UTF-8Van Der Waals: Antibody - Antigen Specificity240228207
Antibody view:
Antigen view:
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<font face="Verdana, Arial, Helvetica, sans-serif" size="5" color="#FFFFFF"><strong>Van Der Waals Attractions:</strong> Your Immune System</font>
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<font face="Verdana, Arial, Helvetica, sans-serif" size="4">Your immune
system works by making molecules called <strong>antibodies</strong> that
stick to other "bad" molecules in your system. These bad molecules are
called <strong>antigens</strong> and might be a toxin produced by a
microbe or a molecule on the surface of a bacteria or virus. Van der Waals
attractions are the binding force used to link antibody with antigen. </font>
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<strong><font size="5" face="Verdana, Arial, Helvetica, sans-serif" color="#A86938">3D
Exploration of Bound Antibody & Antigen</font></strong>
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<font face="Verdana, Arial, Helvetica, sans-serif" size="4">To the left,
part of an antibody (green) is shown bound to an antigen (white). As you
learned earlier, how well two molecules stick to each other can be related
to how well the shapes of the molecules fit together.</font><br>
<ul>
<li>
<font face="Verdana, Arial, Helvetica, sans-serif" size="4">Use the
controls below the model to explore how well the antibody and antigen
fit together.</font>
</li>
<li>
<font face="Verdana, Arial, Helvetica, sans-serif" size="4">Then <strong>take
a snapshot which shows the excellent fit between antibody and anitgen</strong>.</font>
</li>
<li>
<font face="Verdana, Arial, Helvetica, sans-serif" size="4">In
addition to the controls below you can drag or shift-drag the molecule
to change the view. </font>
</li>
</ul>
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<strong><font size="5" face="Verdana, Arial, Helvetica, sans-serif" color="#A86938">Design
Your Own Antibody</font></strong>
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<font face="Verdana, Arial, Helvetica, sans-serif" size="4">The attraction
between antibody and antigen often utilizes both types of van der Waals
attraction: dipole-dipole and London dispersion.<strong> Your job is to
design an antibody</strong> that will form the strongest attraction to the
antigen below. To do this you will <strong>select the shape of the
antibody, add charge, dock the antigen to your antibody, and then take a
snapshot</strong> of your work. </font>
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<strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Design
Your Antibody</font> </strong>
</div>
<p>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">- <strong>Select
a the initial molecule shape</strong> for the antibody by clicking on
one of these images:</font>
</p>
<p align="center">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><img usemap="#Map" width="240" src="antibodyChoice.gif" height="147" border="0">
</font>
</p>
<p>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">- <strong>Add
charge</strong> to the antibody by using the charge tools <img width="15" src="addPositiveCharge.gif" height="15">
and <img width="15" src="addNegativeCharge.gif" height="15"> in the
toolbar. To charge part of the antibody, select the appropriate charge
tool and then click on the atoms you want to charge.<br>- <strong>Run
the model, click on the green star, and "dock" the antigen to your
antibody</strong>.<br>- <strong>Take a snapshot</strong> of your best
creation. </font>
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<font face="Verdana, Arial, Helvetica, sans-serif" size="4">Take a
snapshot of your best antibody. If you have time, try using another
shape. What would be the second best design for an antibody that
will attract strongly to the antigen?</font>
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