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Alchemical free energy calculations are widely used in predicting pKa, andbinding free energy calculations in biomolecular systems. These calculationsare carried out using either Free Energy Perturbation (FEP) or ThermodynamicIntegration (TI). Numerous efforts have been made to improve the accuracy andefficiency of such calculations, especially by boosting conformationalsampling. In this paper, we use a technique that enhances the conformationalsampling by temperature acceleration of collective variables for alchemicaltransformations and applies it to the prediction of pKa of the buried Asp 26residue in thioredoxin protein. We discuss the importance of enhanced samplingin the pKa calculations. The effect of the solvent models in the computed pKavalues is also presented.

Computational Study of pKa shift of Aspartate residue in Thioredoxin: Role of Configurational Sampling and Solvent Model