Hydrophobicity scales, which measure the polarity of amino acids, are important tools for rationalizing protein structure and function. A common technique utilizes hydrophobicity scales for calculating the degree of polarity for regions in a protein, but these techniques implicitly assume that hydrophobicity is not affected by environment � that is, that the hydrophobic effect is additive. Here, we test this additivity assumption using, molecular dynamics (MD) simulations applied to a small set of dipeptides and side chain analogs to compare free energies of hydration. Our goal is to assess how strongly amino acid environment affects its hydration free energy; when the environment plays a strong role, hydration free energies can be said to be non-additive and conventional hydrophobicity scales will fail to make useful predictions. Two water models, explicit and implicit, were employed during this study for comparison and to support the proposition that hydrophobicity is not an additive property. In fact, we find significant non-additivity in many cases. Here we discuss our results and implications.

Hydration free energy calculations show that amino acid hydrophobicity is strongly environment-dependent

245th National Meeting (2013)

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