Structural analysis of the N‐ and C‐termini in a peptide with consensus sequence

We present a structural analysis of a peptide, the sequence of which includes amino acids that show preferences for specific positions near the N‐ and C‐termini in protein helices. This peptide has the sequence ac‐YMSEDELKAAEAAFKRHGVP‐amide, which includes a strong version of an N‐terminal Harper‐Rose capping box structure as well as a Gly located close to the C‐terminus designed to elucidate its role in C‐terminal capping. The sequence of five residues at the middle is inserted to separate effects at the two ends via a helix‐stabilizing linker. Application of a simulated annealing procedure using interproton distance constraints derived from ¹H NOESY experiments in water reveals the presence of a C‐terminal structure in this model. The C‐terminus forms a folded back structure in a significant fraction of structures generated by the annealing, in most of which Gly assumes an α_L conformation. This structure occurs within a highly flexible region of the molecule and hence is occupied only a fraction of the time.