Why Protein Modifications Matter for Digestibility: The Case of Ara h 1 Peanut Allergen and Trypsin Cleavage

Trypsin is the principal intestinal endopeptidase and proteomics digestion tool, yet the impact of protein modifications (PMs) on digestibility and allergenicity remains underexplored. We employed a proteomic approach to assess trypsin cleavage efficacy (TCE) at modified versus unmodified K/R residues in Ara h 1, a major peanut allergen. Seven of 17 PM sites showed ≥20% difference in TCE, with carbamoylation + methylation and dihydroxylation retaining significance after multiple-testing correction. The 20% threshold aligns with the 19 ± 1% baseline of porcine trypsin miscleavages. Molecular docking confirmed reduced binding affinity due to steric hindrance from methylation at R259. These findings suggest that impaired digestion at PM sites may enhance peptide sensitization potential. This study provides a basis for machine learning-driven models using public proteomic data sets to predict the influence of PMs on protease performance.