A Comprehensive Study of Factors Affecting the Prediction of the p K a Shift of Asp 26 in Thioredoxin Protein.

The stable protonation state of ionizable amino acids in a protein can be predicted by computing the p K a shift of that residue within the protein environment. Thermodynamic Integration (TI) is an ideal molecular dynamics-based approach for predicting the p K a shift of ionizable protein residues. Here, we probe TI-based simulation protocols for their ability to accurately predict the p K a shift of Asp 26 in thioredoxin. While implicit solvent models can predict the p K a shift accurately, explicit solvent models result in substantial errors. To understand the underlying reason for this surprising discrepancy, we investigate the role of various factors such as solvent models, conformational sampling, background charges, and polarization.