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Protein Conservation 4
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Protein Folding: Solvent Effects
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<font face="verdana, arial, helvetica, sans-serif" size="5">Almost all
proteins fold into a specific shape in order to function. Without that
shape, the protein can't work - it's broken. When the protein is first
made, as it folds up, the side chains of the amino acids interact with the
solvent, with each other, and with the main chain. </font>
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-392113
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org.concord.modeler.text.LineIcon710.0305515<html><body align="center"><strong><font size="5" face="Verdana, Arial, Helvetica, sans-serif" color="rgb(051, 051, 051)">The Environment for Folding: Polar or Non-Polar</font></strong></body></html>-46544255
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<font face="verdana, arial, helvetica, sans-serif" size="4"><b>Folding in
Polar/Non-Polar Solvents</b><br>The model at left shows a peptide (short
protein) consisting entirely of non-polar amino acids in water, a polar
solvent. </font>
<ul>
<li>
<font face="verdana, arial, helvetica, sans-serif" size="4">Notice the
shape of the unfolded peptide, and that one amino acid <img src="highlightedAA.gif">
is a different color than the rest, so you can find it easily later. </font>
</li>
<li>
<font face="verdana, arial, helvetica, sans-serif" size="4">Run the
model until the peptide's folded shape is stable, and answer the first
two questions below. </font>
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<font face="verdana, arial, helvetica, sans-serif" size="4">Then
change the solvent to oil, run the model, and answer the last two
questions.</font>
</li>
</ul>
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Reminder: the highlighted amino acid is non-polar,<br> just like all the rest in this short chain. Its is colored<br> differently only to make it easy to see.
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<b>When the peptide folds in water, how does the shape of the folded peptide compare to the unfolded shape?
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<b>In water, where does the highlighted amino acid end up?
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<b>Answer this question after you run the model in oil. Remember that oil is a non-polar solvent. <br>Explain the difference between what the peptide does in water, and what it does in oil, using the words "polar", "non-polar", and "hydrophobic".
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<b>Predict how the peptide would fold in oil, if all the amino acid side chains were polar instead of non-polar.
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Use what you have learned on previous pages<br> of this activity to make your prediction. <br> Remember how polar amino acids behave<br> in a non-polar solvent.
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<font face="verdana, arial, helvetica, sans-serif" size="2">A note on our
simplified protein folding description: Protein folding is a complex
process that is not yet fully understood. However, it is very clear that
in addition to solvent/side chain/main chain interactions, 'helper'
proteins called chaperones are essential to the correct folding of most
proteins.</font>
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