Efficient deduction of encoded local response within a thermodynamically perturbed folded protein.

Abstract

Externally imposed perturbations can subtly reshape protein structure and mechanics prior to the emergence of global unfolding signatures. Delineating locally sensitive zones, however, can pose immense challenges. Subjecting a small folded protein to isotropic pressure spanning 0.001-10 kbar, we develop a simplified and interpretable computational framework to characterize local responses embedded within its conformational ensemble. Pairwise mechanical stiffness descriptors are treated as high-dimensional mechanical fingerprints and projected using linear discriminant analysis (LDA) to identify the pressure ranges that maximally separate conformational populations. To attribute the discriminative mechanical changes to specific residues, we combine the LDA model with SHapley Additive exPlanations, yielding a ranked set of locally responsive sites. While the overall rigidity landscape of the protein shows only modest pressure dependence, the top-ranked residues exhibit pronounced, pressure-specific alterations in solvent association. Radial distribution functions and tetrahedral order metrics reveal significant reorganization of hydration structure around the leading hotspot across the LDA-inferred transition region, whereas low-ranked sites display weak or nonspecific hydration changes. Together, these results connect global thermodynamic perturbation to localized mechanical and hydration responses and suggest a practical route for prioritizing mutation sites and mechanistic hypotheses in perturbed biomolecular systems.