Importance of potential interhelical salt-bridges involving interior residues for coiled-coil stability and quaternary structure.

Coiled coils are formed by two or more alpha-helices that align in a parallel or an antiparallel relative orientation. Polar interactions involving residues at the interior a and d positions are important for determining the quaternary structure of coiled coils. In the model heterodimeric coiled-coil Acid-a1-Base-a1, a buried a-d' Asn-Asn interaction is sufficient to specify both a dimeric structure and an antiparallel relative helix orientation.

The role of helix stabilizing residues in GCN4 basic region folding and DNA binding.

Basic region leucine zipper (bZip) proteins contain a bipartite DNA-binding motif consisting of a coiled-coil leucine zipper dimerization domain and a highly charged basic region that directly contacts DNA. The basic region is largely unfolded in the absence of DNA, but adopts a helical conformation upon DNA binding. Although a coil --> helix transition is entropically unfavorable, this conformational change positions the DNA-binding residues appropriately for sequence-specific interactions with DNA.