Hoelzer Sandbox: Difference between revisions

We started our physical model of the β2-adrenergic receptor by opening the pdb file 2rh1.pdb in the protein viewing software Rasmol.  We started by opening our pdb file in Rasmol as a spacefill model  <scene name='Hoelzer_Sandbox/Building_our_model/8'>(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.