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Home  >  Problems  >  Chapter 10

  1. Download the Rasmol program from the Rasmol home Web site. (Note that the browser can be set up to start Rasmol automatically when a pdb mime-type is received.)
  2. Follow the instructions below in Problem 4 to view representatives of the major protein structural classes.
  3. Choose one or two representatives for downloading from each site visited for viewing by Rasmol.
  4. Submit a list of the major classes that you encountered, including the name of a protein in each class.

  1. Go to the SCOP Web site, also reachable by a Web search.
  2. Go to the top of the structural hierarchy and note the links to a more detailed classification of the protein structural classes. The first icon of the three shown for each class will be an image model that can be viewed by the browser.
  3. Follow the hierarchy to lower and lower levels, eventually reaching a link to a Protein Data Bank (PDB) entry. PDB files are large tables that give atomic coordinates of atoms in proteins and other information and may be downloaded and viewed as described below.
  4. There are a number of display programs for viewing PDB files. We will use Rasmol. Choose two PDB files for downloading and viewing by Rasmol. (Note that the PDB identification code is a combination of numbers and letters, e.g., 1gc1.)

  1. Go to PDB (the protein structure databank) at Rutgers University and retrieve two PDB files of interest to your research.

  1. Start Rasmol and open the pdb file. Rasmol presents a number of drop-down windows for varying the views. Behind this window is a command window where commands may be typed (see point 2, below, for commands).
    1. Rotating molecule: Move mouse.
    2. Moving molecule across screen: Move mouse while holding down command or option key.
    3. Display options: Use the various display options (especially wireframe, ribbons, and cartoon) to see the effects.
    4. Colors: Try various options (especially group options).
    5. Stereo: Eyes either have to look straight ahead or else be crossed so that each eye is viewing a different image. The image in the middle will be stereo. Visual devices may be available.
    6. Labels: Label amino acids. The view will need to be zoomed to see the labels (see command window, below). Another way of identfying the amino acid is to click on the molecule; the atom or amino acid will be identified in the command window.
  2. Rasmol command window:
    1. Choose command on the drop-down window.
    2. Type "help commands" to view all available commands.
    3. To zoom the molecule, type "zoom" followed by a number. Zoom 100 is the standard view; a zoom less than 100 is smaller and a view larger than 100 is bigger. Zoom 500 will allow one to view the individual amino acids.

  1. Find the nearest Pfam Web site and become familiar with the top 20 protein families. Pfam is a database of conserved protein domains in a large number of related protein families.
  2. Click the "browse Pfam" link to view the protein families in the database. There are links to SCOP, the structural classification pages.
  3. Follow these links and examine the structure of one or two proteins using the image display option.
  4. You can also obtain the PDB file and use Rasmol to display the molecule, as described in the previous problem.

  1. Find the INTERPRO database.
  2. Search for domains in the yeast SNF2 transcription factor, Swiss-prot P22082.

In addition to Pfam, there are a number of other Web sites that may be used to search a query protein sequence for domains that represent a protein family, including INTERPRO and the BLAST server at NCBI (rpsblast and cdart), which search several of these domain databases at the same time.

  1. Retrieve a protein sequence of your choice that was listed in the SCOP structural hierarchy and obtain the sequence from the sequence link.
  2. Paste the sequence into the sequence entry window on the 3DPSSM server. This server searches a sequence (no more than 800 amino acids at a time) using a set of position-specific scoring matrices that are based on alignments of proteins that have the same structural fold and a similar sequence. A match to one of these matrices thus identifies a potential three-dimensional structure. The results are sent back by E-mail or to a designated Web site.
  3. How does the prediction compare roughly to the SCOP structure?


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