Hints for Discovery in Protein Explorer Revised Sept. 2004.

These hints are numbered to correspond to the longer list of questions.

Important: if you don't know where to find parts of Protein Explorer mentioned below, look in the Help/Index/Glossary! You get it by clicking the circled green question mark at the top of every control panel (except FirstView, where it is near the bottom). There is also a link on the FrontDoor page, under "About Protein Explorer" (right-most gray column).

  1. In FirstView, how many different colors of chains are visible? In QuickViews, how many chains are listed on the SELECT menu? At FirstView, click on backbone trace for more information.
    Click on an "elbow" of each chain and look at the report in the message window to see if it is made of amino acids or nucleotides.
    1. Optional: Open the PE Site Map, and use the Sequences display to look for chains with identical sequences, and for gaps (rows of dots ...... within a chain). Help linked to the Sequences page gives more information on types of gaps.
      To distinguish DNA from RNA, SELECT Nucleic, and use the link in the middle window.

  2. Disulfide bonds are displayed in FirstView. (To get back to FirstView, open the PE Site Map, from which Reset Session.)

  3. In either Features of the Molecule or QuickViews, press the gray button labeled 2o. (When in QuickViews, read the help in the middle frame after each operation.)

  4. At Features of the Molecule, a section near the bottom of the control panel (scroll down) lists all ligands, including their full names. You can click on each one to locate where it is in the molecular image.
    1. Optional: In QuickViews: SELECT Ligand, DISPLAY Contacts. If there is more than one ligand molecule, use SELECT Clicks (one residue per click) to select just one before doing DISPLAY Contacts.

  5. (Skip unless you are doing the optional questions.) Optional:
    1. For active site information, start at Features of the Molecule. If the authors of your protein model designated sites in the PDB structure data file (header), they will be listed here. Clicking on their names will locate each in the molecular image. If the authors did not include site information in the structure data file, or to find additional sites, use PE's Site Map to go to External Resources. If you find the sequence numbers of residues in a site of interest, use Seq3D (from PE's Site Map) to highlight them in the molecular image. You can also use ConSurf (External Resources, or in QuickViews: SELECT Evolution) to identify surface patches that are highly conserved during evolution. These are often active sites.
    2. With the key residues of the active site displayed (e.g. as ball and stick, with the remainder of the protein in backbone), COLOR by Structure.

  6. SELECT Protein, DISPLAY Spacefill, COLOR Polarity2 (or Polarity3). Use the [Slab] button to view the core.
    1. Use the [Slab] button to restore the entire surface.
    2. For soluble and insoluble reference proteins, at the FrontDoor, under More Quick-Start Molecules, click on Protein Comparator to see hemoglobin and the potassium channel side by side.

  7. SELECT Protein, DISPLAY Spacefill, COLOR Polarity5.
    1. Optional: Pay attention to the middle frame!

  8. (No hints for "interesting, surprising or unusual".)

  9. To find biological functions, first look at PE's Features of the Molecule control panel. As another strategy, see if your molecule happens to be described in a "Protein Documentary" (search the web for the name of your molecule plus "documentary"). If not, do a general web search for your molecule. Or look it up in a biology or biochemistry textbook.
    1. Optional: The primary literature reference may also help with the function. It is available at PE's Features of the Molecule control panel.

  10. Use the link to the PE Site Map (on every control panel in PE) to access External Resources. There, go to Probable Quaternary Structure.

  11. In QuickViews, DISPLAY Evolution, or use the link to the PE Site Map (on every control panel in PE) to access External Resources. There, go to ConSurf.

  12. (Skip unless you are doing the optional questions.)
    1. Optional: At the FrontDoor, click (in the middle gray block) on Find your molecule for a list of sites that search the PDB.
    2. & C. Available in Features of the Molecule.