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3 10 ‐Helix adjoining α‐helix and β‐strand: Sequence and structural features and their conservation
Author(s) -
Pal Lipika,
Dasgupta Bhaskar,
Chakrabarti Pinak
Publication year - 2005
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20266
Subject(s) - helix (gastropod) , context (archaeology) , collagen helix , crystallography , alpha helix , chemistry , structural element , protein secondary structure , protein structure , triple helix , stereochemistry , circular dichroism , materials science , composite material , biology , biochemistry , ecology , paleontology , snail
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 3 10 ‐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–3 10 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 proline 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 3 10 ‐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 3 10 –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–3 10 and 3 10 –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 3 10 ‐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. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 147–162, 2005 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com