CropStabDB: a protein stability resource and Engineering Atlas of orthologue-supported substitutions for 30 plant proteomes

Abstract

Protein stability, the capacity to maintain a folded structure and function, matters as much for transporters and regulators as for enzymes, and heat erodes it. Wheat, rice, maize and soybean supply two-thirds of human caloric intake, and warming reduces yields. Rubisco activase variants selected for thermostability increased photosynthesis, biomass and yield under heat. They came from gene shuffling; no method proposes residues at proteome scale. Genome editing has made such changes routine, yet predictors estimate melting temperature, name no residue, and have not been reported for a plant proteome. Here we present CropStabDB: 1,425,716 proteins from 30 plant species scored on six interpretable components, with an Engineering Atlas of 2,097,576 candidate substitutions in 51,440 proteins, 785,622 at Engineering Confidence Score ≥ 0.70. Every candidate is a residue a more stable orthologue carries at that column. Substitution-type scores match the direction of measured folding free energies in 842 of 926 domains (90.9%). On three proteomes from families absent from training, the model reaches an area under the curve of 0.919. Applied blind to wheat, the score reproduces the measured thermostability ranking of the Rubisco activase isoforms in all three subgenomes. CropStabDB is freely available without registration at https://cropstab.org.