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.

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.

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.

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[[Image:Smart Teams photo 5.jpg|right|120px]]

~~This Proteopedia page was created with help from the Milwaukee School of Engineering's Center for BioMolecular Modeling (CBM).~~ SMART (Students Modeling A Research Topic) ~~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 see other SMART Team Projects or to learn~~ more about ~~SMART Teams~~, visit the ~~[[SMART Teams|SMART Teams Proteopedia Page home page~~.]]

SMART Teams (Students Modeling A Research Topic)is a science outreach program developed by the MSOE Center for BioMolecular Modeling. In this program, teams of high school students work with a local resarch lab to design and build a physical model of a protein that is being investigated by the lab. The goal of the SMART Team program is to introduce students to the real world of scince --- as it exists in a local research lab. This developement of this program was supported by grants from the NIH-NCRR SEPA program (Science Education Partnership Award) and an HHMI Precollege Science Education Award. For more information about this program, visit the CBM web site at www.rpc.msoe.edu/cbm.

Hoelzer Sandbox: Difference between revisions

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@@ Line 19: / Line 19: @@
 <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/8'/>
+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.
+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.
@@ Line 41: / Line 50: @@
 [[Image:Smart Teams photo 5.jpg|right|120px]]
-This Proteopedia page was created with help from the Milwaukee School of Engineering's Center for BioMolecular Modeling (CBM).  <font color = 'red'>SMART (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 see other SMART Team Projects or to learn more about SMART Teams, visit the [[SMART Teams|SMART Teams Proteopedia Page home page.]]
+<font color = 'red'>SMART  Teams (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)is a science outreach program developed by the MSOE Center for BioMolecular Modeling.  In this program, teams of high school students work with a local resarch lab to design and build a physical model of a protein that is being investigated by the lab.  The goal of the SMART Team program is to introduce students to the real world of scince --- as it exists in a local research lab.  This developement of this program was supported by grants from the NIH-NCRR SEPA program (Science Education Partnership Award) and an HHMI Precollege Science Education Award.  For more information about this program, visit the CBM web site at www.rpc.msoe.edu/cbm.