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

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||00:08
 
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|| In this tutorial, we will learn to:  * '''Load''' structure of '''Human Pancreatic Hexokinase''' on '''Jmol panel'''
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||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 residue'''s at the active site.       
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||Highlight '''amino acid residue'''s at the active site.       
  
 
|-
 
|-
 
||00:25
 
||00:25
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||* Highlight '''substrate''' and '''cofactor'''s of the enzyme.
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||Highlight '''substrate''' and '''cofactor'''s 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
 
   
 
   
 
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||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'''.
  
 
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||01:28
 
||01:28
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|| To do so, open the  '''File''' menu, scroll down and click on '''Get PDB''' option.
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||To do so, open the  '''File''' menu, scroll down and click on '''Get PDB''' option.
  
 
|-
 
|-
 
||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''' dialog-box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''',  that is, '''3IDH'''  in the text-box.  
  
 
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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.   
  
 
|-
 
|-
 
||02:06
 
||02:06
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|| Click on '''OK''' button.
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||Click on '''OK''' button.
  
 
|-
 
|-
 
||02:09
 
||02:09
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|| 3D structure of  '''hexokinase''' also known as '''glucokinase''' opens on the screen.
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||3D structure of  '''hexokinase''' also known as '''glucokinase''' opens on the screen.
  
 
|-
 
|-
 
||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.
  
 
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||02:34
 
||02:34
 
||On the panel, we have the '''ball and stick''' model of '''hexokinase'''.
 
||On the panel, we have the '''ball and stick''' model of '''hexokinase'''.
 +
 
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||02:40
 
||02:40
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|-
 
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||02:56
 
||02:56
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|| '''Hexokinase''' is a '''monomeric protein''' of 465 amino acids.
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||'''Hexokinase''' is a '''monomeric protein''' of 465 amino acids.
  
 
|-
 
|-
 
||03:02
 
||03:02
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|| It has two '''domains''', a large domain and a small domain.
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||It has two '''domains''', a large domain and a small domain.
  
 
|-
 
|-
 
||03:07
 
||03:07
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|| The '''active-site''' for this '''enzyme'''  is located in the '''cleft''' between the two domains.
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||The '''active-site''' for this '''enzyme'''  is located in the '''cleft''' between the two domains.
 +
 
 
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||03:14
 
||03:14
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||03:34
 
||03:34
 
||Now, let us go back to the Jmol panel.
 
||Now, let us go back to the Jmol panel.
 +
 
|-
 
|-
 
||03:38
 
||03:38
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||We can select and highlight the components  of  enzymes like :  '''Substrate, Cofactors''' or '''Amino acid residues''' at the active site.
+
||We can select and highlight the components  of  enzymes like '''Substrate, Cofactors''' or '''Amino acid residues''' at the active site.
 +
 
 
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|-
 
|| 03:49
 
|| 03:49
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||04:14
 
||04:14
 
||Also, amino acids are  grouped under headings like: '''Polar''', '''Non-polar''', '''Basic''', '''Acidic''', '''Uncharged''' etc.
 
||Also, amino acids are  grouped under headings like: '''Polar''', '''Non-polar''', '''Basic''', '''Acidic''', '''Uncharged''' etc.
 +
 
|-
 
|-
 
||04:26
 
||04:26
 
||Listed in the '''Hetero''' menu, are the metal ion '''potassium''' and '''substrate glucose'''.
 
||Listed in the '''Hetero''' menu, are the metal ion '''potassium''' and '''substrate glucose'''.
 +
 
|-
 
|-
 
||04:34
 
||04:34
 
||We can modify the display of '''enzyme''' to easily locate the '''substrate binding site'''.`
 
||We can modify the display of '''enzyme''' to easily locate the '''substrate binding site'''.`
 +
 
|-
 
|-
 
||04:41
 
||04:41
 
||Let us change the display and color of the atoms of the protein.
 
||Let us change the display and color of the atoms of the protein.
 +
 
|-
 
|-
 
||04:46
 
||04:46
 
||Open the pop-up menu, go to '''Select''' and scroll down to '''Protein''' option. Click on '''All'''.
 
||Open the pop-up menu, go to '''Select''' and scroll down to '''Protein''' option. Click on '''All'''.
 +
 
|-   
 
|-   
 
||04:55
 
||04:55
 
||Open the pop-up menu again, scroll down to '''Style''', then to '''Scheme'''. And click on '''Sticks''' option.  
 
