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Protein Conservation 7
255229185
Sequence Similarity
Open the "Side Chain Properties" chart
Open the "Side Chain Properties" chart
page 9 of 11
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<font face="verdana,arial,sans-serif" size="5">One of the steps toward
discovering the function of a newly found protein is to search online
databases for a similar sequence or sequences. Proteins that are related
through evolution have similar amino acid sequences, and consequently,
similar functions. So finding a protein with a similar sequence can
provide a huge clue to the function of the new protein. </font>
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org.concord.modeler.text.LineIcon700.0305515<html><body align="center"><strong><font size="5" face="Verdana, Arial, Helvetica, sans-serif" color="rgb(051, 051, 051)">Similarity Using the Single Letter Code</font></strong></body></html>-46544255
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<font face="verdana,arial,sans-serif" size="4">When searching for similar
proteins in sequence databases, we use the single letter code of the amino
acids. So first let's get some practice using the single letter code.<br><b>Open
the "Side Chain Properties" chart using the link below.</b> Use
the chart to look up the single letter code and to evaluate which amino
acids would make conservative substitutions. </font>
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<b><font size="4" face="verdana,arial,sans-serif">Using the single letter code for the amino acids, which of the following
amino acids would be a conservative substitution for arginine (R)? <br><br>
<center>L, D, K, or F</center>
<br><Br>
Type your answer (a single letter) here:</font></b>
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K
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<p>
<font size="4" face="verdana,arial,sans-serif"><b>Sequence Similarity
Challenge</b><br>Suppose that a newly discovered protein in humans
contains the amino acid sequence,<br>GSTDYGI. Using an online database,
you find similar sequences in many other species, and see that the amino
acids at four of the seven spots in this sequence are identical in all
of these species. In the other three spots, conservative substitutions
have occurred.</font>
</p>
<p>
<font size="4" face="verdana,arial,sans-serif">Using the letters of the
four identical amino acids with blanks to represent where the
substitutions are, the sequence looks like this: _ST_YG_. <b>Your job </b>is
to fill in the blanks with conservative changes.</font>
</p>
<ul>
<li>
<font size="4" face="verdana,arial,sans-serif"><b>For example:</b><br>Reference
peptide:       GGRGGAG<br>Challenge
peptide:       GG_GG_G<br>Your
answer might be: GGKGGCG because K and C are conservative
substitutions for R and A. </font>
</li>
</ul>
<font size="4" face="verdana,arial,sans-serif"><b>Reference peptide:
GSTDYGI<br>Challenge peptide:  _ST_YG_</b><br></font>
<ul>
<li>
<font face="verdana,arial,sans-serif" size="4"><b>Use the "Side Chain
Properties" chart</b> to find 3 similar amino acids to fill in
the blanks with conservative substitutions. </font>
</li>
<li>
<font face="verdana,arial,sans-serif" size="4"><b>Type your new,
7-letter sequence in the blank below.</b></font>
</li>
</ul>
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Type your 7-letter sequence here:
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<font face="verdana,arial,helvetica,sans-serif" size="4"><strong>Explain why you chose each of those three amino acids:</strong></font>
</form>
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<font face="verdana, arial, helvetica, sans-serif" size="4">Regions of a
protein can look very similar, but the side chain properties may have
important differences. </font>
<ul>
<li>
<font face="verdana, arial, helvetica, sans-serif" size="4">Use the
controls at right to explore the peptides below. </font>
</li>
<li>
<font face="verdana, arial, helvetica, sans-serif" size="4">Compare
the reference peptide (in the middle) to the other two. </font>
</li>
<li>
<font face="verdana, arial, helvetica, sans-serif" size="4">Take a
snapshot of the peptide that is most conserved compared to the
reference peptide. Annotate it to explain your choice.</font>
</li>
</ul>
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<p>
 
</p>
<table width="100%" cellspacing="0" cellpadding="5" border="1">
<tr>
<td>
<font face="verdana, arial, sans-serif" size="3"><strong>Color by:</strong></font>
</td>
<td>
<font face="verdana, arial, sans-serif" size="3"><strong>Display as:</strong></font>
</td>
</tr>
<tr>
<td width="66%">
<strong><font size="3" face="verdana, arial, sans-serif"><input value="radio" name="RadioGroup1" script="script:jmol:1:select all; color cpk; script:jmol:2:select all; color cpk; script:jmol:3:select all; color cpk" type="radio" checked="checked">
element<br><input value="radio" name="RadioGroup1" script="script:jmol:1:select all; color amino; select [thr]; color pink; select [glu]; color purple; select all; script:jmol:2:select all; color amino; select [thr]; color pink; select [glu]; color purple; select all; script:jmol:3:select all; color amino; select [thr]; color pink; select [glu]; color purple; select all;" type="radio">amino
acid identity<br><input value="radio" name="RadioGroup1" script="script:jmol:1:select polar; color magenta; select hydrophobic; color gray; select all; script:jmol:2:select polar; color magenta; select hydrophobic; color gray; select all; script:jmol:3:select polar; color magenta; select hydrophobic; color gray; select all" type="radio"></font><font color="#ff00ff" size="3" face="verdana, arial, sans-serif">polar,
</font><font color="#999999" size="3" face="verdana, arial, sans-serif">non-polar
</font><font size="3" face="verdana, arial, sans-serif">amino acids </font></strong>
</td>
<td width="34%">
<form>
<strong><font size="3" face="verdana, arial, sans-serif"><input value="radio" name="RadioGroup2" script="script:jmol:1:select all; cpk 25%; wireframe 0.3; script:jmol:2:select all; cpk 25%; wireframe 0.3; script:jmol:3:select all; cpk 25%; wireframe 0.3;" type="radio" checked="checked">
ball & stick<br><input value="radio" name="RadioGroup2" script="script:jmol:1:select all; cpk off; wireframe 0.3; script:jmol:2:select all; cpk off; wireframe 0.3; script:jmol:3:select all; cpk off; wireframe 0.3;" type="radio">stick<br><input value="radio" name="RadioGroup2" script="script:jmol:1:select all; cpk; script:jmol:2:select all; cpk; script:jmol:3:select all; cpk;" type="radio">spacefill
</font></strong>
</form>
</td>
</tr>
</table>
<br>
<br>
<font size="4" face="verdana, arial, helvetica, sans-serif"><b>Click and
drag on the peptides to rotate them; </b></font><b><font size="3" face="verdana, arial, helvetica, sans-serif">SHIFT</font><font size="4" face="verdana, arial, helvetica, sans-serif">-drag
to zoom in or out.</font></b>
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<b>Substitutions of similar amino acids are called conservative because they tend to <i>conserve</i> (meaning 'keep much the same') the properties of the side chain. Explain how the peptide that you chose above will help to conserve the properties of the side chains in the reference peptide.</b></html>
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