protein structure for high schoolers

From: James Whittle
Date: 20 January 2012 21:41

Hi-

I am trying to help my former chemistry teacher set up a demonstration of protein structure for her class. I'd like to include electron density maps, and maybe show an enzyme active site. Are there suggestions from the BB on the easiest way to do this? Would pymol be the program of choice, or is there a simpler program that could show electron density? Has anyone already created such a demonstration they could and have advice on it?

James

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From: Boaz Shaanan

Hi,

I think that spdbv (deepview) and the tutorial has some of what you need. The program is very simple to implement on any Mac or PC, although it's not the nicest program to use in the long run. It'll take you 5 minutes to install and test the features you'd like from the tutorial.

  Cheers,

               Boaz

 

 

Boaz Shaanan, Ph.D.  

 

                

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From: Yoder, Marilyn

Hi,

 

I've given a couple talks/demos to HS students.  As much as I love enzymes, I found it more effective to show structures of proteins binding to other biological molecules (not just other proteins).  I typically show phosphatidylinositol binding protein (PITP) bound to phosphatidylcholine, simply because that is a structure I solved and am comfortable with.  I think DNA binding proteins would also be effective.  p53 might be a good candidate, especially because of its association with cancer – that will get their attention.

 

I used pymol, it was easy to install on the teachers computer, then they could easily use it after I left. 

 

Regards,

Marilyn

 

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From: Andrew Orry

James,

I would like to recommend the free ICM-Browser http://www.molsoft.com/icm_browser.html . It is widely used for teaching structural biology and it is easy to make fun and interesting fully interactive 3D slides and animations of protein structures.

The students can view the fully interactive 3D files in the browser, PowerPoint or on the web using ActiveICM http://www.molsoft.com/activeicm.html  The files can also be viewed on the  iPad/iPhone using iMolview http://www.molsoft.com/iMolview.html

We will be happy to send you some examples if you would like them.

Thanks,
Andy

--  Andrew Orry Ph.D.

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From: Sabuj Pattanayek

foldit doesn't do electron densities and I don't recall if there are
any puzzles in it that mention active sites/docking (it's been more
than a year since I "played" it), but it's worth a mention.

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From: Nadir T. Mrabet

I would suggest MolProbity along with KiNG (on Firefox!) would be most appropriate (http://kinemage.biochem.duke.edu/).

HTH,

Nadir

Pr. Nadir T. Mrabet

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From: Joel Sussman

6-Feb-2012

Dear Marilyn

Have you looked at Proteopedia [www.proteopedia.org], see e.g.

http://proteopedia.org/w/DNA

http://proteopedia.org/w/Forms_of_DNA

http://www.proteopedia.org/w/HIV-1_protease

http://www.proteopedia.org/w/Proton_Channels

and many more.

n.b. How the green links cause the 3D Jmol images to change so as to reflect what the test says.

Pls let me know what you think of these pages.

best regards,

Joel