Pre-lab assignment 1


Name:                                                                                                                                                     Score:                     /5


In the course materials folder on the server is a folder called "University of Illinois" in there are materials related to a powerful molecular modeling program called Virtual Molecular Dynamics (VMD).


Using a PC, work through section 1 of the tutorial (vmd-tutorial.pdf in the vmd-tutorial-files folder) using the protein ubiquitin (1UBQ.pdb) as an example.  Please answer the following questions:



1)      Is ubiquitin a globular or fibrous protein?




2)      Identify how many helices, beta sheets and random sequences are present in ubiquitin




3)      Using the structure, determine if the very C-terminal residues acidic, basic, polar or non-polar?



4)      Save the image you created in section 1.6 of the tutorial to the “Drop box” folder on the server.  Be sure to use your name or initials in the filename to insure credit.




5)      There are two proline residues adjacent in the sequence.  What are their numbers?  What secondary structure are they involved in? What is their impact on the tertiary structure?




Notebook assignment:                          /5


Complete your notes on the reaction mechanism, make sure this is a useful tool for the remainder of the semester.


Obtain a copy of J. Mol. Biol. (1996), 262, 202-224.  Write a brief description of what the authors were trying to communicate in Figure 8.