Tom Sandbox: Difference between revisions

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/2'>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 aforementioned image how the grey hydrophobic regions are between the helices, while the pink hydrophobic regions protrude outwards.

{{STRUCTURE_1ysa|  PDB=1ysa  |  SCENE=  }}  

The two main domains are labeled 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 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.