Hoelzer Sandbox: Difference between revisions

=<font color = 'red'>Madison West High School</font> SMART Team Molecular Story<font color = 'red'> of β2-Adrenergic Receptor</font>=

[[Image:Madison_West_SMART_Team.jpg|left|Madison West SMART Team|630 px]]

<applet load='2rh1.pdb' size='400' frame='true' align='left' caption='Madison West SMART Team Model - β2-Adrenergic Receptor' scene='Hoelzer_Sandbox/Building_our_model/1'/>

 

We started our physical model of the β2-adrenergic receptor by opening the pdb file 2rh1.pdb in the protein viewing software Rasmol.  The default format for a newly opened .pdb file in Rasmol is a thin wireframe <scene name='Hoelzer_Sandbox/Building_our_model/1'>(STEP ONE)</scene>.  Our SMART Team wanted to focus on the binding portion of the receptor so we only displayed residues 29-230 and 263-342 in backbone format <scene name='Hoelzer_Sandbox/Building_our_model/2'>(STEP TWO)</scene>.  Next, we colored the alpha helices green, the turns gray, the first amino acid on the N-terminal end blue, and the last amino acid on the C-terminal end magenta. <scene name='Hoelzer_Sandbox/Building_our_model/3'>(STEP THREE)</scene>.  Then we added the cholesterol ligands located on the side of the seven helix portion of the protein.  We displayed them in ball and stick format and colored them red <scene name='Hoelzer_Sandbox/Building_our_model/4'>(STEP FOUR)</scene>.  One of the most important portions of our model is the beta blocker Carazolol which we displayed in ball and stick format and colored orange <scene name='Hoelzer_Sandbox/Building_our_model/5'>(STEP FIVE)</scene>.  The last step was adding the main sidechains involved in the binding of the beta blocker.  We displayed Phe 193, Trp 286, Phe 289, and Phe 290 in ball and stick format and colored them cyan <scene name='Hoelzer_Sandbox/Building_our_model/6'>(STEP SIX)</scene>.  Once our model designs were complete in Rasmol, we added monitor lines to help support the model for building and saved the 3D file for printing <scene name='Hoelzer_Sandbox/Building_our_model/7'>(STEP SEVEN)</scene>.  Our model was built by the Center for BioMolecular Modeling at the Milwaukee School of Engineering where they are able to use rapid prototyping technology to build any model designed in the computer environment.   

 

This Proteopedia page was created with help from the Milwaukee School of Engineering's Center for BioMolecular Modeling (CBM).  SMART (<font color = 'red'>S</font>tudents <font color = 'red'>M</font>odeling <font color = 'red'>A</font> <font color = 'red'>R</font>esearch <font color = 'red'>T</font>opic) Teams are a multi-faceted program where high school students explore protein structure and science as a process and not just a collection of facts.  Students work closely with a researcher to understand and model the structure-function relationship of a protein the researcher studies.  After designing and building a model of the protein using Rapid Prototyping technology, SMART teams create an oral presentation explaining their work to a lay audience and a poster which is presented to a scientific audience. To learn more about SMART Teams or the Center for BioMolecular Modeling, visit their website at [http://www.rpc.msoe.edu/cbm/cbm http://www.rpc.msoe.edu/cbm/].