THE PREFERENCE FUNCTIONS METHOD FOR PREDICTING PROTEIN HELICAL TURNS WITH MEMBRANE PROPENSITY

The prediction of secondary structure conformation of membrane-buried segments of integral membrane proteins is done in this work by using t he method of preference functions (Juretic et al. In Theoretical and C omputational Chemistry; Parkanyi, C., Ed.; Elsevier Science: Amsterdam , 1998; Vol 5, Chapter 13, p 405). The method is here extended by pred icting sequence location, hydrophobic moments, and transmembrane orien tation of helical segments. Independent evaluation of the method with ubiquinol-cytochrome c reductase subunits is performed before some alr eady known details of the crystal structure of that respiratory comple x are released. Tests with potassium channels revealed that their char acteristic supersecondary structure in the pore region can be recogniz ed by performing the analysis with preference functions and with hydro phobic moment threshold functions.