Peptide Backbone Effect on Hydration Free Energies of Amino Acid Side Chains

We have studied the hydrophobicity of amino acid side chains by computing conditional solvation free energies that account for effects of the peptide backbone on the side chains’ solvent environment. The free energies reported herein correspond to a gas–liquid transfer process, which mimics solvation of the side chain under the condition that the backbone has been solvated already, and have been obtained on the basis of free energy calculations with empirical force field models. We find that the peptide backbone strongly impacts the solvation of nonpolar side chains, while its effect on the polar side chains is less pronounced. The results indicate that, in the presence of the short peptide backbone, nonpolar amino acid side chains are less hydrophobic than what is expected based on small molecule (analogue) solvation data