Difference between revisions of "Jmol-Application/C4/3D-Models-of-Enzymes/English-timed"
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Revision as of 10:54, 10 March 2015
| 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. |
| 10:00 | If you do not have a good bandwidth, you can download and watch it. |
| 10:04 | The Spoken Tutorial Project Team: |
| 10:07 | Conducts workshops and distributes certificates. |
| 10:10 | For more details, please write to us. |
| 10:14 | Spoken Tutorial Project is a part of the Talk to a Teacher project. |
| 10:19 | It is supported by the National Mission on Education through ICT, MHRD, Government of India. |
| 10:25 | More information on this Mission is available at this link |
| 10:30 | This is Snehalatha from IIT Bombay signing off. Thank you for joining. |
