UNIT 8.11 Structure-Based pK_a Calculations Using Continuum Electrostatics Methods

Abstract

Electrostatic free energy is useful for correlating structure with function in proteins in which ionizable groups play essential functional roles. To this end, the pK_a values of ionizable groups must be known and their molecular determinants must be understood. Structure-based calculations of electrostatic energies and pK_a values are necessary for this purpose. This unit describes protocols for pK_a calculations with continuum electrostatics methods based on the numerical solution of the linearized Poisson-Boltzmann equation by the method of finite differences. Critical discussion of key parameters, approximations, and shortcomings of these methods is included. Two protocols are described for calculations with methods modified empirically to maximize agreement between measured and calculated pK_a values. Applied judiciously, these methods can contribute useful and novel insight into properties of surface ionizable groups in proteins.