Exercises
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- An Introduction to Molecular Models
and Computer Visualization of Amino Acids Using Chime
-
- Introduction: The purpose of this exercise is to familiarize
you with some conventions of molecular modeling with both solid
three-dimensional representations and computer visualizations.
For this exercise we will use a simple visualization plug-in
(mini-program) called Chime. Chime is free and available on the
net. If you want your own copy (Mac or PC or etc.) you may download
it from the MDL download page at:
- http://www.mdli.com/chemscape/chime/download.html
- ((If you are on campus the only computers that have Chime
loaded are those in SA 364. Note also that Chime is currently
only on the Mac side.)
-
- For this exercise we will be using molecular models on a
site maintained by Dr. William McClure in the Biology Department
of Carnegie-Mellon University in Pittsburgh. Its address is:
- http://info.bio.cmu.edu/Courses/BiochemMols/AAViewer/AAVFrameset.ham
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- Building Molecular Models: Researchers in chemical
education have found that computer models have little or no meaning
for many students until they have become familiar with physical
models which they have held and manipulated. Thus for this exercise
we will begin with building a few ball and stick models using
standard model kits. Working in pairs, build the following (keep
the models for comparison later):
- Two glycines (one each): H3N+CH2CO2-
Arrange the two models so they are mirror images. Are the two
molecules the same (can they be superposed)?
- Compare your glycine models with the CPK (space-filling)
model provided: arrange the models so they represent the same
conformations and identify each atom in each model type.
- Two alanines (one each): H3N+CHCH3CO2-.
Arrange the two models so they are mirror images (you may have
to interchange two side groups around the central carbon to do
so). Are the two molecules the same (can they be superposed)?
- Compare your alanine models with the CPK model of L-alanine
provided: identify which of your two models corresponds to L-alanine,
the amino acid found in proteins. The other model represents
D-alanine. Why do you think only one is used in proteins (assume
only one t-RNA codes for alanine)?
Computer Models: Go to the amino acid site on the web
(click on the address below). You can open a New Web Browser
by going under the File menu or pressing command N. You
will now have two Netscape windows open, one of which you can
use for these instructions, the other for the models:
http://info.bio.cmu.edu/Courses/BiochemMols/AAViewer/AAVFrameset.ham
When you get to the site you should
see a split window as shown in the figure to the right. Note the
amino acid structure in the right frame of the window, with some
instructions in the left frame. Note that above each frame there
is a box with an amino acid name (the default amino acid is alanine
in the right frame, with a description in the left frame). If
you click and hold on this box for either frame you can slide
down and select the amino acid (aa) of your choice. Begin by selecting
glycine to appear in the right frame. (It may take a moment
to come up, after all its being shipped from Pittsburgh!) It will
rotate a couple of times, then stop. Click and hold down on the
molecule and move the cursor, you should be able to rotate the
molecule randomly around any axis. (Sometimes it takes a bit of
practice; if you hold the mouse button down too long without moving
the mouse a pop-up window will appear.) Now take the ball and
stick model of glycine you constructed earlier and try to manipulate
it so that it looks like the computer image. You will probably
have to adjust its conformation as well as its orientation
in order to get the two models into correspondence.
Now take the model in your hand and flip it vertically. Next
go back to the computer and rotate the glycine to match the model
in your hand. Try flipping both horizontally and vertically, then
match the computer model to it.
Next let's look at the computer representation corresponding
to the CPK model click and hold-down without moving the
mouse go to Display, then Spacefill, then
Van der Waals Radii in the submenus, and release, as in
the figure below:
You should now see an image like that shown below:
Compare this model to your CPK model. Again you may need to
change both the conformation (careful, these models are
more fragile and may fall apart if you rotate bonds to quickly.
You may also have to rotate groups out of the way of each other
as you rotate around another bond) and orientation of your
CPK model to match it to the computer image. Flip the model in
your hand around and then match the computer model to it.
Now pick up your L-alanine models and select alanine as the
amino acid in the left frame on the computer. Compare these physical
and computer models for alanine as you did for glycine. Then manipulate
the images of the two amino acids to compare features.
You can explore some other aspects of these amino acids by
clicking on the "X" boxes below the images (the images
will revert to stick models). Finally, you should tryout some
of the other visualization options such as Wireframe and
Ball & Stick under the Display submenu. There
are also a couple of nice displays under the Options submenu.
If you know how to "cross" your eyes for 3-D displays
(topo maps etc) there is a Stereo Display option which
will show two images to give a stereo view, either with your eyes
properly skewed or with a viewer.
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- Last modified 22 August 2001
- © R. Paselk 1999
Laboratory
