Helix capping in the GCN4 leucine zipper

Capping interactions associated with specific sequences at or near the ends of alpha-helices are important determinants of the stability of protein se condary and tertiary structure. We investigate here the role of the helix-c apping motif Ser-X-X-Glu, a sequence that occurs frequently at the N termin i of alpha helices in proteins, on the conformation and stability of the GC N4 leucine zipper. The 1.8 Angstrom resolution crystal structure of the cap ped molecule reveals distinct conformations, packing geometries and hydroge n-bonding networks at the amino terminus of the two helices in the leucine zipper dimer. The free energy of helix stabilization associated with the hy drogen-bonding and hydrophobic interactions in this capping structure is -1 .2 kcal/mol, evaluated from thermal unfolding experiments. A single cap thu s contributes appreciably to stabilizing the terminated helix and thereby t he native state. These results suggest that helix capping plays a further r ole in protein folding, providing a sensitive connector Linking alpha-helix formation to the developing tertiary structure of a protein. (C) 1999 Acad emic Press.