title: Disposition of amphiphilic helices in heteropolar environments.
abstract: It is known that alpha helices in globular proteins usually consist of two types of residues, hydrophobic and hydrophilic, with the number of each type being roughly equal. Except for many transmembrane helices, alpha-helices are generally amphiphilic to some degree. This is not entirely surprising because alpha-helices typically reside in heteropolar environments that arise from the polar aqueous solution that surrounds a protein and the apolar "hydrophobic core" located at its center. The packing of alpha-helices in such heteropolar environments is driven by the minimization of free energy brought about by placing hydrophobic sidechains into apolar environments and hydrophilic sidechains into polar environments. The interface between the two environments can be characterized by an interfacial plane, called the demarcation plane, that optimally separates the two classes of residues. The inclination angle omega between the axis of the helix and the demarcation plane provides a measure of the degree of amphiphilicity of an alpha-helix. For highly amphiphilic helices, omega approximately 0. The inclination angle provides a new measure of amphiphilicity that complements the hydrophobic moments of Eisenberg et al. Based on the simple physical model described above, an algorithm is developed for predicting the helix inclination angle. The calculated results show that the inclination angle for most alpha-helices extracted from globular proteins is less than 25 degrees in magnitude. This suggests that helices found in globular proteins tend to be reasonably amphiphilic with half their face dominated by hydrophobic residues and the other half by hydrophilic residues. A new two-dimensional representation that characterizes the disposition of hydrophobic and hydrophilic residues in alpha-helices, called a "wenxiang diagram," is presented. The wenxiang diagram can also be used as an important element to represent a protein molecule.
authors.affiliation: Computer-Aided Drug Discovery, Pharmacia and Upjohn, Kalamazoo, Michigan 49007-4940, USA.
authors.forename: K C
authors.initials: KC
authors.lastname: Chou
authors.forename: C T
authors.initials: CT
authors.lastname: Zhang
authors.forename: G M
authors.initials: GM
authors.lastname: Maggiora
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001053:Apolipoproteins / Q000737:chemistry; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D006110:Grasshoppers / Q000737:chemistry; D008433:Mathematics; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary
chemical_list: D001053:Apolipoproteins