Guiding Peptide Kinetics via Collective-Variable Tuning of Free-Energy Barriers

While recent advances in AI have transformed protein structure prediction, protein function is also strongly influenced by the thermodynamic and kinetic features encoded in its underlying free-energy surface. Here, we propose a framework to rationally reshape this landscape in order to control conformational transition rates, built on the Collective Variables for Free Energy Surface Tailoring (CV-FEST) framework, and validate it on point mutations of the miniprotein Chignolin. The framework relies on Harmonic Linear Discriminant Analysis (HLDA)-based collective variables (CVs) constructed from short molecular dynamics trajectories confined to metastable basins, requiring only limited sampling within each basin. Notably, the HLDA CV derived solely from the wild-type system already provides residue-level scores that predict whether mutations at specific positions are likely to accelerate or slow unfolding transitions. Furthermore, we find that the leading HLDA eigenvalue associated with the derived CV, a quantitative measure of the one-dimensional statistical separation between folded and unfolded ensembles, is significantly correlated with transition rates across mutations. Together, these results suggest that kinetic effects of point mutations can be inferred from minimal local sampling, providing a practical route for guiding the engineering of transition rates without exhaustive simulations or large training data sets.