EVOLUTIONARY CONSERVATION OF BOTH THE HYDROPHILIC AND HYDROPHOBIC NATURE OF TRANSMEMBRANE RESIDUES

An algorithm (HRG), developed to allow the pairwise comparisons of the aligned residues of several members of large gene families of polytop ic integral membrane proteins is described. Using hydrophobicity scale s, application of this algorithm allows the number and size of the mem brane-spanning domains of bacteriorhodopsin, a polytopic protein whose structure has been partially determined, to be predicted with a high degree of accuracy (sensitivity 94%, specificity 82% for predicting th e membrane embedded or extramembranous location of residues). As oppos ed to previously reported structure-prediction algorithms, delineation of putative transmembrane segments from connecting loops is also more clearly evident with the application of the HRG algorithm, even with proteins from widely divergent species. This indicates strong evolutio nary pressure for the conservation of both the hydrophobic and hydroph ilic character of residues in membrane-embedded regions of polytopic p roteins, such as those of the G-protein-coupled receptor superfamily. These and other structural and functional implications evident from th e application of the HRG algorithm are considered.