Employing AlphaFold and TED to Explore the Structural Impacts of Stress-associated Mutations in Rice

Abstract

Plants have evolved adaptive mechanisms to handle environmental stress. However, Genome-Wide-Association-Studies have identified genetic variations associated with stress resistance, yet their structural and functional impacts remain poorly understood. This limits our ability to develop more resilient crops. Using predicted three-dimensional protein structures from the AlphaFold Database, chopped into domains by The Encyclopedia of Domains, we analyzed how mutations identified in Genome-Wide-Association-Studies affect protein structure and function. The analysis revealed 102 mutations in 76 high-quality protein domains likely to impact structure and function. Thirty-nine mutations were positioned within 5 Angstroms of predicted functional sites, including those near post-translational-modification sites (3), allosteric sites (5), protein-protein interaction sites (25), ligand-binding sites (15), and conserved regions (9). We identified potential interaction partners for 18 proteins with mutations at predicted interfaces and modeled their complex structures. Six mutations were predicted to enhance binding affinity with their protein partners. This study utilized only open-access tools and could strengthen plant defense mechanisms. However, experimental validation is essential to confirm the relevance and applicability of these findings for plant breeding programs.