Hoelzer Sandbox: Difference between revisions

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Mark Hoelzer, Tim Herman

Revision as of 18:20, 21 January 2009 view source Tim Herman (talk \| contribs) 59 edits No edit summary ← Older edit		Revision as of 18:21, 21 January 2009 view source Tim Herman (talk \| contribs) 59 edits No edit summary Newer edit →
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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.