title: Occurrence, conformational features and amino acid propensities for the pi-helix.
abstract: The most abundant helix type in proteins is the alpha-helix, accounting for about 31% of amino acid secondary structure states, while the 3(10)-helix accounts for about 4%. The pi-helix appears to be extremely rare and is considered to be unstable. Existing secondary structure definition methods find very few within the Protein Data Bank. Using an improved pi-helix definition algorithm to search a non-redundant subset of high-resolution and well-refined protein structures, we found that almost every tenth protein contained a pi-helix. This enabled us to show for the first time that the pi-helix has structural parameters that are different from the hypothesized model values. It also has distinctive amino acid preferences and it is conserved within functionally related proteins. Features that may contribute to the stability of the pi-helical structure have also been identified. In addition to hydrogen bonds, several other factors contribute to the stability of pi-helices. The pi-helix may have some functional advantages over other helical structures. Thus, we describe cases where the side chains of functionally important residues at every fourth position within a pi-helix could be aligned and brought close together in a way that would not be allowed by any other helix type.
authors.affiliation: Department of Molecular Biophysics, Center for Chemistry and Chemical Engineering, University of Lund, Box 124, SE-221 00 Lund, Sweden.
authors.forename: M N
authors.initials: MN
authors.lastname: Fodje
authors.forename: Salam
authors.initials: S
authors.lastname: Al-Karadaghi
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000596:Amino Acids / Q000378:metabolism*; D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D006860:Hydrogen Bonding
chemical_list: D000596:Amino Acids