Decoding the Post-translational Modification Crosstalk: Functional Implications of Phosphorylation, Acetylation, and...

Post-translational modifications (PTMs) such as phosphorylation, acetylation, and methylation critically expand proteome function by regulating protein structure and interactions. Hydropathy changes serve as a main driving force; however, a quantitative, mechanistic understanding of how their distinct chemical changes alter local protein hydropathy remains limited. To bridge this gap, we extend the Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) scale, a residue-level hydropathy scale, to systematically evaluate PTM-induced physicochemical changes. By applying this method, we quantify the effect and magnitude of hydropathy shifts at modification sites and map how these perturbations influence the local protein environment. Our analysis reveals that phosphorylation exerts a strong, consistent hydrophilic effect, significantly increasing PARCH values due to the introduction of a large, charged phosphate group. In contrast, N-lysine acetylation, which neutralizes charge, shows context-dependent effects, predominantly increasing the hydrophobicity but occasionally enhancing the local hydrophilicity. Methylation presents the most complex signature, with no uniform trend, where increased side chain bulk can paradoxically increase water exposure despite the modification's nonpolar nature. This study establishes the PARCH scale as a powerful quantitative tool for deciphering how PTMs regulate the local hydropathy landscape of proteins, providing a predictive foundation for understanding their structural, hydropathy, and functional consequences.