||Open the pop-up menu again, scroll down to '''Style''', then to '''Scheme'''. And click on '''Sticks''' option.  
 +
 
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||05:05
 
||05:05
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||05:11
 
||05:11
 
|Now, to change the color- open the pop-up menu again, go to '''Color''' >> '''Atoms''' and click on '''Blue''' option.
 
|Now, to change the color- open the pop-up menu again, go to '''Color''' >> '''Atoms''' and click on '''Blue''' option.
 +
 
|-
 
|-
 
||05:23
 
||05:23
 
||We have, on the screen, the model of '''hexokinase''' in blue color and in '''sticks''' display.
 
||We have, on the screen, the model of '''hexokinase''' in blue color and in '''sticks''' display.
 +
 
|-
 
|-
 
||05:30
 
||05:30
 
||Observe the substrate '''Alfa-D-Glucose''' in '''ball and stick''' display in the cleft.
 
||Observe the substrate '''Alfa-D-Glucose''' in '''ball and stick''' display in the cleft.
 +
 
|-
 
|-
 
||05:38
 
||05:38
 
||To highlight the substrate- open the pop-up menu, go to '''Select''', then '''Hetero''' and click on '''GLC-ALFA-D-GLUCOSE'''.
 
||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
 
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||06:00
 
||06:00
 
||To change the color- open the pop-up menu again, go down to '''Color''' >> '''Atoms''' and click on '''White''' option.  
 
||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
 
||On the 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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||06:20
 
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||06:32
 
||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.  
 
||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.  
 +
 
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||06:50
 
||06:50
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||07:27
 
||07:27
 
||Observe that the atoms of  '''aspargine residue''' now in orange color.
 
||Observe that the atoms of  '''aspargine residue''' now in orange color.
 +
 
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||07:33
 
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||07:39
 
||07:39
 
||Edit the amino acid position to '''231''' and color of atoms to red.
 
||Edit the amino acid position to '''231''' and color of atoms to red.
 +
 
|-
 
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||07:48
 
||07:48
 
||Press '''Enter'''.
 
||Press '''Enter'''.
 +
 
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||07:51
 
||07:51
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||08:06
 
||08:06
 
||and,color of atoms to green and press '''Enter'''.  
 
||and,color of atoms to green and press '''Enter'''.  
 +
 
|-
 
|-
 
||08:13
 
||08:13
 
|| 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
 
||Also highlighted in the model is the '''potassium''' atom shown here, in purple color.  
 
||Also highlighted in the model is the '''potassium''' atom shown here, in purple color.  
 +
 
|-
 
|-
 
||08:30
 
||08:30
 
||We can also show '''ramachandran plots''' for a particular protein in jmol.  
 
||We can also show '''ramachandran plots''' for a particular protein in jmol.  
 +
 
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||08:36
 
||08:36
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||08:45
 
||08:45
 
||press '''Enter'''.  
 
||press '''Enter'''.  
 +
 
|-
 
|-
 
||08:47
 
||08:47
 
||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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||09:00
 
||09:00
 
||Change the display of secondary structure.
 
||Change the display of secondary structure.
 +
 
|-
 
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||09:04
 
||09:04
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||09:14
 
||09:14
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||* Modify the display of secondary structure.
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||Modify the display of secondary structure.
  
 
|-
 
|-
 
||09:17
 
||09:17
−
||* Highlight '''amino acid residue'''s at the active site.
+
||Highlight '''amino acid residue'''s at the active site.
 +
 
 
|-
 
|-
 
||09:21
 
||09:21
−
||* Highlight '''substrate''' and '''cofactor'''s of the '''enzyme'''.  
+
||Highlight '''substrate''' and '''cofactor'''s of the '''enzyme'''.  
  
 
|-
 
|-
 
||09:25
 
||09:25
 
||And, view '''ramachandran''' plot for  proteins.
 
||And, view '''ramachandran''' plot for  proteins.
 +
 
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||09:30
 
||09:30
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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
−
|| conducts workshops and distributes certificates.
+
||conducts workshops and distributes certificates.
  
 
|-
 
|-
 
||10:10
 
||10:10
 
||For more details, please write to us.
 
||For more details, please write to us.
 +
 
|-
 
|-
 
||10:14
 
||10:14

Latest revision as of 15:29, 28 October 2020

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 dialog-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.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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