Factors that affect the stabilization of alpha-helices in short peptides by a capping box

It was reported recently that the capping box sequences of four N-terminal residues are very important for the stabilization of alpha-helices in proteins and peptides. To elucidate factors that affect the stabilization of alpha-helices in short peptides by this motif, we analyzed conformational properties of side chains of five N-terminal residues in several analogs of neuropeptide Y (NPY). The analysis revealed three previously unreported factors that appear to be important for stabilization of an alpha-helix: (a) a second capping box hydrogen bond for the side chains of Ser, Thr, and Cys; (b) long-range electrostatic interactions between the first (N-cap) and fifth (N4) residues; and (c) capping interactions of alpha-amino groups with the N4 residue. These factors were incorporated into the parameter set of a recently published, statistical mechanics approach that showed excellent accuracy in the prediction of the helical propensities of short peptides in water [Munoz, V., & Serrano, L. (1995) J. Mol. Biol. 245, 275-296, 297-308]. A significant improvement in the agreement between theoretical predictions and experimental data was achieved. The present results also clarify the nature of capping box stabilization of alpha-helices in peptides and proteins, indicating that the total influence of hydrogen bonding, local interactions between side chains, helix macrodipole-charge/dipole interactions, and solvation possibilities must all be taken into account. All these factors are associated with approximately the same energy, but with different residues at the N-cap position, they may have opposite effects on the helix stability of peptides. Thus, a delicate balance of interactions of different types controls the stabilization properties of N-cap residues in alpha-helices.