Tom Sandbox: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
Alan Tom (talk | contribs)
111 edits
No edit summary
Alan Tom (talk | contribs)
111 edits
No edit summary
Line 6: Line 6:




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 amino acid control 'derepression response' in yeast and binds upstream of several amino acid biosynthetic genes.<ref>PMID:3464968</ref> It is one of the main response factors for amino acid starvation.  
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 amino acid control 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.  


GCN4 is known as a B zip 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/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>
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/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>


===Hydrophobic Stability===
===Hydrophobic Stability===
Line 22: Line 22:
===Binding with DNA===
===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 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>
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>


===Heptad Repeat===
===Heptad Repeat===
Line 42: Line 42:
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 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 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, protenating 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.
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:ph effects.jpg|center|500px]]
Retrieved from "https://proteopedia.org/Tom_Sandbox"