CHIME EXERCISE

2OR1: Complex between 434 Phage Repressor and Target DNA

The structure to the right is that of Phage Repressor complexed with DNA. Use the following instructions to identify key characteristics of the complex:

 

1) Display the complex as wireframe, then select the DNA and display it as either Backbone or Ribbon.

  • Identify the Major and Minor grooves of the DNA

2) Select all, and display as Cartoon

  • Identify the protein dimer, and note the symmetry of the subunits. How many helices does a subunit have?

  • Which helix is in the major groove? This helix is known as the "recognition helix."

  • Note that the two successive major grooves of DNA are occupied, each by one helix of a subunit.

  • Find the helix-turn-helix (HTH) motif and note which helices are involved. 

  • Note the proximity of the C-terminal helices -- there appears to be some interaction, but it's not the main protein-protein interaction (the main interaction is between 2 C-terminal domains not shown here)

3) Select all, and display as wireframe. Now, select the protein and display it as spacefill. 

  • Note how the protein conforms to the DNA backbone and major grooves.

4) Select all, and display as cartoon.  Then select protein sidechains and display as ball and stick.

  • Identify a few of the sidechains on the recognition helix that appear to interact with bases in the major groove of the DNA.

  • Identify sidechains on the other helices near the DNA that appear to interact with the DNA backbone.

5) Select the helices and identify the loop part of the HTH motif.

  • What residues comprise the loop?

6) Select the water residues and display as ball and stick.

  • Do they seem to play a role in the protein-DNA interactions?

7) Using a spacefill display for the DNA, and another display for the protein, try to identify a few residues that might be involved in VDW contacts.  Find some nonpolar residues and display them as ball and stick to see if they're in touching distance.

 

As a result of the DNA-Protein interaction, the DNA is bent in an arc of radius ~65 A. This has two geometric consequences:

      (1) Minor groove is compressed ~2.5 A at the center

      (2) Minor groove widens ~2.5 A at the ends.