Structures of N-termini of helices in proteins

We have surveyed 393 N-termini of α-helices and 156 N-termini of 310- helices in 85 high resolution, non homologous protein crystal structures for N-cap side-chain rotamer preferences, hydrogen bonding patterns, and solvent accessibilities. We find very strong rotamer preferences that are unique to N-cap sites. The following rules are generally observed for N-tapping in α- helices: Thr and Ser N-cap side chains adopt the gauche- rotamer, hydrogen bond to the N3 NH and have ψ restricted to 164 ± 8°. Asp and Ash N-cap side chains either adopt the gauche- rotamer and hydrogen bond to the N3 NH with ψ = 172 ± 10°, or adopt the trans rotamer and hydrogen bond to both the N2 and N3 NH groups with ψ = 107 ± 19°. With all other N-caps, the side chain is found in the gauche+ rotamer so that the side chain does not interact unfavorably with the N-terminus by blocking solvation and ψ is unrestricted. An i, i + 3 hydrogen bond from N3 NH to the N-cap backbone C=O in more likely to form at the N-terminus when an unfavorable N-cap is present. In the 310-helix Asn and Asp remain favorable N-caps as they can hydrogen bond to the N2 NH while in the trans rotamer; in contrast, Ser and Thr are disfavored as their preferred hydrogen bonding partner (N3 NH) is inaccessible. This suggests that Ser is the optimum choice of N-cap when α- helix formation is to be encouraged while 310-helix formation discouraged. The strong energetic and structural preferences found for N-caps, which differ greatly from positions within helix interiors, suggest that N-caps should be treated explicitly in any consideration of helical structure in peptides or proteins.