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

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(Created page with "{| border=1 || '''Time''' || '''Narration''' |- ||00:01 ||Hello everyone. Welcome to this tutorial on '''3D Models of Enzymes in Jmol '''. |- ||00:08 || In this tutorial,...")
 
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||00:01
 
||00:01
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||Hello everyone. Welcome to this tutorial on '''3D Models of Enzymes in Jmol '''.  
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||Hello everyone. Welcome to this tutorial on '''3D Models of Enzymes in Jmol '''.  
  
 
|-
 
|-
 
||00:08
 
||00:08
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|| In this tutorial, we will learn to Load structure of '''Human Pancreatic Hexokinase''' on '''Jmol panel'''.
+
|| In this tutorial, we will learn to:  * '''Load''' '''structure''' of '''Human Pancreatic Hexokinase''' on '''Jmol panel'''.
  
 
|-
 
|-
 
||00:16
 
||00:16
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||Modify the display of secondary structure .
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||* Modify the display of secondary structure .
  
 
|-
 
|-
 
||00:20
 
||00:20
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||Highlight amino acid residues at the active site.       
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||* Highlight amino acid residues at the active site.       
  
 
|-
 
|-
 
||00:25
 
||00:25
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|| Highlight substrate and cofactors of the enzyme.
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||* Highlight substrate and cofactors of the enzyme.
  
 
|-
 
|-
 
||00:30
 
||00:30
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|| And view '''Ramachandran plot''' for protein  
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||* And view '''Ramachandran plot''' for protein.
 
                
 
                
 
|-
 
|-
 
||00:35
 
||00:35
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|| To follow this tutorial you should have Knowledge of basic biochemistry.
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|| To follow this tutorial, you should have Knowledge of basic biochemistry
 
   
 
   
 
|-
 
|-
 
||00:41
 
||00:41
−
||And familiar with  basic operations from  '''Jmol Application window'''.
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||and familiar with  basic operations from  '''Jmol Application window'''.
 
        
 
        
 
|-
 
|-
 
||00:46
 
||00:46
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||Please view  the tutorial '''Proteins and Macromolecules''' in the Jmol Application series.
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||Please view  the tutorial '''Proteins and Macromolecules''' in the '''Jmol Application''' series.
 
        
 
        
 
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||00:57
 
||00:57
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||To record this tutorial I am using, '''Ubuntu''' Operating System version 12.04 .
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||To record this tutorial, I am using: * '''Ubuntu''' Operating System version 12.04  
  
 
|-
 
|-
 
||01:05
 
||01:05
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||'''Jmol''' version 12.2.2.
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||* '''Jmol''' version 12.2.2.
  
 
|-
 
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||01:08
 
||01:08
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|| '''Java''' version 7. and '''Mozilla Firefox browser''' 22.0
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||* '''Java''' version 7. and * '''Mozilla Firefox browser''' 22.0
  
 
|-
 
|-
 
||01:16
 
||01:16
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||Open the Jmol window and load the structure of '''hexokinase'''  enzyme.
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||Open the '''Jmol''' '''window''' and '''load''' the structure of '''hexokinase'''  enzyme.
  
 
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||01:37
 
||01:37
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||An Input dialogue box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''',  that is '''3IDH'''  in the text box.  
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||An '''Input''' dialogue box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''',  that is '''3IDH'''  in the text box.  
  
 
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|-
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|-
 
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||01:55
 
||01:55
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|| If you do not have a working Internet connection: Open the existing '''pdb''' file using '''open a file''' icon on the tool bar.   
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|| If you do not have a working Internet connection: Open the existing '''pdb''' file using '''Open a file''' icon on the tool bar.   
  
 
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||02:16
 
||02:16
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|| Open the console window using the '''File''' menu.
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|| Open the '''console''' window using the '''File''' menu.
  
 
|-
 
|-
 
||02:21
 
||02:21
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||As shown on the Console, The structure on the panel is for '''Human Pancreatic Glucokinase''' along with substrate '''Glucose'''.
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||As shown on the Console, the structure on the panel is for '''Human Pancreatic Glucokinase''' along with substrate '''Glucose'''.
  
 
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||02:34
 
||02:34
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||On the panel we have the ball and stick model of '''hexokinase'''.
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||On the panel, we have the '''ball and stick''' model of '''hexokinase'''.
 
|-
 
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||02:40
 
||02:40
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||02:53
 
||02:53
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||About '''hexokinase''' Enzyme.
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||About '''hexokinase''' Enzyme-
  
 
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||03:30
 
||03:30
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||'''Alpha-D-Glucose''' is the substrate for this enzyme.
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||'''Alpha-D-Glucose''' is the '''substrate''' for this enzyme.
  
 
|-
 
|-
 
||03:34
 
||03:34
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||Now let us go back to the Jmol panel.
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||Now, let us go back to the Jmol panel.
 
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||03:38
 
||03:38
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|-
 
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|| 03:49
 
|| 03:49
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||To select a particular component Open the pop-up menu using the right click.  
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||To select a particular component- Open the pop-up menu using the right-click.  
  
