Gene Families, Structural and Functional Contexts Shape Protein Thermostability and Paralog Divergence in Arabidopsis

Protein family membership may constrain protein thermal stability, but the extent of this effect remains unclear. We reanalyzed a published thermal proteome dataset containing 3917 Arabidopsis thaliana proteins. Proteins within the same family showed significantly smaller pairwise Tm differences than size-matched random groups, and family membership explained 67.6% of total Tm variation. Although thermal stability was generally conserved within families, some paralogs displayed marked divergence beyond that expected from sequence similarity. This exceptional divergence was not associated with duplication mode or overall structural distance, whereas differences in disulfide-bond density showed the clearest structural association. Gene Ontology cellular-component divergence was also positively associated with thermal divergence. Overall, thermal stability is strongly organized at the gene-family level, while exceptional divergence among paralogs appears to arise through heterogeneous, pair-specific structural and functional changes.