We have examined the secondary structure of the protein and its atomic spatial structure. However, since we cannot distinguish single amino acids in this display, we cannot determine the location of the active site. In order to overcome this obstacle we will display the entire protein in a secondary structure display, except for the amino acids composing the active site, which will be displayed in a different way and in a different color. Even though in the Balls and Sticks display each atom, as well as the chemical bonds between the atoms, can be seen, it is difficult to distinguish the secondary structures of the protein. The secondary structure of the protein is the structure displaying the protein according to basic repeating structures: alpha helices appearing in pink, and beta sheets in yellow, and the areas connecting them: turns and loops in white. We will return to the Jmol workspace and change the protein display to the secondary structure display (Cartoon).

  1. What command do we perform in the workspace? After writing it down, try to perform it in the workspace

Since we selected only some of the amino acids in the previous command (the hydrophobic amino acids), we must first select all of the amino acids in the protein, and in fact all of the atoms composing the structure, and only then change the model display. These are the commands:

  • Right click the mouse. In the additional options menu, pick Select ➔ All.
  • Right click the mouse and pick Style ➔ Scheme ➔ Cartoon.

The protein is now displayed in the secondary structure display. Now we will use the Select command to select the amino acids comprising the active site and display them in the model. This action requires two stages (Figure 10): selecting the area on which to perform the action, in this case selecting the amino acids of the active site using the Select command; and in the next stage displaying the bonds between the atoms of the selected amino acids so that they become visible. Return to the workspace and perform the following actions:

Figure 10: Displaying the bonds between the atoms in the amino acids comprising the active site is a two stage process

Figure 10: Displaying the bonds between the atoms in the amino acids comprising the active site is a two stage process

  • We will open the console (screen 7):
  • In the workspace menu bar pick File ➔ Console… or right click the mouse and in the additional options menu pick Console
Screen 7: Opening the console

Screen 7: Opening the console

Selecting the amino acids comprising the active site: enter the following command in the console select 214, 216, 270 (the command can be copied using ctrl+C or “copy”, and placed on the screen using ctrl+V, or “paste”) and press Enter. With this command we have selected the amino acids comprising the active site, by entering the position numbers of the amino acids in the active site, separated by commas. Notice the Jmol tool notifies that 28 atoms have been selected, which comprise the three amino acids in the active site. There was no change in the protein display after selecting the amino acids.

  • Displaying the bonds between the atoms of the amino acids comprising the active site: right click the mouse in the workspace.
  • In the options menu pick Style➔ Bonds ➔ 0.3 Å (screen 8).
Screen 8: The command to display the bonds between the atoms of the selected amino acids in the desired width

Screen 8: The command to display the bonds between the atoms of the selected amino acids in the desired width

  • Rotate the protein and see what has changed in the protein model before you.
  • Changing the color of the bonds: right click the mouse in the workspace. In the additional options menu, pick Color ➔ Bonds ➔ Cyan.

11. Rotate the protein again, zoom in and out and see what has changed in the protein model before us.

Choose one answer:

  1. The model of the entire protein is displaying the bonds between the atoms.
  2. The bonds between the atoms are displayed only for the amino acids selected by the scientists.
  3. The bonds between the atoms of the amino acids selected by the scientists, were colored in cyan.
  4. Answer b and c are correct.

The correct answer is: D. By using the command Style ➔ Bonds ➔ 0.3 Å we are in fact requesting that the width of the chemical bonds displayed will be spaced at 0.3Å. Å (Ångström) is a unit of length equal to 10-10 meter, which is equal to one-hundredth of a millionth of a centimeter. Notice that this does not mean that the size of the atoms or the bonds in the molecule have changed, only their display. This display allows us to see the chemical bonds clearly.

By using the command Color ➔ Bonds ➔ Cyan  we are in fact requesting that those chemical bonds be colored in Cyan, and in this way we will be able to see them clearly.

12. In the spatial structure of the protein, are the amino acids comprising the active site close or far from each other?

Choose one answer:

  1. Close to each other.
  2. Far from each other.
  3. Two amino acids are close to each other, and the third one is far from them.
  4. It is impossible to know.

The correct answer is: A. All three amino acids comprising the active site are close to each other in the spatial structure of the enzyme. The location of the three amino acids comprising the active site can be seen in screen 9.

Screen 9: The amino acids comprising the active site (Cyan) are close to each other. You can zoom in to the desired area by using the Zoom in command in the menu.

Screen 9: The amino acids comprising the active site (Cyan) are close to each other. You can zoom in to the desired area by using the Zoom in command in the menu.