Characterisation of hydrophobic interactions of ubiquinol with AtAOX and EsAOX isoforms by site-directed mutagenesis, molecular dynamics and docking.
Alternative oxidase (AOX) is cyanide insensitive terminal oxidase of plant mitochondrial electron transport chain serving as important bypass from classical cytochrome pathway for reduction in generation of reactive oxygen species (ROS) and for maintenance of redox homeostasis under diverse stress conditions. While many studies have emphasised on AOX structure in premature form, the mitochondria localised mature form which is biologically relevant for substrate interaction is not much explored. In the current study, we have performed comparative structural and molecular docking analysis of mature AOX isoforms from stress-sensitive Arabidopsis thaliana and extremophile Eutrema salsugineum to elucidate molecular determinants of ubiquinol binding and stress tolerance. Homology models of AOX isoforms were constructed and validated through SWISS-MODEL, GalaxyWEB, and Ramachandran plot. Docking of activators (pyruvate, glyoxylate, oxaloacetate, 2-oxoglutarate) and substrate (ubiquinol) revealed strong hydrophobic interactions, predominantly Pi-Pi alkyl bonds, within conserved catalytic domains. Among all isoforms, AtAOX1a and EsAOX1a exhibited highest binding affinities with ubiquinol. In-silico site-directed mutagenesis and molecular dynamics simulations demonstrated that substitution of conserved hydrophobic residues, Val184 in AtAOX1a and Val118 in EsAOX1a, with aspartic acid (V→D) did not alter structural stability but significantly disrupted ubiquinol-binding pocket and reduced binding affinity indicating conserved valine residues as hydrophobic anchors crucial for substrate stabilisation. The study underscores hydrophobic interactions as key determinant of AOX function proposing valine as potential site for in-vitro mutagenesis to modulate AOX-mediated stress responses. The findings serve as foundation for future experimental studies addressing AOX mediated stress responses and exploring strategies for improving plant stress tolerance.