Why is understanding protein shape important? Understanding how a protein folds into a specific shape is one of the most important and challenging problems of modern science. If we could predict how a particular sequence of amino acids would fold, we could build protein-based molecular machines similar to those found in a cell. For example, if we understood the way a misfolded protein is responsible for a serious illness, we could probably design the right medicine to help those with the illness.
Why should we use the Folding Polymer model, with its water and oil? Every protein in a living cell is surrounded by water or by lipids. The surrounding plays a very important role in the shaping of a protein. To explore the role of the surrounding water or lipids on protein folding, we will work with a dynamic model of a string of beads surrounded by either water or lipids (oil). Every "bead" in the string represents an amino acid, all beads are linked to each other with covalent bonds, and the whole string represents a fragment of a protein, such as a hemoglobin fragment or a piece of bee venom's protein, or some other cellular component or machine. Working with the dynamic model, we will explore how water or lipids affects the folding of the protein chain. We will investigate the role of different amino acids in this process and find out how the changes in their sequence within a protein chain can affect the shape of a folding protein.
Review How to Use Folding Polymer model if necessary.
What is the effect of placing a protein chain in different environments?
For a amino acid to become part of a protein, it should have at least two covalent bonds to connect it to its neighbors. When amino acids are linked in a protein chain, the amino group and carboxyl group are bonded or "taken." The key part of the amino acid that is left to interact with water is the group of atoms we call a side-chain, residue or radical. Let's find out more about the side-chains and their response to water.
A. Water and Oil - What's the difference to a protein?
1. You can launch your model in one of two ways:
A. From your browser. Click the link below.
Folding Polymer: 20 Alanine Residues: http://xeon.concord.org:8080/modeler/webstart/protein/ala20.jnlp
B. By going through the Molecular Workbench application on your computer (workbench.jar). Then you should click the following links: Student Pages, Protein Folding, A Polymer with 20 Alanines.
It may take a short while to launch the Molecular Workbench the first time.
2. Make sure the "Select a solvent type" is set to "Vacuum."
3. Click the "Run" button, and observe what happens to the polymer chain.
4. Set the "Select a solvent type" window to "Water."
5. Click the "Run" button, and observe what happens to the polymer chain.
6. What is the property of alanine that helps explain its reaction to water?
7. Set the "Select a solvent type" window to "Oil." Click the "Run" button, and describe and draw what happens to the polymer chain.
8. What is the difference between the protein's response to water and to lipids (oil)?
B. What is the effect on the shape of a polymer chain in water of replacing just a single amino acid "bead"?
1. Before starting, make sure the "Select a solvent type" window shows "Water".
2. This time, change the first amino acid from alanine to glutamic acid, and run. Draw what you observe.
3. Now change the first two and last two alanine amino acids to glutamic acid and run. Draw what you observe.
4. Explain how just a change of one or two amino acids have such an effect.
C. What happens when a significant part of a polymer chain is water-fearing and another part is water-loving?
1. Make sure the "Select a solvent type" window shows "Water."
2. Build a polymer chain with a set of 10 hydrophilic amino acids next to each other in the middle of the chain. Run the model.
3. Describe and draw what happens to the shape of the protein.
4. The drawing below represents a whole protein in water.
Where would you expect to find water-fearing, hydrophobic amino acids, at location A, B or C?
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