Biomolecular Structure   Chem 791B - Assignment #1 (Due 2/12)

• This class assignment can be carried out either in the CRC (where everything is installed) or can be done at your home or lab (in which case you will need to download the appropriate software - see below).
  • In your browser go to the SwissPDBViewer tutorial.
  • With that running, launch the SwissPDBViewer program and follow the instructions in the tutorial. Work through the following sections, going back and forth between the tutorial and the program:
    1. Getting Started
    2. Windows and Help
    3. Manipulating the Model
    4. Selecting and Displaying
    5. Coloring
    6. Measuring and Labeling
    7. Mutating and Changing Side-Chain Conformations (OPTIONAL)
    8. Using a Ramachandran Plot
    9. Judging the Quality of Models - check out the electron density map demo!
• This ought to take 1-2 hours, so give yourself a solid block of time on which to work through this.

• As a second project, go to the Protein Database and try to find a protein as follows. Download it, check it out in SwissPDBViewer, and verify that it has the structural element indicated. EMail the name of the protein and its PDB code to me before Thursday. You can use the text to help you find such a protein, but I'd prefer that you come up with a different one from the classics in the text. Hint: look up one from the text and then use the "Search for structural neighbors" link on the newer PDB site.
• For extra credit, find a motif that I have not listed below...
• Clarification: Each person should come up with his or her own example of the motif associated with his or her name. Working in groups is encouraged (and groups can be cross-motif), but in the end everyone should know how to find and download structures. You will be doing more of this soon.
  • Four helix bundle: Irina Alimov, Vivek Prabhu, Renuka Sivendran
  • Up-down beta barrel: Carlotta Cancelliere, Binu James
  • Greek Key: Jesse Charette, Hordur Kristinsson
  • Beta strand propellor: Shujun Chen, Catherine McIntosh
  • Coiled-coil: Robert Yi-Te Chou, Anton Manuilov
  • Jelly roll: Edward A Esposito, Rebecca Whitfield
  • Beta helix: Greg Gallagher, Charu Taneja
  • Beta-alpha-beta barrel: George DeBusk, James MacGregor Smith
  • Beta-alpha-beta non-barrel: Jenny Habink, Matthias Ober