Investigation of salt bridge stability in a generalized born solvent model

Potentials of mean force (PMFs) of salt bridge formation between oppositely charged amino acid side chains were calculated both in explicit solvent and in a Generalized Born (GB) continuum solvent model to quantify the potential overstabilization of side chain ion pairs in GB relative to explicit solvation. These show that salt bridges are too stable by as much as 3-4 kcal/mol in the GB solvent models that we tested, consistent with previously reported observations of significantly different structural ensembles in GB models and explicit solvent for proteins containing ionizable groups. We thus investigated a simple empirical correction, wherein the intrinsic GB radii of hydrogen atoms bound to charged nitrogen atoms are reduced, effectively increasing the desolvation penalty of the positively charged groups. The thermodynamics of salt bridge formation were considerably improved, as exemplified by the close match of the corrected GB PMF to the reference explicit solvent PMF, and more significantly by our ability to closely reproduce the experimental temperature melting profile of the TC5b Trp-cage miniprotein, which is otherwise highly distorted by prevalent non-native salt bridges when using standard GB parameters.