Department of Biochemistry and Molecular Biophysics, Columbia University, New York
bental@cumbnd.bioc.columbia.edu
A unique hydropathy (hydrophobicity) scale, based on the free energies of transfer of the amino acids from aqueous phase to lipid bilayers, is presented. Unlike other hydropathy scales (e.g. Kyte and Doolittle) which assume that the free energies of transfer are proportional to some inherent property (an individual atom, a chemical group or an amino acid), our scale was derived using a theoretical model that accounts for the amino acids in the context of an alpha-helix embedded in implicit solvent. The scale will be used to predict the location of bilayer spanning helices in membrane proteins. The results will be compared to experimental data, to predictions using other hydropathy scales, and to prediction algorithms that are based on data base derived propensities. The hydropathy scale and the prediction algorithm will be analyzed, and suggestions for improvements will be made. This is a first stage in developing an energy based prediction scheme for transmembrane helices using structural information.