Difference between revisions of "Jmol-Application/C4/3D-Models-of-Enzymes/English"

Title Slide

Welcome to this tutorial on 3D Models of Enzymes in Jmol .

Learning Objectives

• Load structure of Human Pancreatic Hexokinase on Jmol panel.
• Modify the display of secondary structure .
• Highlight amino acid residues at the active site.

Learning Objectives

• Highlight substrate and cofactors of the enzyme.
• And view Ramachandran plot for protein

Pre-requisites

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.

System Requirement

• Ubuntu Operating System version 12.04 .
• Jmol version 12.2.2.
• Java version 7. and
• Mozilla Firefox browser 22.0

Open the File menu, scroll down and click on Get PDB option.

Type 3IDH in the text box.

The structure on the panel is for Human Pancreatic Glucokinase along with substrate Glucose. Close the Console.

This process is explained in detail in the Jmol tutorial Proteins and macromolecules.

Hexokinase

• 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.

Hexokinase

• Aspergine at 204,
• Aspergine at position 231 and
• Glutamic acid at 256.

Alpha-D-Glucose is the substrate for this enzyme.

• Substrate
• Cofactors or
• Amino acid residues at the active site.

Go to Select option.

Open the pop-up menu using the right click. Scroll down to Select option.

From the submenu select By Residue name option. Point to the amino acid residues in the list.

We have individual amino acid residues listed here. Click on the name of the amino acid to select it.

Polar, Non-polar, Basic, Acidic, Uncharged etc.

Go to Hetero menu, select By HETATM option. Show K-Potassium and GLU-Alfa-D-glucose.

Scroll down the Protein option. Click on All option.

Click on All.

Click on Sticks option.

And click on Sticks option.

Now to change the color.

Click on GLC-Alfa-D-glucose.

Open the pop-up menu, go to Select, then Hetero and click on GLC-ALFA-D-GLUCOSE.

Open the pop-up menu again, go down to Color, Atoms and click on White option.

To do so, we have to type commands in the Console window.

Aspergine at position 204

Aspergine at position 231 and

Glutamic acid at 256.

I am using Kmag Screen magnifier to magnify the console window.

Press enter key on the keyboard.

select within square brackets Asn for aspergine close the bracket, 204 i.e the position semicolon color atoms orange. Press enter.

Delete 204 and type 231

And edit the command. Edit the amino acid position to 231 and color of atoms to red.

Delete ASN. Type GLU. Edit the position number to 256. Press enter key.

And color of atoms to green. Press Enter .

Select potassium (K) from the Select menu and change the color to yellow.

Shown here in purple color.

Press Enter key.

Press Enter .

Change the display of secondary structure

Summary

• Load structure of Human Pancreatic Hexokinase using PDB code.
• Modify the display of secondary structure.
• Highlight amino acid residues at the active site.

Summary

• Highlight substrate and cofactors of the enzyme.
• And View ramachandran plot for proteins.

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.

Acknowledgement

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This is Snehalatha from IIT Bombay signing off. Thank you for joining.