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-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_interaction/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) 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>
+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. It is required for the general control of amino acid levels in yeast and binds upstream of several amino acid bio-synthetic genes.<ref>PMID:3464968</ref> Its primary function is to act as one of the main response factors for amino acid starvation by initiating transcription, however the exact mechanism of initiation is still being debated (see Binding with DNA).
+GCN4 is known as a bZip protein after its basic region and leucine zipper domains. The first 'leucine zipper' model was coined by Landshulz et al. in 1988 after their initial X-Ray crystallography structure was solved. Today, while the name has stayed the same, we no longer view the leucine binding region in an inter-collated manner like the teeth of a zipper, but as Leucines  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) <scene name='Tom_Sandbox/Leu_leu_and_val_val/1'>Here</scene> the Leucines are represented as red and the Valines are shown as orange. A close up of the leucine-leucine pairing can be seen <scene name='Tom_Sandbox/Leu-leu_interaction/2'>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===
+===Hydrophobic Stability===
-GCN4 is composed of two identical 58 residue alpha helix chains that grouped together to form a parallel coiled-coil dimer. The dimer binds through interlocking leucine amino acids and hydrophobic residues near the C terminus, while pinching in on the major groove of DNA in the N terminal end via basic residues. These two main domains are thus labled the leucine zipper dimerization domain and the basic DNA-binding domain. <ref name="ph"> Sharma, G.; Rege, K.; Budil, D. E.; Yarmush, M. L.; Mavroidis, C. Int J Nanomedicine. 2008 December; 3(4): 505–521. </ref> The basic residues are the reason the class of binding interactions is commonly referred to as bZIP or basic region leucine zipper proteins<ref name="Voet"> Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008. </ref>. The X-ray structure of the 33-residue polypeptide corresponding to the leucine zipper of GCN4 was determined by Peter Kim and Thomas Alber<ref>PMID:1948029</ref>
+GCN4 is composed of two identical 58 residue alpha helix chains that grouped together to form a parallel coiled-coil dimer. Roughly 33 of the 58 total residues are located in the Leucine Zipper region. The dimer binds through interlocking leucine amino acids and <scene name='Tom_Sandbox/Hydrophobic_and_philic_regions/3'>hydrophobic residues</scene> near the C terminus, while pinching in on the major groove of DNA in the N terminal end via basic residues.  The aforementioned image shows how the hydrophobic regions are between the helices, while the hydrophobic regions protrude outwards.
-====Heptad Repeat====
+{{STRUCTURE_1ysa|  PDB=1ysa  |  SCENE=  }}
-GCN4 is said to have a heptad repeat, or seven unit repeated sequence. Here the heptad repeat is a leucine, every seven units. When the structure of the alpha helices is taken into account, it is clear that each leucine is being stacked on top of the last one, every seven units. This creates the zipper-like repeated projections from the two polypeptide chains. Below we see a pictorial representation of the sequence of amino acids as we look down the length of the coiled coil structure.
+===Zipper and Binding Domains===
-[[Image:Coiledcoil-wheelcartoon.gif|center|300px]]
+The two main domains are labeled the <scene name='Tom_Sandbox/Acidic_and_basic_regions/2'>acidic leucine zipper dimerization domain and the basic DNA-binding domain</scene>. <ref name="ph"> Sharma, G.; Rege, K.; Budil, D. E.; Yarmush, M. L.; Mavroidis, C. Int J Nanomedicine. 2008 December; 3(4): 505–521. </ref> Here the acidic region is represented in red and the basic region in blue. The basic residues are the reason the class of binding interactions is commonly referred to as bZIP or basic region leucine zipper proteins<ref name="Voet"> Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008. </ref>. The basic region at the N-terminal of the two chains clamps in on the DNA in a scissor-like manner, making contact with both the <scene name='Tom_Sandbox/Binding_with_dna/3'>phosphate backbone</scene> and the <scene name='Tom_Sandbox/Binding_with_dna/4'>nucleotide bases</scene> of DNA.
