Coiled coils leucine-zippers

Lumb, K. J., Carr, C. M., and Kim, P. S. (1994). Subdomain folding of the coiled-coil leucine-zipper from the bZIP transcriptional activator GCN4. Biochemistry. 33, 7361-7367. 

Figure 2 The change in fraction folded of a coiled-coil leucine zipper peptide, GCN4-P1, as a function of temperature and peptide concentration. The concentrations range from 1 pM with the lowest Tu to 20 pM with the highest T. The enthalpy of unfolding was 35.0 1.1 koal moM (monomer) which compared to that of 34.7 0.3 koal moM measured by calorimetry. Abstracted with permission from data in Thompson KS, Vinson CR and Freire E (1993) Biochemistry Z2 5491-5496. Copyright 1993 American Chemical Society.

Residues 50-64 of the GAL4 fragment fold into an amphipathic a helix and the dimer interface is formed by the packing of these helices into a coiled coil, like those found in fibrous proteins (Chapters 3 and 14) and also in the leucine zipper families of transcription factors to be described later. The fragment of GAL4 comprising only residues 1-65 does not dimerize in the absence of DNA, but the intact GAL4 molecule does, because in the complete molecule residues between 65 and iOO also contribute to dimer interactions. 

Figure 10.18 Side-chain interactions in the leucine zipper structure, (a) The hydrophobic side chains in spikes a and d (see Figure 10.17) form a hydrophobic core between the two coiled a helices, (b) Charged side chains in spikes and g can promote dimer formation by forming complementary charge interactions between the two a helices.

The coiled-coil structure of the leucine zipper motif is not the only way that homodimers and heterodimers of transcription factors are formed. As we saw in Chapter 3 when discussing the RNA-binding protein ROP, the formation of a four-helix bundle structure is also a way to achieve dimerization, and the helix-loop-helix (HLH) family of transcription factors dimerize in this manner. In these proteins, the helix-loop-helix region is preceded by a sequence of basic amino acids that provide the DNA-binding site (Figure 10.23), and... 

Dimerization of the Ce-zinc cluster transcription factors involves an a-helical coiled coil in the dimerization region. Coiled coils, often called leucine zippers, are also found in a large group of transcription factors that do not contain zinc. The leucine zipper is made up of two a helices in a coiled coil with every seventh residue leucine or some other large hydrophobic residue, such as isoleucine or valine. Leucine zipper transcription factors (b/zip) include factors characterized by heterodimerization, for example Fos and Jun. The a-helical DNA-binding motifs of the heterodimers recognize quite different base sequences and are continous with the a helices of the zipper. 

O Shea, E.K., et al. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254 539-544, 1991. 

The leucine zipper DNA-binding proteins, described in Chapter 10, are examples of globular proteins that use coiled coils to form both homo- and heterodimers. A variety of fibrous proteins also have heptad repeats in their sequences and use coiled coils to form oligomers, mainly dimers and trimers. Among these are myosin, fibrinogen, actin cross-linking proteins such as spectrin and dystrophin as well as the intermediate filament proteins keratin, vimentin, desmin, and neurofilament proteins. 

Harbury, P.H., et al. A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 262 1401-1407, 1993. 

A leucine zipper is a structural motif present in a large class of transcription factors. These dimeric proteins contain two extended alpha helices that grip the DNA molecule much like a pair of scissors at adjacent major grooves. The coiled-coil dimerization domain contains precisely spaced leucine residues which are required for the interaction of the two monomers. Some DNA-binding proteins with this general motif contain other hydrophobic amino acids in these positions hence, this structural motif is generally called a basic zipper. 

The leucine zipper motif was recently successfully employed for the construction of native-like triple-stranded coiled-coil in solution [29]. 

B) Helical wheel representation of residues 2-31 of the coiled coil portion of the leucine zipper (residues 249-281) of the related transcription factor GCN4 from yeast. The view is from the N terminus and the residues in the first two turns are circled. Heptad positions are labeled a-g. Leucine side chains at positions d interact with residues d and e of the second subunit which is parallel to the first. However, several residues were altered to give a coiled coil that mimics the structure of the well-known heterodimeric oncoproteins Fos and Jun (see Chapter 11). This dimer is stabilized by ion pairs which are connected by dashed lines. See John et al.172... 

Each of the monomeric proteins c-jun and c-fos, as well as other members of the leucine zipper family, has an N-terminal DNA-binding domain rich in positively charged basic amino acid side chains, an activation domain that can interact with other proteins in the initiation complex, and the leucine-rich dimerization domain.363 The parallel coiled-coil structure (Fig. 2-21) allows for formation of either homodimers or heterodimers. However, cFos alone does not bind to DNA significantly and the cjun/cFos heterodimer binds much more tightly than does cjun alone.364 The yeast transcriptional activator protein GCN4 binds to the same 5 -TGACTCA sequence as does the mammalian AP-1 and also has a leucine zipper structure.360 364 365... 

Similarly, we have studied the preferential heterodimer parallel coiled-coil formation of the transcription factors Max and c-Myc leucine zippers.161 The sequence of the coiled-coil regions of Max and c-Myc is shown in Scheme 8 along with the cross-section of the Max/ c-Myc heterodimer, which shows many favorable electrostatic interactions not identified in the homodimers of either c-Myc or Max. Similarly, air oxidation and redox equilibrium experiments in Figure 9 clearly show the preferential heterodimer formation. 

Hu, J.C., O Shea, E.K., Kim, P.S. Sauer, R.T. (1990). Sequence requirements of coiled-coils analysis with X. repressor-GCN4 leucine zipper fusions. Science 250, 1400-3. 

Fig. 3. The structure of the 33-residue region of yeast transcription factor GCN4 is a two-stranded coiled coil, and is viewed here perpendicular to its long axis. The chains each have a heptad substructure and an a-helical conformation. Because GCN4 contains leucine residues in each d position, except for the most C-terminal one, the structure is commonly referred to as a leucine zipper (PDB coordinate reference number 2ZTA). The pitch length of the left-handed coiled coil has an average value of about 20.4 nm (Harbury et al, 1993 Kuhnel et al, 2004).

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