Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications

We have determined hydrophobicity parameters for the side chains of 22 common post- or cotranslationally modified amino acyl residues and for the standard unmodified amino acids as well. This "comprehensive" parameter set is the first such reported. Parameters determined for the side chains of the standard 20 amino acids correlate well with those of widely accepted sets. Our parameters have also been evaluated by hydrophobicity profiles and by transverse hydrophobic moment calculations on cytosolic, secreted, and membranous model proteins, with favorable results. Many of the hydrophobicity parameters for the post- or cotranslationally modified derivatives are of remarkable magnitude, especially those for oligosaccharide-bound Asn and fatty-acylated Cys or amino terminus. Thus, the comprehensive parameter set determined here greatly extends our ability to analyze homology, membrane directedness, and folding potential of proteins.