Single-engineered-residue solvation perturbations regulate global protein architecture and function

Protein-water interactions fundamentally shape the structure, stability, dynamics, and functionality of proteins. However, the heterogeneous nature of the protein-water interface and the disparity in their dynamic interplay make it challenging to understand how local water perturbations influence protein structural dynamics over space and time. In this study, we introduce a photochromic molecule, spiropyran, to modify a specific residue of proteins, thereby achieving a reversible, residue-specific, and amplified perturbation on the hydrophobicity of protein surfaces. With the aid of controlled, amplified hydrophobic perturbations, we reveal that even residue-level changes in hydrophobicity induce significant global alterations in protein hydration patterns. These hydration shifts propagate in an amino acid sequence-dependent manner, initiating dramatic influences on overall protein architecture and catalytic performance. Our findings establish that interfacial water networks not only capture the surface physicochemical patterns of proteins but also mediate the propagation of local perturbations into broader structural and functional fluctuations. By shifting the paradigm from “structure-function” to “structure-hydration-function”, our work provides innovative perspectives into understanding protein architecture and guiding future drug design strategies.