A critical evaluation of the hydropathy profile of membrane proteins

New membrane-preference scales are introduced for categories of membrane proteins with different functions. A statistical analysis is carried out with several scales to verify the relative accuracy in the prediction of the transmembrane segments of polytopic membrane proteins. The correlation between some of the scales most used and those calculated here provides criteria for selecting the most appropriate methods for a given type of protein. The parameters used in the evaluation of the hydropathy profiles have been carefully ascertained in order to develop a reliable methodology for hydropathy analysis. Finally, an integrated hydropathy analysis using different methods has been applied to several sequences of related proteins. The above analysis indicates that (a) microsomal cytochrome P450 contains only one hydrophobic region at the N-terminus that is consistently predicted to transverse the membrane: (b) only four of the six or seven putative transmembrane helices of cytochrome oxidase subunit III are predicted and correspond to helices I, III, V and VI of the previous nomenclature; (c) the product of the mitochondrial ATPase-6 gene (or the chloroplast ATPase-IV gene) of F0-F1-ATPase shows that helix IV is not consistently predicted to traverse the membrane, suggesting a four-helix model for this family of proteins.