Review of protein structure-based analyses that illuminate plant stress mechanisms
Fatima Shahid, Neeladri Sen, Hawa Najibah Rasni, Nurulhikma Md Isa, Nyuk Ling, Christine Orengo, Su Datt Lam
Abstract
Plants face formidable challenges due to environmental stresses, including pathogens, salt, drought, cold, heat, heavy metal exposure, and flooding, all of which affect growth and agricultural productivity. To combat these stresses, plants have evolved various adaptive mechanisms, including the expression of stress-response proteins. Exploring the three-dimensional structures of plant proteins can be valuable for discovering and characterising stress tolerance mechanisms at the molecular level. Until recently, large-scale analyses were not feasible due to the limited number of experimentally determined plant protein structures. However, the recently developed AlphaFold, RoseTTA-Fold, and ESM-fold protein structure prediction methods, along with their associated portals, now provide hundreds of millions of high-quality predicted 3D models, covering a wide range of plant proteins. This review highlights insights from recent structural investigations into plant stress response using experimental or predicted protein structures. We include analyses of diverse paralogs and isoforms and insights from molecular docking and molecular dynamics simulations. We consider the value of using experimental and predicted structural data in understanding the mechanisms of common stress-modulating plant proteins. Studying the structures of these proteins together with their inferred functions can aid improvements in crop productivity, help foster sustainable agriculture, and contribute to global food security efforts.