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Protein Conservation 5
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Protein Folding in 3D
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<font face="verdana, arial, helvetica, sans-serif" size="5">So far we've
looked at folding using 2D models, which can help with understanding
proteins, but that doesn't let us see what a folded protein really looks
like. To see this, we can use 3D models that show real proteins, and
change the display to see different aspects of the protein.</font>
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<font face="Verdana, Arial, Helvetica, sans-serif" color="rgb(051, 051, 051)" size="5"><strong>Folds
in Real Proteins</strong></font>
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<center>
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<table cellpadding="10" width="280">
<tr>
<td>
<font face="verdana, arial, helvetica, sans-serif" size="4"><b>3D
Protein Folds</b><br>This model shows a real protein's folded
shape.<br><br><b>Use the controls below to explore the different
displays of this protein and answer the questions below.</b></font>
</td>
</tr>
</table>
<table border="1" width="280">
<tr>
<td>
<center>
<table border="0" width="100%">
<tr>
<td colspan="2">
<font face="verdana, arial, sans-serif" size="3"><b>Display
style:</b></font>
</td>
</tr>
<tr>
<td width="35%" valign="top">
<font face="verdana, arial, sans-serif" size="3"><input value="radio" type="radio" script="script:jmol:1:select all; cpk off; wireframe off; trace off; cartoon on; backbone off;" name="RadioGroup2" checked="checked">
cartoon<br><input value="radio" type="radio" script="script:jmol:1:select all; cpk 25%; wireframe 0.3;trace off; cartoon off; backbone off;" name="RadioGroup2">ball
& stick<br><input value="radio" type="radio" script="script:jmol:1:select all; cpk; trace off; backbone off; cartoon off;" name="RadioGroup2">spacefill
</font>
</td>
<td valign="top">
<font face="verdana, arial, sans-serif" size="3"><input value="radio" type="radio" script="script:jmol:1:select all; cpk off; wireframe off; trace off; cartoon off; backbone 0.25;" name="RadioGroup2">
backbone<br><input value="radio" type="radio" script="script:jmol:1:select all; cpk off; wireframe off; backbone off; cartoon off; trace 0.25;" name="RadioGroup2">smooth
backbone<br></font>
</td>
</tr>
<tr>
<td colspan="2">
<hr>
<b><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Color:</font></b>
</td>
</tr>
<tr>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input value="radio" type="radio" script="script:jmol:1:select all; color monomer" name="RadioGroup3" checked="checked">
rainbow<br><input value="radio" type="radio" script="script:jmol:1:select all; color cpk" name="RadioGroup3">element
</font>
</td>
<td>
<input value="radio" type="radio" script="script:jmol:1:select all; color structure" name="RadioGroup3">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">structure<br></font><input value="radio" type="radio" script="script:jmol:1:select polar; color magenta; select not polar; color [x999999]" name="RadioGroup3"><font face="Verdana, Arial, Helvetica, sans-serif" color="#cc00cc" size="3">polar</font><font face="Verdana, Arial, Helvetica, sans-serif" size="3">/</font><font face="Verdana, Arial, Helvetica, sans-serif" color="#333333" size="3">non-polar</font>
</td>
</tr>
</table>
</center>
</td>
</tr>
</table>
</center>
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<font face="verdana, arial, helvetica, sans-serif" size="4"><b>Take
snapshots and use the text annotation button <img src="textannotation.gif">
to show the anwers to the following questions: </b></font>
<ol>
<li>
<font face="verdana, arial, helvetica, sans-serif" size="4">Which
display style do you think shows the folding of the protein best? </font>
</li>
<li>
<font face="verdana, arial, helvetica, sans-serif" size="4">Find a
part of the protein that folds into a spiral or helix type of shape. </font>
</li>
<li>
<font face="verdana, arial, helvetica, sans-serif" size="4">Find a
region of the protein that has folded into four flat strips that run
parallel to each other. </font>
</li>
<li>
<font face="verdana, arial, helvetica, sans-serif" size="4">Which
combination of display styles and colors is good for seeing the
overall shape of the protein?</font>
</li>
</ol>
</body>
</html>
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