Hydration Free Energies of Amino Acids: Why Side Chain Analog Data Are Not Enough

Using molecular dynamics based free energy simulations, we computed relative solvation free energies for pairs of N-acetyl-methylamide amino acids (Ala-Ser, Val-Thr, Phe-Tyr, Val-Ala, Thr-Ser, Phe-Ala, and Tyr-Ser) and compared the results with the relative solvation free energies of the corresponding pairs of side chain analogs. We observed differences in (relative) solvent affinity ΔΔΔA between amino acids and side chain analogs of up to 66% or, in absolute numbers, 4.9 kcal/mol (Ala-Ser). To rationalize these findings, we estimated separately contributions from what we refer to as solvent exclusion and self-solvation. While the former accounts for the reduction in solute−solvent interactions as one part of the solute occludes other parts of the solute, the latter turned out to be the determining contribution for small polar amino acids and could be shown to arise from interactions between the polar backbone and the polar functional group of the respective side chain in the gas phase. Consequently, the solvent affinity of small polar amino acids depends strongly on the backbone conformation. Our results indicate that the still widely used group additivity−solvent exclusion assumption to estimate solvation free energies for large(r) molecules (such as peptides and proteins) from model compound data (such as side chain analogs) is insufficient. To illustrate practical consequences, we compare the explicit solvent results with those of implicit solvent models. While approaches based on the generalized Born model give results in (mostly) good agreement with explicit solvent, approaches relying (primarily) on the group additivity−solvent exclusion assumption fail to reproduce ΔΔΔA. Finally, we briefly discuss the implications of our results for hydrophobicity scales.