Protein Engineering Protocols - Mycobacteriology research center

36 Mason et al.Fig. 1. Dimeric parallel coiled coil. (A) Helical wheel diagram looking down thehelix axis from the N-terminus to the C-terminus. Heptad positions are labeled a to gand a′ to g′, respectively. Positions a, d, e, and g are in different shades of gray. (B) Sideview. The helical backbones are represented by cylinders, the side chains by knobs. Thepath of the polypeptide chain is indicated by a line wrapped around the cylinders. Forsimplicity, the supercoiling of the helices is not shown. While residues at positions a(dark gray) and d (light gray) make up the hydrophobic interface, residues at positionse (medium gray) and g (black) pack against the hydrophobic core. They can participatein interhelical electrostatic interactions between residue i (g position) of one helix andresidue i′ + 5 of the other helix (e′ position, belonging to the next heptad), as indicatedby the hatched bars. (C,D) Coiled-coil domain of the yeast transcription factor GCN4(see Note 1) as ribbon plot (Protein Data Bank code: 2ETA; ref. 6) to indicate supercoilingand g/e′ interactions. The plot was made using Pymol (7).is the parallel (i.e., both helices run N to C alongside each other) dimeric, lefthandedvariety. In this class, the periodicity of each helix is seven, with anywherefrom 2 (in designed coiled coils; ref. 4) to 200 of these repeats in aprotein (5). In this repeat, the residues are designated (a-b-c-d-e-f-g) nin onehelix, and (a′-b′-c′-d′-e′-f′-g′) nin the other (Fig. 1). In this model, a and d areusually nonpolar core residues found at the interface of the two helices, conversely,e and g are partially solvent exposed polar “edge” residues that givespecificity between the two helices through electrostatic interactions. Finally,the remaining three residues (b, c, and f) are typically hydrophilic and exposedto the solvent. The apparent simplicity of the coiled coil structure, with itsheptad periodicity, has led to extensive study. Remarkably, interaction between