Discussion:
Human Homeodomain
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 bondbetween 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.