-{{STRUCTURE_1ysa|  PDB=1ysa  |  SCENE=  }}
+===Binding with DNA===
+The basic region binding domain of GCN4 inserts itself into the <scene name='Tom_Sandbox/Major_groove/2'>major groove</scene> of the DNA. This causes a bend in both the AP-1 and ATF/CREB binding sites of DNA<ref name="bind">PMID:15459288</ref>. AP-1 refers to a group of activator proteins that bind to the same 9 residue semi-palindromic region for transcription activation. ATF/CREB refers to a fully palindromic 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>. The bending mechanism was determined by adding fluorophores to the ends of U shaped manufactured DNA segments with the specific binding sites AP-1 or ATF/CREB inserted into the center. The shift in the fluorophore positioning showed the effect of bending on the DNA due to GCN4 binding. 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"/> This is thought to be the mechanism for inducing transcription, however the actual bending of DNA is still debated.<ref>DOI: 10.1021/bi970215u</ref><ref>DOI: 10.1021/bi990053x</ref>
-'''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)
+===Heptad Repeat===
+GCN4 is said to have a heptad repeat, or seven unit repeated sequence. Here the heptad repeat is a leucine, every seven units. When the structure of the alpha helices is taken into account, it is clear that each leucine is being stacked on top of the last one, every seven units. This creates the zipper-like repeated projections from the two polypeptide chains. Below we see a pictorial representation of the sequence of amino acids as we look down the length of the coiled coil structure.
-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 <scene name='Tom_Sandbox/Leu-leu_interaction/1'>Leucines</scene> must not in fact be oriented as a zipper, but on the same levels.
+[[Image:Coiledcoil-wheelcartoon.gif|center|300px]]
-[[Image:Asymmetric_helices.jpg|center|400px]]
+'''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)
-'''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.'''
+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:zipper_motif.jpg|center|400px]]
+'''Image 2: The figure above comes from the paper - Secondary Structure of a Leucine Zipper Determined by NMR.<ref name="abc"/> Figure A represents the interdigitated zipper model and figure B shows the coiled coil symmetric model that is now the accepted structure.'''
-====The Leucine Zipper====
+===The Leucine Zipper Nano-Tweezer===
-The leucines themselves come on every other level of the alpha helix and do not actually interchange one over the other like a zipper, but instead make side to side contact. This was noted in 1990 due to the symmetric nature of the two subunits. If the leucines showed interdigitation the subunits would be asymmetric <ref name="abc"/>.
+The X-ray structure of the 33-residue polypeptide corresponding to the leucine zipper of GCN4 was determined by Peter Kim and Thomas Alber in 1991<ref>PMID:1948029</ref>. As stated above, the leucines themselves come on every other level of the alpha helix and do not actually interchange one over the other like a zipper, but instead make side to side contact. This was noted in 1990 due to the symmetric nature of the two subunits. If the leucines showed interdigitation the subunits would be asymmetric <ref name="abc"/>.
-The Leucine Zipper of GCN4, as expected, operates under a specific pH. It has been shown that at lower pH values the zipper will reversibly protenate and open up, losing its hydrophobic stability. Researchers are looking into this opening and closing reaction as a form of nano-tweezers. <ref name="ph"/>
+The Leucine Zipper of GCN4, as expected of a protein, operates under a specific pH. It has been shown that at lower pH values the zipper will reversibly protenate and open up. This occurs because it loses its hydrophobic stability, protonating its polypeptide chains. Researchers are looking into this opening and closing reaction to be used purposefully as a form of nano-tweezers to grab onto and hold very-very small particles. <ref name="ph"/> A diagram of this mechanism is shown below.
 [[Image:ph effects.jpg|center|500px]]
 '''Image 3: A schematic representation of the Leucine Zipper acting as nano-tweezers under different pH conditions<ref name="ph"/>.
-===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>.
 ==See Also==
 [[2zta]]
 [[1ysa]]
+<ref>DOI:10.1016</ref>
 ==Reference==
 <references/>