Hello everyone. Welcome to this tutorial on 3D Models of Enzymes in Jmol .
In this tutorial, we will learn to: * Load structure of Human Pancreatic Hexokinase on Jmol panel
Modify the display of secondary structure
Highlight amino acid residues at the active site.
Highlight substrate and cofactors of the enzyme.
And, view Ramachandran plot for protein.
To follow this tutorial, you should have knowledge of basic biochemistry
and familiar with basic operations from Jmol Application window.
Please view the tutorial Proteins and Macromolecules in the Jmol Application series.
It is available at the following link.
To record this tutorial, I am using: * Ubuntu Operating System version 12.04
Jmol version 12.2.2.
Java version 7 and * Mozilla Firefox browser 22.0.
Open the Jmol window and load the structure of hexokinase enzyme.
I am connected to internet. So, I will load the structure directly from the PDB website.
To do so, open the File menu, scroll down and click on Get PDB option.
An Input dialogue-box appears on the screen. Type the four letter PDB code for hexokinase, that is, 3IDH in the text-box.
This code was obtained from the Protein Data Bank website.
If you do not have a working internet connection: Open the existing pdb file using Open a file icon on the tool bar.
Click on OK button.
3D structure of hexokinase also known as glucokinase opens on the screen.
Open the Console window using the File menu.
As shown on the Console, the structure on the panel is for Human Pancreatic Glucokinase along with substrate Glucose.
Close the Console.
On the panel, we have the ball and stick model of hexokinase.
Remove the water molecules from the protein model on the panel.
This process is explained in detail, in the Jmol tutorial Proteins and macromolecules.
About hexokinase Enzyme-
Hexokinase is a monomeric protein of 465 amino acids.
It has two domains, a large domain and a small domain.
The active-site for this enzyme is located in the cleft between the two domains.
Active-site for hexokinase has 3 amino acid residues: Aspergine at 204, Aspergine at position 231 and Glutamic acid at 256.
Alpha-D-Glucose is the substrate for this enzyme.
Now, let us go back to the Jmol panel.
We can select and highlight the components of enzymes like Substrate, Cofactors or Amino acid residues at the active site.
To select a particular component- Open the pop-up menu using the right-click.
Scroll down to Select option.
From the sub-menu, Proteins, select By Residue name.
We have individual amino acid residues listed here.
Click on the name of the amino acid to select it.
Also, amino acids are grouped under headings like: Polar, Non-polar, Basic, Acidic, Uncharged etc.
Listed in the Hetero menu, are the metal ion potassium and substrate glucose.
We can modify the display of enzyme to easily locate the substrate binding site.`
Let us change the display and color of the atoms of the protein.
Open the pop-up menu, go to Select and scroll down to Protein option. Click on All.
Open the pop-up menu again, scroll down to Style, then to Scheme. And click on Sticks option.
Now we have, on the panel, the protein in sticks display.
Now, to change the color- open the pop-up menu again, go to Color >> Atoms and click on Blue option.
We have, on the screen, the model of hexokinase in blue color and in sticks display.
Observe the substrate Alfa-D-Glucose in ball and stick display in the cleft.
To highlight the substrate- open the pop-up menu, go to Select, then Hetero and click on GLC-ALFA-D-GLUCOSE.
Open the pop-up menu again, scroll down to Style >> Scheme and click on Sticks option.
To change the color- open the pop-up menu again, go down to Color >> Atoms and click on White option.
On the panel is the model of hexokinase with position of the substrate clearly highlighted.
We can change the color of the amino acids at the active site to highlight them.
To do so, we have to type commands in the Console window.
As mentioned earlier, the amino acids involved at the active-site are Aspergine at position 204, Aspergine at position 231 and Glutamic acid at 256.
Open the console window using File menu. Click on Console.
I am using Kmag Screen magnifier to magnify the console window.
At the $ (dollar) prompt, type: "select" within square brackets "Asn" for aspergine close the bracket, "204" i.e the position semicolon "color atoms orange".
Press Enter.
Observe that the atoms of aspargine residue now in orange color.
Press up-arrow button on the key board and edit the command.
Edit the amino acid position to 231 and color of atoms to red.
Press Enter.
Press up-arrow key again and edit the name of the amino acid to GLU, that is, glutamic acid and position to 256.
and,color of atoms to green and press Enter.
We have, on the panel, a 3D model of hexokinase with substrate and the active site highlighted.
Also highlighted in the model is the potassium atom shown here, in purple color.
We can also show ramachandran plots for a particular protein in jmol.
On the console, at the dollar($) prompt, type: plot ramachandran
press Enter.
On the screen, we have a ramachandran plot for hexokinase.
Try to load different enzymes using pdb files from the database.
Change the display of secondary structure.
Let's summarize. In this tutorial, we learnt to: * Load structure of Human Pancreatic Hexokinase using PDB code.
Modify the display of secondary structure.
Highlight amino acid residues at the active site.
Highlight substrate and cofactors of the enzyme.
And, view ramachandran plot for proteins.
As an assignment: Load the dot pdb file of enzyme Lysozyme on Jmol panel.
Highlight the substrate bound to the enzyme.
Highlight the amino acids at the active site.
Hint: Get the pdb file of Lysozyme from PDB database.
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