2009-2010 UMBC SMART Teams
1. Go to the Protein Databank and download the 3EE9 pdb file of the NS-1 protein of Influenza A.
2. Go to the 3DMD http://cbm.msoe.edu/stupro/smart/resources.html and download RP-RasMol. You will be asked to apply for a password and it may take 24 hours to receive your password. You may use the free version of RasMol to do the initial design, but you will need RP-RasMol to complete your design with monitor lines. Only one copy of RP-Rasmol will be provided to each SMART Team. Everyone on the SMART Team may download the free version of Rasmol. http://cbm.msoe.edu/stupro/smart/resources.html
3. Read the primary citation for the PDB file, as well as the Gack (2009) et. al background paper. After reading this information, complete qualification tasks 2-4.
To help determine what important features you want to include in your molecular story and model, answer the following questions:
- What is the “hook” or “big picture” regarding this protein? Why do we care about this protein?
- What is the function of this protein?
- What are the important features that you want to highlight on your model? This does not need to be specific with respect the precise amino acids, but rather what features are you going to include in your model? For example, are you planning on highlighting the secondary structures? What are the significant amino acids involved in the function of the protein (is there an active site? A binding site?)? Is there a ligand that you wish to display?
- Why is the significance of these selected features? Why are you going to highlight them on your model?
Send answers to Task #2 to Julie by Friday, October 16 th.
For information on SMART Teams at UMBC, or to become a SMART team teacher or research mentor, contact Julie Wolf at 410-455-2146 or jwolf@umbc.edu |
