Leucine zipper peptide

The stability of peptides is generally increased when natural amino acids are substituted by fluorinated analogs (e.g., tri- or hexafluoroleucine, hexafluorova-line). Such stabilization augments with the number of hexafluoroleucine residues introduced [77]. Native-like structure was preserved, but the peptides had a more structured backbone and less fluid hydrophobic core. Substitution of four leucine residues by trifluoroleucines in the leucine zipper peptide GCN4-p1d led to a substantial gain in thermal stability and resistance to chemical denaturation of the... 

Thus, the question in coiled-coil prediction and design is what specific replacements are superimposed on the basic HPPHPPP pattern to direct the functional oligomerization state This question was first tackled by Conway and Parry, who analyzed natural coiled-coil sequences that formed dimers and trimers (Conway and Parry, 1990, 1991). Woolfson and Alber (1995) advanced this approach by comparing amino-acid profiles for these two structures directly. The work that made the biggest impact on this issue, however, was the collaborative experimental study from the Kim and Alber laboratories using the GCN4 leucine-zipper peptide model system and mutants thereof. 

Returning to the a and d sites of coiled-coil interfaces, they are not the exclusive province of hydrophobic residues polar residues are found here and, in many cases, they are highly conserved. In retrospect, this is also apparent in the amino-acid profiles of dimeric and trimeric coiled coils (Conway and Parry, 1990, 1991 Lupas et al., 1991). Furthermore, inspection of these profiles reveals trends in the data for instance, basic residues occur frequently at the a sites of dimeric coiled coils (Conway and Parry, 1990). The real importance of such inclusions, however, only became apparent with the determination of the structure of the leucine-zipper peptide GCN4-pl (O Shea et at, 1991). 

Woolfson et al. reported the design of a self-assembling fiber (SAP) system [73] that comprises two complementary de novo designed leucine zipper peptides. Due to complementary interactions in the core and flanking ion pairs, the two peptides combine rapidly to form partly helical staggered heterodimers. These heterodimers have sticky ends to promote their lateral noncovalent association into extended coiled-coil fibers. 

Ghosh and coworkers demonstrate that discrete supramolecular assemblies can be formed from leucine-zipper peptides tethered to a dendrimer core. These give fibrous structures when two complementary discrete dendrimer-peptide assemblies are combined this is one of the first examples where both discrete and repeated assemblies can be formed using the same system (Figure 18a). 

Initial studies to characterize the behavior of fluorinated amino acids within coiled-coil systems were conducted independently by the Tirrell group at CalTech and the Kumar group at Tufts. Work focused on incorporation of tri-fluoroleucine and trifluorovaline into the well-characterized leucine zipper peptides that readily assemble into dimeric ensembles in order to act as DNA-binding elements within transcription factors. The yeast transcriptional factor GCN4 contains a 56-amino acid DNA-binding segment known... 

Fig. 4 Multidomain leucine zipper proteins designed to form reversible hydrogels. Helices represent leucine zipper peptides Lines represent central polyelectrolyte domains. Reproduced from [22] with permission of the publisher...

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.

Figure 5 Plots of the Logarithmic Capacity Factor, In k, versus the Reciprocal of the Absolute Temperature (1/7) (A) and In k versus the Volume Fraction of the Organic Solvent, ip, (B) for the 37-mer Peptide, HIV-1 gpl60 Leucine Zipper [N558-Q595] Polypeptide,24 ab...

Stereo view of the sixty propane minima (thick lines) obtained with the modified force field (see text) on the surface of the A peptide chain (medium lines) of the GCN4 leucine zipper (PDB code 2ZTA). Although the peptide chain was removed during the MCSS procedure, its backbone and hydrophobic side chains are also drawn (thin lines) to show how the propane minima match the aliphatic groups of chain B. Hydrophobic residues are labeled at their Ca atom.Five clusters of propane minima that do not match the hydrophobic side chain of the helix involved in the interhelical interactions are labeled from A (top right) to E (bottom center) and discussed in the text. 

Several mammalian leucine zipper proteins bind to the CCAAT sequence (Table 28-1) and are, therefore, as a family designated C/EBP.361 366 367 A 30-residue segment of C/EBP contains four leucine residues at 7-residue intervals. When plotted as a helical wheel (Fig. 2-20) the four leucines are aligned on one side.368 Similar sequences are present in the proteins cMyc, cjun, and cFos and in GCN4. These observations suggested that if the peptide sequence forms an a helix, the leucine side chain from two identical subunits or closely related proteins might interdigitate in... 

The disulfide-bridged leucine zipper dimers (Scheme 8) were prepared by air oxidation of the appropriate reduced peptides containing a Cys-Gly-Gly linker at the amino terminus.[9) Typically, the ap-... 

Related to these ideas, Pandya et al. (2004) have described the design of an antiparallel coiled-coil (helix-loop-helix) peptide, which is stabilized by a disulfide bridge between the termini of the peptide. Reduction of the disulfide triggered a switch to a dimeric leucine zipper. 

Ryadnov et al. (2003) have designed a coiled coil-based nanoscale linker system dubbed Belt-and-Braces. The system was novel in a number of respects. Though based on a leucine-zipper dimer design, it was a ternary system in which one peptide (the Belt ) templated the assembly of two half-sized peptides (the Braces ) thus, the system was the first and simplest example of a coiled-coil vernier assembly (Kelly et al., 1998). The Belt-and-Braces design employed all of the key design rules for a... 

Stevens et al (2004) reported a similar leucine-zipper-like linker system. This comprised two six-heptad peptides (d = Leu, a = Val, Ala, and lie), one of which was basic with predominantly Lys at e and g, while the other was acid with predominantly Glu at e and g. Assembly was confirmed by CD spectroscopy and visualized by coupling the peptides to gold nanoparticles followed by TEM. A nice touch in this work was the use of different size nanoparticles to create binary assemblies including satellite structures, in which 8.5 nm particles (derivatized with the acid peptide) were organized around 53 nm particles (derivatized with the basic peptide). 

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