Hoelzer Sandbox: Difference between revisions

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Virtually any image of a protein that can be created in the computer environment of RP-RasMol, can be converted into a physical model of the protein using rapid prototyping technology.   
  Virtually any image of a protein that can be created in the computer environment of RP-RasMol, can be converted into a physical model of the protein using rapid prototyping technology.   


To design our model of the β2-adrenergic receptor, we used the atomic coordinates for this structure as reported in the pdb file 2rh1, from the Ray Stevens laboratory at the Scripps Research Institute.  Our model represents <scene name='Hoelzer_Sandbox/Image_1/1'>amino acids 29-230 and 263-342 </scene>.  Starting with a cpk-colored, spacefilled representation of the protein, we simplified this image by converting it to an <scene name='Hoelzer_Sandbox/Image_2/1'>alpha-carbon backbone representation</scene>.  We colored the seven trans-membrane alpha helices green --- connected by loops that we colored gray.  We then displayed four sidechains <scene name='Hoelzer_Sandbox/Spacefilled_4/7'>(Phe 193, Trp 286, Phe 289, and Phe 290)</scene> involved in the binding of a beta-blocker, and colored them blue.  The beta-blocker, <scene name='Hoelzer_Sandbox/Spacefilled_4/6'>Carazolol</scene>, was then added in a ball-and-stick format, colored orange.  The <scene name='Hoelzer_Sandbox/Spacefilled_4/8'>three cholesterol molecules </scene> resolved in this structure, bound to the outside surface of the protein, were added and displayed in a ball-and-stick format, colored red.  Finally, <scene name='Hoelzer_Sandbox/Spacefilled_4/9'>the N-terminal end </scene>of the protein was colored blue, and <scene name='Hoelzer_Sandbox/Spacefilled_4/10'>the C-terminal end </scene>was colored magenta.
To design our model of the β2-adrenergic receptor, we used the atomic coordinates for this structure as reported in the pdb file 2rh1, from the Ray Stevens laboratory at the Scripps Research Institute.  Our model represents <scene name='Hoelzer_Sandbox/Image_1/1'>amino acids 29-230 and 263-342 </scene>.  Starting with a cpk-colored, spacefilled representation of the protein, we simplified this image by converting it to an <scene name='Hoelzer_Sandbox/Image_2/1'>alpha-carbon backbone representation</scene>.  We colored the seven trans-membrane alpha helices green --- connected by loops that we colored gray.  We then displayed four sidechains <scene name='Hoelzer_Sandbox/Spacefilled_4/7'>(Phe 193, Trp 286, Phe 289, and Phe 290)</scene> involved in the binding of a beta-blocker, and colored them blue.  The beta-blocker, <scene name='Hoelzer_Sandbox/Spacefilled_4/6'>Carazolol</scene>, was then added in a ball-and-stick format, colored orange.  The <scene name='Hoelzer_Sandbox/Spacefilled_4/8'>three cholesterol molecules </scene> resolved in this structure, bound to the outside surface of the protein, were added and displayed in a ball-and-stick format, colored red.  Finally, <scene name='Hoelzer_Sandbox/Spacefilled_4/9'>the N-terminal end </scene>of the protein was colored blue, and <scene name='Hoelzer_Sandbox/Spacefilled_4/10'>the C-terminal end </scene>was colored magenta.


A ply file describing this final structure was exported from RP-RasMol and sent to the MSOE Center for BioMolecular Modeling, where it was constructed from plaster powder, using a color ZCorp 3D printer.   
A ply file describing this final structure was exported from RP-RasMol and sent to the MSOE Center for BioMolecular Modeling, where it was constructed from plaster powder, using a color ZCorp 3D printer.   
We started our physical model of the β2-adrenergic receptor by opening the pdb file [[2rh1|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. 


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