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

ABSTRACT Like the-turns,which are charac-terized by a limiting distance between residues two positions apart (i, i3), a distance criterion (involv-ing residues at positions i and i4) is used here to identify -turns from a database of known protein structures. At least 15 classes of -turns have been enumerated based on the location in the , space of the three central residues (i1 to i3)—one of the major being the class AAA, where the residues oc-cupy the conventional helical backbone torsion angles. However, moving towards the C-terminal end of the turn, there is a shift in the , angles towardsmore negative, such that the electrostatic repulsion between two consecutive carbonyl oxy-gen atoms is reduced. Except for the last position (i4), there is not much similarity in residue compo-sition at different positions of hydrogen and non-hydrogen bonded AAA turns. The presence or ab-sence of Pro at i1 position of - and -turns has a bearing on whether the turn is hydrogen-bonded or without a hydrogen bond. In the tertiary structure, -turns are more likely to be found in -hairpin loops. The residue composition at the beginning of the hydrogen bonded AAA -turn has similarity with type I -turn and N-terminal positions of heli-ces, but the last position matches with the C-terminal capping position of helices, suggesting that the existence of a “helix cap signal ” at i4 position prevents -turns from growing into helices. Our results also provide new insights into -helix nucleation and folding. Proteins 2004;55:305–315. © 2004 Wiley-Liss, Inc. Key words: -turn; -turn; conformation; second-ary structure; protein folding; sequence preferenc