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Protein Conservation 6
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Amino Acid Similarity in 3D
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<font face="verdana, arial, helvetica, sans-serif" size="5">An amino acid
substitution can cause a peptide to fold differently, or not, depending on
how similar the new amino acid is to the original. When the substitution
of an amino acid is similar to the original, the change is called <b>conservative</b>.
If the amino acid is quite different, it is called a <b>non-conservative</b>
substitution.<!--A
non-conservative substitution it is more likely to lead to a change in
protein structure and function than a conservative change.-->
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<font face="Verdana, Arial, Helvetica, sans-serif" color="rgb(051, 051, 051)" size="5"><strong>Conservative
Substitutions</strong></font>
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<font face="verdana,arial,sans-serif" size="4"><b>Can you pick the most
conservative substitution in 3D?</b> Click and drag each amino acid to
rotate it in 3D. Compare the Reference amino acid to the three below it.
From them, pick the one that is the most conservative (similar)
substitution for the Reference amino acid. Take a snapshot and use the
annotation button <img src="textannotation.gif"> to explain why it would
be a conservative substitution.<br><br><b>Click and drag on the amino
acids to rotate them; </b></font><b><font face="verdana, arial, helvetica, sans-serif" size="3">SHIFT</font><font face="verdana, arial, helvetica, sans-serif" size="4">-drag
to zoom in and out. </font></b>
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Hint
Comparing the amino acids will be easier
if you first rotate them so their main chains
are all oriented in the same way.
Hint
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Take a snapshot of AA #1
Take a snapshot of AA #1
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Take a snapshot
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Take a snapshot of AA#2
Take a snapshot of AA#2
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Take a snapshot
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Take a snapshot of AA#3
Take a snapshot of AA#3
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Take a snapshot
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<p>
<font face="verdana, arial, helvetica, sans-serif" size="4"><strong>Challenge
set. </strong>The button below will load a new set of amino acids into
the models above. This time, choose a <b>non-conservative</b>
substitution for the reference amino acid, take a snapshot, and annotate
to show your reasons for choosing it. </font>
</p>
<br>
<input value="Load challenge set" type="submit" script="script:jmol:1:load phe.pdb; script:jmol:2:load tyr.pdb; script: jmol:3:load trp.pdb; script: jmol:4:load his.pdb;" name="loadModels">
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