Challenge I

November 2002

Answers are due December 18th, 2002

Please submit your response to challenge@waksman.rutgers.edu
Include the name of your team, your high school, and the names of each team member.

The Three Dimensional Shape of Thioredoxin

Proteins, the machines of living cells, have complicated three dimensional shapes. But, despite their complexity, all proteins share some common regular features. This challenge offers you the opportunity to closely examine the regular and irregular features of a protein. The protein that you will be looking at is called thioredoxin. In order to participate in the Challenge, you must download the three dimensional coordinates of this protein (the position of each of the atoms in the molecule), and a computer program (RasMol) that reads these coordinates and draws a picture of the protein.

On the Internet, go to http://www.rcsb.org/pdb/
Enter 1ERT into the text box. Press the "Find a Structure" button
A list will appear of several different structures of related proteins. Select the Explore link for the 1ERT structure.
Locate the "Download/Display File" hyperlink on the left of the screen. Click on it.
Go the section of the screen marked "Download the Structure File:". Click on the box marked PDB, Compression "none".
< Save the file.
On the Internet, go to the site http://www.openrasmol.org/
Scroll down the page, and click on "RasMolÜprior test version (RasMol 2.7.2)".
Click on the 2.7.2.1 version of RasMol to download the program that is appropriate for your computer. (8 or 32 bit for Macs, 8 bit for MSWINdows machines) You may also want to download the program1s help file. (raw or gz).
Run RasMol. Load the 1ERT.pdb file.
Display the protein in 4 ways: backbone, ball and stick, space fill, and cartoon.

Level 1

What features of the molecule stand out when you look at each view? What information does each view of the protein offer? What are you looking at when you look at the protein backbone?

Level 2

In the cartoon view, color the helical regions of the protein green and the sheet regions blue. Leave the remainder of the molecule colored gray. Identify the N-terminus and the C-terminus of the protein. Send us a "GIF" image of the cartoon display of the molecule, using the colors indicated above. Label the N-terminus and C-terminus of the protein. Tell us the names of the amino acids that are at the N and C-termini of the protein. Tell us the number of alpha helices and beta sheets in the molecule.

Level 3:

Individual cysteine residues can exist in a reduced form. However if two cysteine residues come close together and are in the proper geometry with respect to each other then they can be oxidized to form a disulfide bond, covalently linking the two residues. These bonds can help stabilize the folded structure of a protein or in some cases the oxidation/reduction of these bonds may be part of the enzymatic activity of the protein.

How many cysteine (Cys) residues are in the protein? (One way to find these is to color the protein in CPK mode, in which sulfur groups are displayed in yellow. Remember there are also sulfur atoms in methione (Met) residues.
Disulfide bonds can form if two Cys residues come close to one another. Using the Picking distance function under the Options menu determine the distances between the sulfur atoms of each Cys residue and the other Cys residues in the protein. Indicate which pairs (if any) you think would be able to form a disulfide bond.
Using a textbook or the WWW, find out what this enzyme does. In one paragraph, explain the importance of the cysteine residues in this protein.

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