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-term inal residues are very important for the stabilization of alpha-helice s in proteins and peptides. To elucidate factors that affect the stabi lization 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 thre e previously unreported factors that appear to be important for stabil ization of an alpha-helix: (a) a second capping box hydrogen bond for the side chains of Ser, Thr, and Cys; (b) long-range electrostatic int eractions between the first (N-cap) and fifth (N4) residues; and (c) c apping interactions of alpha-amino groups with the N4 residue. These f actors were incorporated into the parameter set of a recently publishe d, statistical mechanics approach that showed excellent accuracy in th e prediction of the helical propensities of short peptides in water [M unoz, V., & Serrano, L. (1995) J. Mol. Biol. 245, 275-296, 297-308]. A significant improvement in the agreement between theoretical predicti ons and experimental data was achieved. The present results also clari fy the nature of capping box stabilization of alpha-helices in peptide s and proteins, indicating that the total influence of hydrogen bondin g, local interactions between side chains, helix macrodipole-charge/di pole 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 ha ve opposite effects on the helix stability of peptides. Thus, a delica te balance of interactions of different types controls the stabilizati on properties of N-cap residues in alpha-helices.