STRUCTURAL-ANALYSIS OF THE N-TERMINI AND C-TERMINI IN A PEPTIDE WITH CONSENSUS SEQUENCE

We present a structural analysis of a peptide, the sequence of which i ncludes 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 c apping. The sequence of five residues at the middle is inserted to sep arate effects at the two ends via a helix-stabilizing linker. Applicat ion of a simulated annealing procedure using interproton distance cons traints derived from H-1 NOESY experiments in water reveals the presen ce of a C-terminal structure in this model. The C-terminus forms a fol ded back structure in a significant fraction of structures generated b y the annealing, in most of which Gly assumes an alpha(L) conformation . This structure occurs within a highly flexible region of the molecul e and hence is occupied only a fraction of the time.