Michael Pikaart/Biochem StructureIntro: Difference between revisions
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Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /> | Helices have a twist to them, either right handed or left handed. A normal right-tighty screw is a right-handed helix. We take a look at a protein called GCN4, a transcription factor found in yeast that binds DNA and regulates expression of genes responsible for synthesis of amino acids. (For more information, go to [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=GCN4|SGD]). The GCN4 protein has a long section of alpha helix. Part of this helix binds directly to a particular sequence of DNA, while the part of the helix not in direct contact with the DNA binds to a second GCN4 molecule. In fact, GCN4 must bind to a second GCN4 molecule in order to bind DNA; GCN4 thus binds DNA as a homodimer. Thus the alpha helix of GCN4 provides both its DNA binding domain and its dimerization domain. We'll start with looking at the GCN4 dimer bound to DNA. It looks kind of like you're picking up a pencil between two fingers.<applet load='1ysa' size='400' frame='true' align='right' caption='GCN4 homodimer bound to DNA' /> | ||
Take a minute to play around with this structure. By grabbing the image with a left-click, you can rotate it around. If you hold the Shift key as you left-click, you can either zoom, by moving your mouse up and down, or rotate in the z axis, by moving your mouse left and right. Right-clicking gives you a bunch of options allowing you to control how the structure appears. Then click the green links below to walk through a number of close-ups of the molecule. | |||
Let's take a closer look at a bit of the alpha helix. | |||