Problem Set #6: Proteins on the Web

Due October 28th at the beginning of class


So far we have used several tools on the web for exploring protein structure.  This week I would like you to synthesize what we have done before to compare two enzymes, triosephosphate isomerase and dihydroorotate dehydrogenase.  These enzymes are some similarities but have differerent functions.  Examine these proteins using the resources we have used in the first four problem sets to determine how they are similar and different.  In particular, begin thinking about how the structure relates to function: these are enzymes!


Some ways you might explore these proteins might be to

  1. use the PDB to find their structures (human triosephosphate isomerase is 1hti.pdb; human dihydroorotase is 1d3g.pdb).  Look at the headers and the pictures to find out some basic information and see if they have overall similar structures.
  2. Download the files and use Rasmol or SwissPDB Viewer to look at the structures.  What kind of shape do these proteins have, and how are they similar and different? 
  3. Try to draw a topology diagram.  Based on the overall shape and fold, do you see any reason to believe that these proteins may be related?
  4. Look at their active sites.  Both of these proteins are enzymes, which means that they catalyze chemical reactions.  Where are the active sites, what cofactors or side chains are involved in the catalysis, do their substrates have any similarities in size, structure, etc.? 
  5. How related are triosephosphate isomerase and dihydroorotase?  Use SCOP or CATH to determine whether these proteins belong in the same class, family, or whatever.  Do you think they may have evolved from a common ancestor or not? 
  6. Try to overlay the two sequences and/or structures to accentuate their similarities and differences.  You may have to play around with this for a while, because their sequence similarity is low enough that most computer programs have a hard time finding the similar parts.  Places you might try this: the fitting programs in SwissPDB Viewer (copies of the manual are available); the sequence overlaying functions in the NIH-Genebank site “Entrez” (you will have to look up the sequences first; it will help you to know that human dihydroorotase is part of a larger enzyme complex called CAD); the protein comparison web site DALI (; other sites on the internet.
  7. Use the NIH-Genebank website “Entrez” and/or ISI Web of Science to find out more about these proteins, their functions, and their nearest structural/evolutionary neighbors.


Once you have compiled a bunch of information about these proteins, I would like you to synthesize the information into a concise but informative presentation.  An abstract (~1 typed page) plus several figures with figure legends should suffice to get across the major points.  Some hand-drawn figures are fine.