Using Computers to Study Molecular Structure

Tertiary Structure

About tertiary structure

To study tertiary structure, you'll examine the enzyme lysozyme. There are 4 disulfide (-S-S-) bonds in lysozyme. These are covalent bonds that link distant parts of the protein primary structure, and are common in extracellular proteins. They are formed from side chains of the amino acid cys. You can see the yellow sulfur atoms lurking in the middle of the molecule.

The tertiary structure of an enzyme is integral to its ability to bind with specific substrates. The MacMolecule file for lysozyme also has views of the enzyme complexed with a carbohydrate.

Opening the tertiary structure in MacMolecule

When you choose Lysozyme below, MacMolecule will automatically open that file. You can switch back to Netscape by choosing Netscape from the Applications Menu.

Tertiary Structure MacMolecule File

lysozyme

This MacMolecule file contains 3 different views of the molecule. You can switch to a different view by clicking on its title in the Views Pane in the upper right of the MacMolecule window.

View
Original A ball and stick view of the lysozyme molecule
Enyzme-substrate complex A view of lysozyme (the enzyme) complexed with a carbohydrate (the substrate) bound to its active site. The substrate molecule is colored green.
Substrate A ball and stick view of the NAG by itself.

Questions

7. a. Give a brief description of the structure of the enzyme lysozyme.

b. What is the overall shape of the enzyme?

8. How many alpha-helices (blue) and beta-sheets (red) are seen in the structure of lysozyme?
alpha-helices: _____
beta-sheets:______
9. Are there any covalent bonds between lysozyme (the enzyme) and NAG (the substrate)?
YES     NO
10. Is the shape of lysozyme any different when NAG is bound? If so, how?

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The Biology Project
University of Arizona
Wednesday, September 9, 1998
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