Molecular visualization of the GCN4-DNA interaction

This web page uses the open-source Java Applet program Jmol, a platform-independent replacement for Chime and Rasmol, neither of which is available in an OS X native version. You will need a relatively recent Java Virtual Machine to use it.

The buttons below are generally intended to be clicked in order.

This tutorial illustrates 1ysa.pdb, the structure of the basic region-leucine zupper protein GCN4 determined by Ellenberger and Harrison, 1992. This shows the classic alpha helices in major groove recogntion. The dimeric protein binds to an inverted repeat recognition site. Protein binding is thermodynamically coupled to protein dimerization.

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Here are the text files that back up the buttons, so you can see the syntax used for Jmol. You should even be able to cut and paste from these files into the Jmol console and reproduce what the buttons do.

  1. Initial view
  2. Focus on Leucine zipper
  3. Focus on basic residues
  4. Focus on Asn 235
  5. Zoom in on interactions
  6. Details of H-bond network
  7. Arg-Guanine