Jmol-Application/C4/3D-Models-of-Enzymes/English-timed

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Time Narration
00:01 Hello everyone. Welcome to this tutorial on 3D Models of Enzymes in Jmol .
00:08 In this tutorial, we will learn to Load structure of Human Pancreatic Hexokinase on Jmol panel.
00:16 Modify the display of secondary structure .
00:20 Highlight amino acid residues at the active site.
00:25 Highlight substrate and cofactors of the enzyme.
00:30 And view Ramachandran plot for protein
00:35 To follow this tutorial you should have Knowledge of basic biochemistry.
00:41 And familiar with basic operations from Jmol Application window.
00:46 Please view the tutorial Proteins and Macromolecules in the Jmol Application series.
00:53 It is available at the following link.
00:57 To record this tutorial I am using, Ubuntu Operating System version 12.04 .
01:05 Jmol version 12.2.2.
01:08 Java version 7. and Mozilla Firefox browser 22.0
01:16 Open the Jmol window and load the structure of hexokinase enzyme.
01:22 I am connected to internet, so I will load the structure directly from the PDB website.
01:28 To do so, Open the File menu, scroll down and click on Get PDB option.
01:37 An Input dialogue box appears on the screen. Type the four letter PDB code for hexokinase, that is 3IDH in the text box.
01:50 This code was obtained from the Protein Data Bank website.
01:55 If you do not have a working Internet connection: Open the existing pdb file using open a file icon on the tool bar.
02:06 Click on OK button.
02:09 3D Structure of hexokinase also known as glucokinase opens on the screen.
02:16 Open the console window using the File menu.
02:21 As shown on the Console, The structure on the panel is for Human Pancreatic Glucokinase along with substrate Glucose.
02:31 Close the Console.
02:34 On the panel we have the ball and stick model of hexokinase.
02:40 Remove the water molecules from the protein model on the panel.
02:44 This process is explained in detail in the Jmol tutorial Proteins and macromolecules.
02:53 About hexokinase Enzyme.
02:56 Hexokinase is a monomeric protein of 465 amino acids.
03:02 It has two domains, a large domain and a small domain.
03:07 The active-site for this enzyme is located in the cleft between the two domains.
03:14 Active-site for hexokinase has 3 amino acid residues: Aspergine at 204, Aspergine at position 231 and Glutamic acid at 256.
03:30 Alpha-D-Glucose is the substrate for this enzyme.
03:34 Now let us go back to the Jmol panel.
03:38 We can select and highlight the components of enzymes like : Substrate, Cofactors or Amino acid residues at the active site.
03:49 To select a particular component Open the pop-up menu using the right click.
03:55 Scroll down to Select option.
03:57 From the sub-menu, Proteins, select By Residue name.
04:04 We have individual amino acid residues listed here.
04:10 Click on the name of the amino acid to select it.
04:14 Also amino acids are grouped under headings like: Polar, Non-polar, Basic, Acidic, Uncharged etc.
04:26 Listed in the Hetero menu, are the metal ion potassium and substrate glucose.
04:34 We can modify the display of enzyme to easily locate the substrate binding site.`
04:41 Let us change the display and color of the atoms of the protein.
04:46 Open the pop-up menu, go to Select, and scroll down to Protein option. Click on All.
04:55 Open the pop-up menu again, scroll down to Style, then to Scheme.

And click on Sticks option.

05:05 Now we have on the panel the protein in sticks display
05:11 Now to change the color, open the pop-up menu again, go to Color, Atoms, and click on Blue option.
05:23 We have on the screen the model of hexokinase in blue color and in sticks display
05:30 Observe the substrate, Alfa-D-Glucose in ball and stick display in the cleft.
05:38 To highlight the substrate, open the pop-up menu, go to Select, then Hetero and click on GLC-ALFA-D-GLUCOSE.
05:52 Open the pop-up menu again , scroll down to Style, Scheme and click on Sticks option.
06:00 To change the color, Open the pop-up menu again, go down to Color, Atoms and click on White option.
06:12 On panel is the model of hexokinase with position of the substrate clearly highlighted.
06:20 We can change the color of the amino acids at the active site to highlight them.
06:26 To do so, we have to type commands in the Console window.
06:32 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.

06:50 Open the console window using File menu. Click on Console.
06:57 I am using Kmag Screen magnifier to magnify the console window.
07:03 At the $ prompt type: select within square brackets Asn for aspergine close the bracket, 204 i.e the position semicolon color atoms orange.
07:25 Press enter.
07:27 Observe that the atoms of aspargine residue now in orange color.
07:33 Press up arrow button on the key board and edit the command.
07:39 Edit the amino acid position to 231 and color of atoms to red.
07:48 Press Enter
07:51 Press up arrow key and again and edit name of amino acid to GLU, that is glutamic acid and position to 256
08:06 Color of atoms to green and Press Enter .
08:13 We have on the panel a 3D model of hexokinase with substrate and the active site highlighted.
08:23 Also highlighted in the model is the potassium atom shown here in purple color.
08:30 We can also show ramachandran plots for a particular protein in jmol.
08:36 On the console, at the $ prompt type plot ramachandran
08:45 Press Enter .
08:47 On the screen we have a ramachandran plot for hexokinase.
08:54 Try to load different enzymes using pdb files from the database.
09:00 Change the display of secondary structure
09:04 Lets summarize, In this tutorial we learnt to, Load structure of Human Pancreatic Hexokinase using PDB code.
09:14 Modify the display of secondary structure.
09:17 Highlight amino acid residues at the active site.
09:21 * Highlight substrate and cofactors of the enzyme.
09:25 And View ramachandran plot for proteins.
09:30 As an Assignment: Load the dot pdb file of enzyme Lysozyme on Jmol panel.
09:38 Highlight the substrate bound to the enzyme.
09:42 Highlight the amino acids at the active site.
09:46 Hint: Get the pdb file of Lysozyme from PDB database.
09:52 Watch the video available at this URL.
09:56 It summarizes the Spoken Tutorial project.
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10:04 The Spoken Tutorial Project Team:
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10:30 This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14