View source for Jmol-Application/C4/3D-Models-of-Enzymes/English-timed

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|| '''Time''' 
|| '''Narration'''

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||00:01
||Hello everyone. Welcome to this tutorial on '''3D Models of Enzymes  in Jmol '''. 

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||00:08
|| In this tutorial, we will learn to  Load structure of '''Human Pancreatic Hexokinase''' on '''Jmol panel'''.

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||00:16
||Modify the display of secondary structure .

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||00:20
||Highlight amino acid residues at the active site.       

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||00:25
||  Highlight substrate and cofactors of the enzyme.

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||00:30
|| And view '''Ramachandran plot''' for protein 
               
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||00:35
|| To follow this tutorial you should have Knowledge of basic biochemistry.
 
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||00:41
||And familiar with  basic operations from  '''Jmol Application window'''.
      
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||00:46
||Please view  the tutorial '''Proteins and Macromolecules''' in the Jmol Application series.
       
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||00:53
||It is available at the following link.

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||00:57
||To record this tutorial I am using,  '''Ubuntu''' Operating System version 12.04 .

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||01:05
||'''Jmol''' version 12.2.2.

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||01:08
|| '''Java''' version 7. and '''Mozilla Firefox browser''' 22.0

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||01:16
||Open the Jmol window and load the structure of '''hexokinase'''  enzyme.

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||01:22
||I am connected  to '''internet''',  so I will load the structure directly from the '''PDB website'''.

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||01:28
|| To do so, Open the  '''File''' menu, scroll down and click on '''Get PDB''' option.

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||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. 

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||01:50
||This code was obtained from the '''Protein Data Bank''' website.

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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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||02:06
|| Click on '''OK''' button.

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||02:09
|| 3D Structure of  '''hexokinase''' also known as '''glucokinase''' opens on the screen.

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||02:16
|| Open the console window using the '''File''' menu.

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||02:21
||As shown on the Console, The structure on the panel  is for '''Human Pancreatic Glucokinase''' along with substrate '''Glucose'''.

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||02:31
||Close the Console.

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||02:34
||On the panel we have the ball and stick model of '''hexokinase'''.
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||02:40
||Remove the '''water molecules''' from the '''protein model''' on the panel. 

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||02:44
||This process is explained in detail in the  Jmol tutorial '''Proteins and macromolecules'''. 

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||02:53
||About '''hexokinase''' Enzyme. 

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||02:56
|| '''Hexokinase''' is a monomeric protein of 465 amino acids.

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||03:02
|| It has two '''domains''', a large '''domain''' and a small '''domain'''.

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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
|| Active-site  for '''hexokinase''' has 3 amino acid residues:  '''Aspergine''' at 204,  '''Aspergine''' at position 231 and  '''Glutamic acid''' at 256.

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||03:30
||'''Alpha-D-Glucose''' is the substrate for this enzyme.

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||03:34
||Now let us go back to the Jmol panel.
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||03:38
||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
||To select a particular component Open the pop-up menu using the right click. 

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|Scroll down to '''Select''' option.

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||From the sub-menu, '''Proteins''', select '''By Residue name'''.

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||We have individual amino acid residues listed here.

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||Click on the name of the amino acid to select it.

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||Also amino acids are  grouped under headings like: '''Polar''', '''Non-polar''', '''Basic''', '''Acidic''', '''Uncharged''' etc.
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||04:26
||Listed in the '''Hetero''' menu, are the metal ion '''potassium''' and '''substrate glucose'''.
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||04:34
||We can modify the display of enzyme to easily locate the substrate binding site.`
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||04:41
||Let us change the display and color of the atoms of the protein.
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||04:46
||Open the pop-up menu, go to '''Select''', and scroll down to '''Protein''' option. Click on '''All'''.
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||04:55
||Open the pop-up menu again, scroll down to '''Style''', then to '''Scheme'''.
And click on '''Sticks''' option. 
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||05:05
||Now we have on the panel the protein in '''sticks''' display 

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||05:11
|Now to change the color, open the pop-up menu again, go to '''Color''', '''Atoms''', and click on '''Blue''' option.
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||05:23
||We have on the screen the model of '''hexokinase''' in blue color and in sticks display
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||05:30
||Observe the substrate, '''Alfa-D-Glucose''' in ball and stick display in the cleft.
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||05:38
||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
||Open the pop-up menu again , scroll down to '''Style''', '''Scheme''' and  click on '''Sticks''' option.

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||06:00
||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
||On  panel is the model of '''hexokinase''' with position of the substrate clearly highlighted.
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||06:20
||We can change the color of the amino acids at the active site to highlight them.

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||06:26
||To do so, we have to type commands in the '''Console''' window.

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||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. 
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||06:50
|| Open the console window using '''File menu'''. Click on '''Console'''.

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||06:57
||I am using '''Kmag''' Screen magnifier to magnify the console window.

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||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'''.

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||Press enter.

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||07:27
||Observe that the atoms of  '''aspargine''' residue now in orange color.
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||07:33
||Press up arrow button on the key board and edit the command.

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||07:39
||Edit the amino acid position to 231 and color of atoms to red.
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||07:48
||Press Enter
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||07:51
||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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||08:06
||Color of atoms to green and Press Enter . 
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||08:13
|| We have on the panel a 3D model of '''hexokinase''' with substrate and the active site highlighted.
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||08:23
||Also highlighted in the model is the '''potassium''' atom shown here in purple color. 
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||08:30
||We can also show '''ramachandran plots''' for a particular protein in jmol. 
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||08:36
||On the console, at the $ prompt type  '''plot ramachandran''' 

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||Press Enter . 
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||08:47
||On the screen we have a '''ramachandran plot''' for '''hexokinase'''.
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||08:54
||Try to load different enzymes using '''pdb files''' from the database.

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||09:00
||Change the display of secondary structure
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||09:04
||Lets summarize, In this tutorial we learnt to,  Load structure of Human Pancreatic Hexokinase using PDB code.

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||09:14
|| Modify the display of secondary structure.

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||09:17
|| Highlight amino acid residues at the active site.
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||09:21
||* Highlight substrate and cofactors of the enzyme. 

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||09:25
||And View '''ramachandran''' plot for  proteins.
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||09:30
||As an Assignment:  Load the dot pdb file of enzyme '''Lysozyme''' on  Jmol panel.

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||09:38
|| Highlight the substrate bound to the enzyme.

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||09:42
|| Highlight the amino acids at the active site.

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||09:46
||Hint: Get the '''pdb''' file of '''Lysozyme'''  from  '''PDB database'''. 

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||09:52
||Watch the video available at this URL.

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||09:56
||It summarizes the Spoken Tutorial project.

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||10:00
||If you do not have a good bandwidth, you can download and watch it.  

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||10:04
|| The Spoken Tutorial Project Team: 

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||10:07
||Conducts workshops and distributes certificates.

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||10:10
||For more details, please write to us.
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||10:14
|| Spoken Tutorial Project is a part of the Talk to a Teacher project. 

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||10:19
||It is supported by the National Mission on Education through ICT, MHRD, Government of India.
 
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||10:25
||More information on this Mission is available at this link 

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||10:30
||This is '''Snehalatha''' from '''IIT Bombay''' signing off. Thank you for joining. 
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