Exercises
WWW Visualization of Protein Structure Using Chime
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- For this exercise we are going to use a site maintained by
Do. William McClure in the Biology Department of Carnegie-Mellon
University in Pittsburgh. Its address is:
- http://info.bio.cmu.edu/Courses/BiochemMols/ProtG/ProtGMain.htm
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- If you need to review the use of these visualizations go
back to our amino
acid exercises. If you'd like to check what you learned earlier,
you might want to do their amino
acids quiz. I found it interesting and informative.
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Protein G B1 Domain
- For today's exercises we will start by looking at the structure
of a particular protein, Protein G, B1 Domain at the CMU site.
(Another interesting protein structure site is Sears' at UCSB,
check out your lecture notes for the addresses.)
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Secondary Structure: Let's
start with the a-helix. Click
here to get to the site. Note the overall structure of the
rotating image of Protein G. The coils represent a-helixes,
while the ribbon-arrows represent beta strands (tail >
point = N-terminal > C-terminal).
- Look at the a-helix by clicking
on the highlighted a-Helix
in the upper frame. This will take you to an image of the a-helix. The visualization tools we saw
earlier with the amino
acid exercises still work here. Stop the rotation and look
at the helix from different angles. Read about the a-helix
in the right panel and try the different toggles. Make sure you
look at wire-frame and space-filling models as well. Check out
the hydrogen bonding using Display Hydrogen Bonds in the
Options submenu.
- Next, click on the highlighted first b-Hairpin
in the upper frame. Note the two anti-parallel b-strands.
Make sure you look at the wire-frame and space-filling models
as well. Again, remember, in our discussion the b-strand
is the secondary structural element.
- What is a hairpin? How is it characterized?
- How would you classify the hairpin in our terms of hierarchical
structure?
- Go on to the second b-hairpin.
What's different?
- When your finished looking at the hairpins click on the Type
1 turns. What relationship do they have to the beta-hairpins?
- Supersecondary structure: Next go to the b-sheet
using the highlighted b-Sheet
in the upper frame, or the b-Sheet
button. Again look at the hydrogen bond pattern as you did for
the a-helix. Stop the rotation, then
click on the buttons to color the hydrophobic and the hydrophilic
side chains.
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- Domain structure: Now look at how the elements go
together to build the protein. Look at the packing of this protein
by clicking appropriately in the upper panel. Does this domain
constitute the protein's tertiary structure? Why or why not?
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- At this point you might like to try their protein
structure quiz, based on Protein G. If you want some more
experience with protein structures, you might look at the examples
below first, and then return to the quiz. The quiz is a challenging
exercise. Expect to make mistakes, sometimes due to the ambiguity
of the questions, but it should prove a good learning experience.
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Other Protein Examples
- Cytochrome
Oxidase - alpha helical structures
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- HIV
Reverse Transcriptase - alpha helix and beta sheets, quaternary
structure of a dimer.
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- Aspartate
Receptor - four alpha helix motif membrane spanning protein
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- Nitrogenase
- complex metaloenzyme, mostly alpha helixes.
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- Green
Fluorescent Protein - cool beta barrel: beta meander type
(beta strands connected by relatively tight loops), very little
alpha helix. Try viewing Display set to Cartoon
for a familiar style of viewing.
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- Proteins
- Click on the Lessons button then Proteins to get to
the list of four structures below: (Note, on these pages, if
you click on any of the buttons with X's you may get message
boxes "JavaScript error...." Just click on the OK boxes
and all will be well.)
- BPTI (bovine pancreatic trypsin inhibitor),
- Hemoglobin: an opportunity to look more carefully at this
protein which we have studied.
- Plastocyanine: a nice beta barrel: beta meander type (beta
strands connected by relatively tight loops).
- Alcohol dehydrogenase: Note the two domains with different
motifs. One has a nice beta sheet with alpha helixes on both
sides, the other has a beta sheet with a few alpha helixes. Which
would be called beta-alpha-beta (super secondary or motif structure)?
Why?
- Molecular
Dynamics - Click on the Lessons button, then Peptides,
then click on Molecular dynamics to study this animated
image. Note that you can view this animation with different representations
just as you can for still forms.
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- Last modified 22 August 2001
- © R. Paselk 1999
Laboratory
