Tom Sandbox: Difference between revisions
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===Structure=== | ===Structure=== | ||
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 | 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 <scene name='Tom_Sandbox/Hydrophobic_and_philic_regions/1'>hydrophobic residues</scene> near the C terminus, while pinching in on the major groove of DNA in the N terminal end via basic residues. It is clear from the image how the grey hydrophobic regions are between the helices, while the pink hydrophobic regions protrude outwards. | ||
{{STRUCTURE_1ysa| PDB=1ysa | SCENE= }} | |||
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. | |||
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'''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.''' | '''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==== | ====The Leucine Zipper==== | ||
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>. 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, 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"/> | ||
