Tom Sandbox: Difference between revisions
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{{STRUCTURE_1ysa| PDB=1ysa | SCENE= }} | {{STRUCTURE_1ysa| PDB=1ysa | SCENE= }} | ||
===Zipper and Binding Domains=== | |||
These 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/2'>bases and phosphate oxygens</scene> of DNA. In this scene, 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. | These 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/2'>bases and phosphate oxygens</scene> of DNA. In this scene, 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. | ||
