Knob-socket packing investigation of bZIP protein dimerization

Abstract

The α-helical coiled coil (CC) is a well-studied protein structural motif. The pseudo-heptad repeat is the distinguishing characteristic of canonical CC, which consists of a repeating seven amino acids at abcdefg positions. Knob-socket (KS) analyses of the CC packing interactions reveal the contribution of amino acids at each position to affinity and specificity by describing the inter-helical packing as well as the intra-helical packing interactions in CC helices. The binding interface between two CC helices can be defined as a hydrophobic seam.