Zipperer

JD Hirst, M Vieth, J Skolmck, CL Brooks III. Predicting leucine zipper structures from sequence. Protein Eng 9 657-662, 1996. 

DA d Avignon, GL Bretthorst, ME Holtzer, A Holtzer. Thermodynamics and kinetics of a folded-folded transition at vahne-9 of a GCN4-hke leucine zipper. Biophys I 76 2752-2759, 1999. 

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. 

Leucine zippers provide dimerization interactions for some eucaryotic transcription factors... 

The leucine zipper motif (see Chapter 3) was first recognized in the amino acid sequences of a yeast transcription factor GCN4, the mammalian transcription factor C/EBP, and three oncogene products, Fos, Jun and Myc, which also act as transcription factors. When the sequences of these proteins are plotted on a helical wheel, a remarkable pattern of leucine residues... 

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 ability of the leucine zipper proteins to form heterodimers greatly expands the repertoire of DNA-binding specificities that these proteins can display. As illustrated in Figure 10.19, for example, three distinct DNA-binding specificities could, in principle, be generated from two types of monomer, while six could be created from three types of monomer and so on. This is an example of combinatorial control, in which combinations of proteins, rather than individual proteins, control a cellular process. It is one of the most important mechanisms used by eucaryotic cells to control gene expression. 

The GCN4 basic region leucine zipper binds DNA as a dimer of two uninterrupted a helices... 

Figure 10.19 Heterodimerization of leucine zipper proteins can alter their DNA-binding specificity. Leucine zipper homodimers bind to symmetric DNA sequences, as shown In the left-hand and center drawings. These two proteins recognize different DNA sequences, as indicated by the red and blue regions in the DNA. The two different monomers can combine to form a heterodimer that recognizes a hybrid DNA sequence, composed of one red and one blue region.

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... 

Figure 10.23 Domain arrangement along the polypeptide chains of three families of transcription factors b/z, b/HLH and b/HLH/z. All three have a basic region (blue) that binds DNA. Dimerization is achieved by the zipper region (purple) in the b/z family, by the Hl-loop-H2 region (red-yellow-green) in the b/HLH family and by a combination of both the zipper and the HLH regions in the b/HLH/z family.

The b/HLH/zip family of transcription factors have both HLH and leucine zipper dimerization motifs... 

Figure 10.28 Schematic diagram of the binding of the transcription factor Max to DNA. The two monomers of Max (blue and green) form a dimer through both the helix-loop-helLx regions which form a four-helix bundle like MyoD, and the zipper regions, which are arranged in a coiled coil. The N-terminal basic regions bind to DNA in a way similar to GCN4 and MyoD. (Adapted from A.R. Ferre-D Amare et al., Nature 363 38-4S, 1993.)...

Figure 10.29 The structure of the Max monomer is essentially built up from two long a helices joined by a loop region (yellow). The basic region (blue) and H1 (red) of the helix-loop-helix region form one continous a helix, and H2 (green) and the zipper region (purple) form a second continous a helix.

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. 

Helix-loop-helix (b/HLH) transcription factors are either heterodimers or homodimers with basic a-helical DNA-binding regions that lie across the major groove, rather than along it, and these helices extend into the four-helix bundle that forms the dimerization region. A modification of the b/HLH structure is seen in some transcription factors (b/HLH/zip) in which the four-helix bundle extends into a classic leucine zipper. 

Ellenberger, T.E., et al. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted a helices crystal structure of the protein-DNA complex. Cell 71 1223-1237, 1992. 

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. 

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