Tom Sandbox: Difference between revisions

GCN4 (PDB [[2zta]] by itself, [[1ysa]] bound to DNA) is a eukaryotic transcription factor first isolated from Saccharomyces cerevisiae, also known as Baker's Yeast. The first 'leucine zipper' model was coined by Landshulz et al. in 1988. Today, while the name has stayed the same, we no longer view the leucine binding region in an inter-collated manner, but as <scene name='Tom_Sandbox/Leu_leu_and_val_val/1'>Leucines</scene>  meeting face to face <ref name="abc"> Oas, T. G.;  McIntosh, L. P.;  O'Shea, E. K.;  Dahlquist, F. W.; and  Kim, P. S. Biochemistry 1990 29 (12), 2891-2894 </ref>. (see heptad repeat section) Here the Leucines are represented as red and the Valines are shown as oragne. A close up of the leucine-leucine pairing can be seen <scene name='Tom_Sandbox/Leu-leu_interaction/1'>here</scene>.GCN4 binds to promoter regions AP-1 and ATF/CREB to induce transcription via the C terminal basic residues of the two symmetric alpha helices.<ref> Hope, I. A.; Struhl,K. Cell, Volume 46, Issue 6, 12 September 1986, Pages 885-894</ref>

===Structure===

===Binding with DNA===

The basic region binding domain of GCN4 inserts itself into the <scene name='Tom_Sandbox/Major_groove/1'>Major Groove</scene> of the DNA. This causes a shift in bothe the AP-1 and ATF/CREB binding sites of DNA<ref name="bind">PMID:15459288</ref>. This was determined by adding fluorophores to the end of U shaped DNA segments with the specific binding sites in the centers. The shift in their positioning showed the effect of bending on the DNA. In total, in the complex with GCN4-bZIP, the ATF/CREB site is bent by (25 ± 2)° and the AP-1 site by (20 ± 2)° toward the minor groove.<ref name="bind"/> AP-1 refers to a group of activator proteins that bind to the same 9 base pair semi-palindromic region for transcription activation. ATF/CREB refers to a fully palendromic region. The AP-1 site sequence is 5′-ATGACTCAT-3′, and the ATF/CREB site is 5′-ATGACGTCAT-3′<ref> Hockings, S. C.; Kahn, J. D.; Crothers, D. M. PNAS February 17, 1998 vol. 95 no. 4 1410-1415 </ref>.  

====Heptad Repeat====

'''Image 1:A pictorial representation of the heptad repeat between the two subunits in a coiled-coil conformation. By following through the wheels alphabetically, it is clear how the leucines will stack every 7 units. The apostrophe denotes the diference between the two polypeptide subunits.'''(from Kgutwin in Wikipedia Commons http://commons.wikimedia.org/wiki/File:Coiledcoil-wheelcartoon.gif)

At every d and d' we have a Leucine, while at the a and a' locations we typically see valine. <ref name="Voet" /> In the opposite positions one tends to see more charged and polar residues. The Leucine and Valine repeats create a strongly hydrophobic region between the two alpha helices. This clearly shows the relationship between coils and shown below, we can see that for the two helices to be symmetrical, the Leucines must not in fact be oriented as a zipper, but on the same levels.

'''Image 2: The figure above comes from the paper - Secondary Structure of a Leucine Zipper Determined by NMR.<ref name="abc"/> The caption was left for clarification.'''

====The Leucine Zipper Nano-Tweezer====