Tom Sandbox: Difference between revisions

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Alan Tom

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 These two main domains are labled the <scene name='Tom_Sandbox/Acidic_and_basic_regions/1'>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 as Orange and the basic region in purple. 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 like a pair of tweezers and makes contact with both <scene name='Tom_Sandbox/Binding_with_dna/1'>the bases and phosphate oxygens</scene> of DNA. In this example, Arginine residues of one of the helices are highlighted. The yellow Arginine binds to the oxygen of the phosphate backbone, while the light green Arginine binds to the inner nucleotide base.
+===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>.
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-====The Leucine Zipper====
+====The Leucine Zipper Nano-Tweezer====
-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>. 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, 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.
 [[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>.