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Protein Folding 4: Hydrophobicity and folding
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Protein Folding
Hydrophobicity
In the model below, you can see hydrophobic amino acids surrounded by water. The differences between this and the model on the previous page are that the amino acids are connected in a chain, and we don't show individual water molecules. This model lets you explore the effect of the solvent (the surrounding molecules, such as water) on the folding of a protein.
Choose a model: Set solvent:
Membrane proteins are not completely surrounded by water. They are partly embedded inside the membrane, where non-polar lipid molecules influence their shape.
1. Click "Hydrophobic amino acids," then use the "Set solvent" controller to put the chain in oil (a kind of lipid), and see how it folds. Putting a chain of hydrophobic amino acids in oil is like setting the slider in the model at the top of the page to "non-polar."
2. Click "Hydrophilic amino acids," and again use the "Set solvent" controller to put the chain in oil. Then, change the solvent to water. Try changing the solvent back and forth a few times.
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<b>Hydrophobicity:</b><br><font size="3"> <img src="blue.gif">
 Hydrophilic<br> <img src="pink.gif"> Hydrophobic<br><br><b>Solvent:</b><br> <img src="water.gif"> Water<br> <img src="oil.gif">
 Oil </font>
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<font face="Verdana, Arial, Helvetica, sans-serif" size="4">Run the model,
and imagine you are one of the hydrophobic amino acids. What do you
experience as the chain folds in water? Describe your interactions with
other amino acids and with water molecules.</font>
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<font face="Verdana, Arial, Helvetica, sans-serif" size="4">Click on
"Hydrophilic amino acids" above, and run the model. Imagine you are one of
the hydrophilic amino acids. Describe your interactions with other amino
acids and with water molecules.</font>
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<font face="Verdana, Arial, Helvetica, sans-serif" size="4">Imagine you
are one of the amino acids in the hydrophilic chain, first in oil and then
in water. Describe your interactions with the solvent molecules in oil and
then in water.</font>
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