Protein Folding Simulation
Name________________________ Per____
Go to bit.ly/MustangProteinFolding to run the protein folding simulation.
Click the play button at the bottom of the screen to watch the chain of amino acids fold into a
protein. The green amino acids are hydrophilic and the gold amino acids are hydrophobic. Try
resetting the simulator several times by clicking on the generate random protein button and
playing simulation over again.
Describe the pattern that you noticed regarding how the hydrophilic and hydrophobic amino acids
arrange themselves during protein folding.
According to the simulation settings, what substance is the protein floating in?
Based on the phenomenon you observed, how would you describe the characteristics of:
Hydrophilic molecules
Hydrophobic molecules
Click the generate random protein button and hit play to allow the protein fold up. Press the
pause button and sketch the general shape of the protein (do not draw each amino acid just sketch
the outline of protein) in the protein 1 box.
Do this a second time by clicking the generate random protein, clicking play to let the protein
fold and then pausing the simulation. Make a second sketch in the box titled protein 2.
Repeat a 3rd and a 4th time and add sketches to the 2 remaining boxes.
Protein 1
Protein 2
Protein 3
Protein 4
As a group discuss the 4 protein molecules that you sketched. Make a list of similarities and
differences.
Similarities
Differences
With your group, brainstorm some possible causes for the difference in shape of the above proteins.




Based on the models that the simulation has created, predict the shape of a protein that has all
hydrophobic amino acids:
What shape would you predict for an all hydrophilic protein?
Now use the simulation to test your predictions:
All Hydrophobic
All Hydrophilic
Question: What happens to a protein when the amino acid sequence is change?
CER: You may use the simulator to generate evidence.
Claim: Changing the sequence of amino acids….
Evidence:
d
Reasoning:
Use the scientific principles of hydrophobic and
hydrophilic nature of amino acids to reason.