Difference between revisions of "Jmol-Application/C4/3D-Models-of-Enzymes/English-timed"
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| − | || In this tutorial, we will learn to: * '''Load | + | || In this tutorial, we will learn to: * '''Load''' structure of '''Human Pancreatic Hexokinase''' on '''Jmol panel''' |
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| − | ||* Modify the display of secondary structure | + | ||* Modify the display of secondary structure |
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| − | ||* And view '''Ramachandran plot''' for protein. | + | ||* And, view '''Ramachandran plot''' for protein. |
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| − | ||* '''Java''' version '''7''' | + | ||* '''Java''' version '''7''' and * '''Mozilla Firefox browser''' '''22.0'''. |
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| − | || | + | || 3D structure of '''hexokinase''' also known as '''glucokinase''' opens on the screen. |
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| − | ||This process is explained in detail in the Jmol tutorial '''Proteins and macromolecules'''. | + | ||This process is explained in detail, in the Jmol tutorial '''Proteins and macromolecules'''. |
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| − | || It has two '''domains''', a large | + | || It has two '''domains''', a large domain and a small domain. |
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| − | || Active-site for '''hexokinase''' has 3 amino acid | + | || Active-site for '''hexokinase''' has 3 '''amino acid residue'''s: '''Aspergine''' at '''204''', '''Aspergine''' at position '''231''' and '''Glutamic acid''' at '''256'''. |
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| − | ||We have individual amino acid | + | ||We have individual '''amino acid residue'''s listed here. |
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| − | |Now, to change the color- open the pop-up menu again, go to '''Color''' | + | |Now, to change the color- open the pop-up menu again, go to '''Color''' >> '''Atoms''' and click on '''Blue''' option. |
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| − | ||Open the pop-up menu again, scroll down to '''Style''' | + | ||Open the pop-up menu again, scroll down to '''Style''' >> '''Scheme''' and click on '''Sticks''' option. |
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| − | ||To change the color- open the pop-up menu again, go down to '''Color''' | + | ||To change the color- open the pop-up menu again, go down to '''Color''' >> '''Atoms''' and click on '''White''' option. |
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| − | ||On panel is the model of '''hexokinase''' with position of the '''substrate''' clearly highlighted. | + | ||On the panel is the model of '''hexokinase''' with position of the '''substrate''' clearly highlighted. |
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| − | ||At the $ (dollar) prompt, type: '''"select"''' within square brackets '''"Asn"''' for aspergine close the bracket, '''"204"''' i.e the position | + | ||At the $ (dollar) prompt, type: '''"select"''' within square brackets '''"Asn"''' for aspergine close the bracket, '''"204"''' i.e the position semicolon '''"color atoms orange"'''. |
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| − | || | + | ||and,color of atoms to green and press '''Enter'''. |
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| − | ||Let's summarize. In this tutorial we learnt to: * '''Load''' structure of '''Human Pancreatic Hexokinase''' using PDB code. | + | ||Let's summarize. In this tutorial, we learnt to: * '''Load''' structure of '''Human Pancreatic Hexokinase''' using PDB code. |
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| − | ||And view '''ramachandran''' plot for proteins. | + | ||And, view '''ramachandran''' plot for proteins. |
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Revision as of 16:25, 2 June 2016
| 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. |
| 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. |
