Expanded turn conformations: characterization and sequence-structure correspondence in α-turns with implications in helix folding

Abstract

Like the β-turns, which are characterized by a limiting distance between residues two positions apart (i, i+3), a distance criterion (involving residues at positions i and i+4) is used here to identify α-turns from a database of known protein structures. At least 15 classes of α-turns have been enumerated based on the location in the φ,ψ space of the three central residues (i+1 to i+3)-one of the major being the class AAA, where the residues occupy the conventional helical backbone torsion angles. However, moving towards the C-terminal end of the turn, there is a shift in the φ,ψ angles towards more negative φ, such that the electrostatic repulsion between two consecutive carbonyl oxygen atoms is reduced. Except for the last position (i+4), there is not much similarity in residue composition at different positions of hydrogen and non-hydrogen bonded AAA turns. The presence or absence of Pro at i+1 position of α- and β-turns has a bearing on whether the turn is hydrogen-bonded or without a hydrogen bond. In the tertiary structure, α-turns are more likely to be found in β-hairpin loops. The residue composition at the beginning of the hydrogen bonded AAA α-turn has similarity with type I β-turn and N-terminal positions of helices, but the last position matches with the C-terminal capping position of helices, suggesting that the existence of a "helix cap signal"at i+4 position prevents α-turns from growing into helices. Our results also provide new insights into α-helix nucleation and folding.