TrIPP: a Trajectory Iterative pK a Predictor

The protonation propensity of ionisable residues in proteins can change in response to changes in the local residue environment. The link between protein dynamics and p K a is particularly important in pH regulation of protein structure and function. Here, we introduce TrIPP (Trajectory Iterative p K a Predictor), a Python tool to monitor and analyse changes in the p K a of ionisable residues during Molecular Dynamics simulations of proteins. We show how TrIPP can be used to identify residues with physiologically relevant variations in their predicted p K a values during the simulations, and link them to changes in the local and global environment. TrIPP is available at https://github.com/fornililab/TrIPP .