310-Helix adjoining α-helix and β-strand: Sequence and structural features and their conservation

Abstract

Does the amino acid use at the terminal positions of an α-helix become altered depending on the context-more specifically, when there is an adjoining 310-helix, and can a single helical cylinder encompass the resultant composite helix? An analysis of 138 and 107 cases of 3 10-α and α-310 composite helices, respectively, found in known protein structures indicate that the secondary structural element occurring first imposes its characteristics on the sequence of the structural element coming next. Thus, when preceded by a 3 10-helix, the preference of praline to occur at the N1 position of an α-helix is shifted to the N2 position, a typical characteristic of the C-terminal capping of the 310-helix. When an α- or a 3 10-helix leads into a helix of the other type, there is a bend at the junction, especially for the 310-α composite, with the two junction residues facing inward and buried within the structure. Thus a single helical cylinder may not properly represent a composite helix, the bend providing a means for the tertiary structure to assume a globular shape, very much akin to what a proline-induced kink does to an α-helix. The tertiary structural context in which β-310 and 310-β composites occurs can be different, causing the angle between the secondary structural elements in the two cases to be different. Composites of 3 10-helices and β-strands are much more conserved among members in families of homologous structures than those between two types of helices; in many of the former instances, the 310-helix constitutes the loops in β-hairpin or β-β-corner motifs. The overall fold of the chain may be more conserved than the actual identify of the secondary structure elements in a composite.