevance. Importantly, it was the only metastate to conserve two residue–residue interactions from docking to the final MD conformation, including the Val201–Phe161 contact also observed in the crystallographic complex. Together, these results highlight metastate 2 as a biologically meaningful conformation, combining energetic favorability, high population frequency, and conservation of key interfacial interactions. This integrative approach demonstrates the value of metastable state analysis for uncovering hidden conformations that shape molecular recognition, offering innovative perspectives for engineering resistance genes and developing novel strategies for crop protection.