One way to get a handle on the multitude of protein structures out there is to arrange or classify them according to the pattern that their polypeptides use to fold and form a tertiary structure. There are several databases available, which classify the domains that a protein contains according to the limited number of folding patterns. These include SCOP (Structural Classification of Proteins) and CATH (Class, Architecture, Topology and Homologous Superfamily). The Protein Data Bank also lets your search for proteins that share similar folds.

Assignment

• Using Jmol, create a website that illustrates the following folds:
  • Four helix bundle (all alpha helix)
  • Antiparallel beta barrel (all beta)
  • Parallel beta barrel (alpha/beta)
• The website should contain four pages, a home page and one page for each of the folds
• Pick two examples of each fold that are contained in proteins with different functions.
  • Use Jmol to display your two examples of each fold. You should limit what is displayed to just the domain that has the described fold.
  • Include in your illustrations any ligands that may be associated with these domains.
• On your website, briefly describe the recognizable features of each fold and the functions for each of your examples.
• Place your site on your username_www share in a folder named Lab10.
• When you are finished, send me an email with the URL for your site.