Amino acids hydrophobic properties in proteins are derived from their atomic polarities

Abstract

Knowledge of the hydrophobicity of amino acids is essential to understanding the structure and function of proteins. One of the most useful tools for this purpose has been the use of hydrophobicity scales. In these scales, each amino acid is attributed with a numerical value that characterizes its hydrophobic or hydrophilic behavior in a protein. These values depend on the particular methodologies used to obtain them. In the present work, we present a way to infer a hydrophobicity scale for all the amino acids from their partial atomic charge from the uniCHARMM force field. All amino acids are more or less soluble in water as they need to be easily bioavailable in the cell medium. It is during the folding process of a polypeptide chain, that an amino acid goes from a soluble state to be part of a folded protein within a cohesive hydrophobic core. In the present work, we have implemented a model and a formula that considers hydrophilicity as the ability of the atoms of amino acids to interact with water, being proportional to the accessibility to the solvent and its partial charge, depending on its sign. On the other hand, hydrophobicity is considered to be more intense the lower the charge on the atom and also proportional to the accessibility of the atom. This procedure improves the accuracy of protein hydrophobicity calculations down to the atomic level.