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The prediction of secondary structure conformation of membrane-buried segments of integral membrane proteins is done in this work by using the method of preference functions (Juretić et al. In Theoretical and Computational Chemistry; Párkányi, C., Ed.; Elsevier Science: Amsterdam, 1998; Vol 5, Chapter 13, p 405). The method is here extended by predicting sequence location, hydrophobic moments, and transmembrane orientation of helical segments. Independent evaluation of the method with ubiquinol-cytochrome c reductase subunits is performed before some already known details of the crystal structure of that respiratory complex are released. Tests with potassium channels revealed that their characteristic super-secondary structure in the pore region can be recognized by performing the analysis with preference functions and with hydrophobic moment threshold functions.
Juretić et al. (Tue,) studied this question.