 
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||04:46
 
||04:46
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||Open the pop-up menu, go to '''Select''', and scroll down to '''Protein''' option. Click on '''All'''.
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||Open the pop-up menu, go to '''Select''' and scroll down to '''Protein''' option. Click on '''All'''.
 
|-   
 
|-   
 
||04:55
 
||04:55
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||Open the pop-up menu again, scroll down to '''Style''', then to '''Scheme'''.
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||Open the pop-up menu again, scroll down to '''Style''', then to '''Scheme'''. And click on '''Sticks''' option.  
−
And click on '''Sticks''' option.  
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|-
 
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||05:05
 
||05:05
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||Now we have on the panel the protein in '''sticks''' display  
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||Now we have, on the panel, the protein in '''sticks''' display.
  
 
|-
 
|-
 
||05:11
 
||05:11
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|Now to change the color, open the pop-up menu again, go to '''Color''', '''Atoms''', and click on '''Blue''' option.
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|Now to change the color- open the pop-up menu again, go to '''Color''', '''Atoms''' and click on '''Blue''' option.
 
|-
 
|-
 
||05:23
 
||05:23
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||We have on the screen the model of '''hexokinase''' in blue color and in sticks display
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||We have, on the screen, the model of '''hexokinase''' in blue color and in sticks display.
 
|-
 
|-
 
||05:30
 
||05:30
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||Observe the substrate, '''Alfa-D-Glucose''' in ball and stick display in the cleft.
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||Observe the substrate '''Alfa-D-Glucose''' in '''ball and stick''' display in the cleft.
 
|-
 
|-
 
||05:38
 
||05:38
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||To highlight the substrate, open the pop-up menu, go to '''Select''', then '''Hetero''' and click on '''GLC-ALFA-D-GLUCOSE'''.
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||To highlight the substrate- open the pop-up menu, go to '''Select''', then '''Hetero''' and click on '''GLC-ALFA-D-GLUCOSE'''.
 
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||05:52
 
||05:52
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||06:00
 
||06:00
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||To change the color, Open the pop-up menu again, go down to '''Color''', '''Atoms''' and click on '''White''' option.  
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||To change the color- Open the pop-up menu again, go down to '''Color''', '''Atoms''' and click on '''White''' option.  
 
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||06:12
 
||06:12
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||06:32
 
||06:32
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||As mentioned earlier the amino acids involved at the active-site are '''Aspergine''' at position 204,  
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||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.  
 
'''Aspergine''' at position 231 and '''Glutamic acid''' at 256.  
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|-
 
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||07:03
 
||07:03
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||At the $ prompt type: '''select within square brackets Asn for aspergine close the bracket, 204 i.e the position semicolon color atoms orange'''.
+
||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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||07:25
 
||07:25
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||Press enter.
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||Press '''Enter'''.
  
 
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|-
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||07:33
 
||07:33
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||Press up arrow button on the key board and edit the command.
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||Press up-arrow button on the key board and '''edit''' the command.
  
 
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|-
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||07:48
 
||07:48
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||Press Enter
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||Press '''Enter'''.
 
|-
 
|-
 
||07:51
 
||07:51
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||Press up arrow key and again and edit name of amino acid to GLU, that is '''glutamic acid''' and position to 256   
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||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
 
||08:06
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||Color of atoms to green and Press Enter .  
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||Color of atoms to green and press '''Enter'''.  
 
|-
 
|-
 
||08:13
 
||08:13
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|| We have on the panel a 3D model of '''hexokinase''' with substrate and the active site highlighted.
+
|| We have, on the panel, a 3D model of '''hexokinase''' with substrate and the active site highlighted.
 
|-   
 
|-   
 
||08:23
 
||08:23
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||08:36
 
||08:36
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||On the console, at the $ prompt type  '''plot ramachandran'''  
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||On the console, at the dollar($) prompt, type: '''plot ramachandran'''  
  
 
|-
 
|-
 
||08:45
 
||08:45
−
||Press Enter .  
+
||press '''Enter'''.  
 
|-
 
|-
 
||08:47
 
||08:47
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||On the screen we have a '''ramachandran plot''' for '''hexokinase'''.
+
||On the screen, we have a '''ramachandran plot''' for '''hexokinase'''.
 
|-
 
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||08:54
 
||08:54
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|-
 
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||09:00
 
||09:00
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||Change the display of secondary structure
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||Change the display of secondary structure.
 
|-
 
|-
 
||09:04
 
||09:04
−
||Lets 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.
  
 
|-
 
|-
 
||09:14
 
||09:14
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|| Modify the display of secondary structure.
+
||* Modify the display of secondary structure.
  
 
|-
 
|-
 
||09:17
 
||09:17
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|| Highlight amino acid residues at the active site.
+
||* Highlight amino acid residues at the active site.
 
|-
 
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||09:21
 
||09:21
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||10:04
 
||10:04
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|| The Spoken Tutorial Project Team:
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|| The Spoken Tutorial Project team
  
 
|-
 
|-
 
||10:07
 
||10:07
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||Conducts workshops and distributes certificates.
+
|| conducts workshops and distributes certificates.
  
 
|-
 
|-
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||10:14
 
||10:14
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|| Spoken Tutorial Project is a part of the Talk to a Teacher project.  
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|| '''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project.  
  
 
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||10:25
 
||10:25
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||More information on this Mission is available at this link  
+
||More information on this mission is available at this link.
  
 
|-
 
|-
 
||10:30
 
||10:30
−
||This is '''Snehalatha''' from '''IIT Bombay''' signing off. Thank you for joining.  
+
||This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.  
 
|-
 
|-
 
|}
 
|}

Revision as of 17:19, 14 September 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 $ (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 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.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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