The structure of the ends of α-helices in globular proteins: Effect of additional hydrogen bonds and implications for helix formation

We prepared a set of about 2000 α‐helices from a relational database of high‐resolution three‐dimensional structures of globular proteins, and identified additional main chain i ← i+3 hydrogen bonds at the ends of the helices (i.e., where the hydrogen bonding potential is not fulfilled by canonical i ← i+4 hydrogen bonds). About one‐third of α‐helices have such additional hydrogen bonds at the N‐terminus, and more than half do so at the C‐terminus. Although many of these additional hydrogen bonds at the C‐terminus are associated with Schellman loops, the majority are not. We compared the dihedral angles at the termini of α‐helices having or lacking the additional hydrogen bonds. Significant differences were found, especially at the C‐terminus, where the dihedral angles at positions C2 and C1 in the absence of additional hydrogen bonds deviate substantially from those occurring within the α‐helix. Using a novel approach we show how the structure of the C‐terminus of the α‐helix can emerge from that of constituent overlapping α‐turns and β‐turns, which individually show a variation in dihedral angles at different positions. We have also considered the direction of propagation of the α‐helix using this approach. If one assumes that helices start as a single α‐turn and grow by successive addition of further α‐turns, the paths for growth in the N → C and C → N directions differ in a way that suggests that extension in the C → N direction is favored. Proteins 2011. © 2010 Wiley‐Liss, Inc.