Hoelzer Sandbox: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Mark Hoelzer, Tim Herman

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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.
-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 amino acids 29-230 and 263-342.  Starting with a cpk-colored, spacefilled representation <scene name='Hoelzer_Sandbox/Spacefilled/1'>TextToBeDisplayed</scene> of the protein, we simplified this image by converting it to an alpha-carbon backbone representation.  We colored the seven trans-membrane alpha helices green --- connected by loops that we colored gray.  We then displayed four sidechains (Phe 193, Trp 286, Phe 289, and Phe 290)  involved in the binding of a beta-blocker, and colored them blue.  The beta-blocker, Carazolol, was then added in a ball-and-stick format, colored orange.  The three cholesterol molecules 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, the N-terminal end of the protein was colored blue, and the C-terminal end was colored magenta.
+To design our model of the β2-adrenergic receptor, we used the atomic coordinates for this structure as reported in the <scene name='Hoelzer_Sandbox/Spacefilled/1'>pdb file 2rh1</scene>, from the Ray Stevens laboratory at the Scripps Research Institute.  Our model represents <scene name='Hoelzer_Sandbox/Spacefilled_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/Spacefilled_3/1'>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_4/2'>(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, Carazolol, was then added in a ball-and-stick format, colored orange.  The three cholesterol molecules 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, the N-terminal end of the protein was colored blue, and the C-terminal end 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.