The Multiple Origins of the Hydrophobicity of Fluorinated Apolar Amino Acids

The substitution of -CH3 with -CF3 groups in the side chain of hydrophobic amino acids often increases their hydrophobicity, but the impact of these substitutions on the thermal stability of proteins is system specific. Here, we investigated this issue by using fixed-charge, all-atom molecular dynamics simulations and an AMBER-compatible library of fluorinated amino acids. We found that the changes in hydration free energy upon fluorination depended strongly on amino acid identity and the location of the fluorinated site. We present a phenomenological model that quantitatively predicts the simulation results. The model demonstrates that changes in hydrophobicity upon fluorination largely arise from steric hindrance of backbone-water hydrogen bonds by -CF3; changes in surface area, often invoked to explain experimental trends, have only a secondary contribution. The model and the force field presented here provide indispensable molecular-scale insight and simulation tools for understanding and predicting the impact of fluorination on protein properties.