1. Find a model of a human homeodomain/DNA complex.
a. How many models do you find?
b. What method of structure determination produced the first of these models?
c. View the first model on the list with QuickPDB or your favorite molecular viewer. What secondary structural element(s) (helix, sheet, coil) interact with DNA?
d. Give beginning and ending residues of main secondary structural element in contact with DNA.
2. Structural Work:
Search the Protein Data Bank for human homeodomain/DNA complexes. ===>View the first model you find with DeepView (Swiss-PdbViewer).
a. PDB File ID: _________ .
b. What patterns does ProSite recognize in this protein?
c. What secondary-structural element (helix, sheet, coil) contains most of the residues that ProSite recognizes as a homeodomain?
d. What secondary-structural element(s) of the homeodomain protein interact(s) directly with DNA?
e. List three residues involved with hydrogen bonds to DNA. List interactions like this: "LYS89-T6" means a hydrogen bond between lysine-89 of the protein and thymine-6 of the DNA.
f. Comment on the quality of this model, especially in areas of protein-DNA interaction.
Go to the PDB at http://www.rcsb.org/pdb/
Put in the search box the following: homeodomain and sapiens
That will search the database for keywords homeodomain AND sapiens (for human, right?)
The first model is 1B72.
It was produced by X-ray Diffraction.
Click on "View Structure."
If you enlargen the still image of the assumed biological molecule (Ribbons: 500x500) you'll find that alpha helices interact with the DNA. In fact there are no sheets at all in this structure. The DNA strands are in red, while the protein helices are in different colours.
Also, you can click on "Summary Information." At the bottom of that page, click on "Summary of PDB Structure." This is a nice page for you'll get nice images of the complex and all kinds of data.