The leucine zipper family: a protein folding motif optimized by nature to fold into a stable α-helical coiled coil. See Figure 1.

Toggle alternate models of leucine zipper region.

The N-terminal half (blue and turquiose) contains basic amino acid residues that interact with the major groove of DNA in a sequence-specific manner.

The C-terminal half (purple and violet) is a leucine zipper. Each chain of the GCN4 leucine zipper domain contains 33 residues. The key leucine residues of each heptad repeat are shown in CPK colors.

Zoom in on the leucine zipper. Toggle spacefill.

Color sidechains by properties (nonpolar, polar and charged). The chains are shown in different shades. Toggle labels on or off.

The end-on view of a two-stranded coiled coil shows that the a and d positions are not structurally equivalent. Residues 63 through 74 comprise the third leucine repeat (-LENEVAR-L).

Leucine side chains in position a face each other across the central axis of the coiled coil and handshaking is easy. The amino acid side chain in position d is oriented away from the central axis and toward the aqueous phase. Toggle spacefill of Leu-67 and Leu-74 sidechains.

Leucine zipper dimers frequently have oppositely charged residues in the d position of one chain and in the e position of the other chain. However, one finds valine in position e in the third heptad of the GCN4 leucine zipper.

Val-71 occurs at position e.

Glu-70 occurs at position d.

Glu-70 in position d pairs with Val-71 in position e of the other chain. Toggle between the two pairs.

Return to backbone model only.

Inter- and intra-helical ionic bonds contribute considerably to stability of coiled coils. Let's look at an intrahelical ionic bond in the third leucine repeat.

Glu-70 (position d) forms an important intrahelical ionic bond with Arg-73 (position g).

The nonpolar –CH2– groups of Glu-70 and Arg-73 interact nicely with the nonpolar side chain of Leu-74 (position a of the next heptad).

An enigma: Is glutamate a hydrophobic amino acid? Why do we find Glu-70 in the d position of the third heptad of the GCN4 leucine zipper?

The –COO^- group of Glu-70 is indeed exposed to the solvent, but its nonpolar –CH2– groups are really in a quasi-nonpolar environment.

View a transparent surface model. The fact that the side chain of Glu-70 is only partially exposed to the solvent becomes immediately clear if you examine the model.

The long-side-chain amino acids, glutamate, lysine, arginine, and glutamine, have not traditionally been considered as nonpolar, yet they are frequently found in position d of leucine zipper motifs. As long as the –COO^- group is neutralized by salt-bridge formation, the glutamate side chain may be considered a nonpolar side chain. We have seen that this is indeed true for Glu-270 in position d of the third heptad repeat of the GCN4 leucine zipper.

The contribution of the two Glu-70···Arg-73 ionic bonds to the thermodynamic stability of the GCN4 leucine zipper has been evaluated experimentally through protein engineering. The double mutant, E70A/R73A, has a melting temperature of 35°C, compared to 55°C for the wild-type protein.

JSmol allows us to model the double mutant. Try it! What do you notice?

In protein engineering, it's generally a safe bet to replace a particular surface residue of interest with alanine. Why is this so?