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 the 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 $ (dollar) 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 again and edit the name of the amino acid to GLU, that is, glutamic acid and position to 256.
08:06 and,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 dollar($) 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 Let's 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.
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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