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

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||'''Slide Number 3
 
||'''Slide Number 3
 
Learning Objectives'''
 
Learning Objectives'''
−
|| In this tutorial, we will learn to
+
||  
 
* Highlight substrate and cofactors of the enzyme.
 
* Highlight substrate and cofactors of the enzyme.
 
* And view '''Ramachandran plot''' for protein                 
 
* And view '''Ramachandran plot''' for protein                 
Line 27: Line 27:
 
And familiar with  basic operations from  '''Jmol Application window'''.
 
And familiar with  basic operations from  '''Jmol Application window'''.
 
        
 
        
−
Please view  the tutorial ''Proteins and Macromolecules' in the Jmol Application series.
+
Please view  the tutorial '''Proteins and Macromolecules''' in the Jmol Application series.
 
        
 
        
−
Macromolecules' in the Jmol Application series
+
It is available at the following link.
 
|-
 
|-
 
||'''Slide Number 5
 
||'''Slide Number 5
 
System Requirement'''
 
System Requirement'''
 
||To record this tutorial I am using,  
 
||To record this tutorial I am using,  
−
* '''Ubuntu Linux''' OS version 12.04 .
+
* '''Ubuntu''' Operating System version 12.04 .
 
* '''Jmol''' version 12.2.2.
 
* '''Jmol''' version 12.2.2.
−
* '''Java''' version 7.
+
* '''Java''' version 7. and
 
* '''Mozilla Firefox browser''' 22.0
 
* '''Mozilla Firefox browser''' 22.0
 
|-
 
|-
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||Cursor on input box.
 
||Cursor on input box.
 
Type '''3IDH''' in the text box.
 
Type '''3IDH''' in the text box.
−
||An Input box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''',  that is '''3IDH'''  in the text box.  
+
||An Input dialog box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''',  that is '''3IDH'''  in the text box.  
 
|-
 
|-
 
||Cursor on the Jmol panel
 
||Cursor on the Jmol panel
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||Cursor on the Console.
 
||Cursor on the Console.
 
||As shown on the Console:
 
||As shown on the Console:
 +
 
The structure on the panel  is for '''Human Pancreatic Glucokinase''' along with substrate '''Glucose'''.
 
The structure on the panel  is for '''Human Pancreatic Glucokinase''' along with substrate '''Glucose'''.
 
Close the Console.
 
Close the Console.
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||Remove the '''water molecules''' from the '''protein model''' on the panel.  
 
||Remove the '''water molecules''' from the '''protein model''' on the panel.  
  
−
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'''.  
 
|-
 
|-
 
||'''Slide Number 6'''
 
||'''Slide Number 6'''
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Hexokinase'''
 
Hexokinase'''
 
|| Active-site  for '''hexokinase''' has 3 amino acid residues:
 
|| Active-site  for '''hexokinase''' has 3 amino acid residues:
−
* Aspergine at 204,
+
* '''Aspergine''' at 204,
−
* Aspergine at position 231 and
+
* '''Aspergine''' at position 231 and
−
* Glutamic acid at 256.
+
* '''Glutamic acid''' at 256.
  
 
'''Alpha-D-Glucose''' is the substrate for this enzyme.
 
'''Alpha-D-Glucose''' is the substrate for this enzyme.
 
|-
 
|-
 
||Cursor on Jmol panel.
 
||Cursor on Jmol panel.
−
||Cursor on Jmol panel.
+
||Now let us go back to the Jmol panel.
 
|-
 
|-
 
||Cursor on Jmol panel with the model of '''hexokinase'''
 
||Cursor on Jmol panel with the model of '''hexokinase'''
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|-
 
|-
 
||Exit the pop-up menu.
 
||Exit the pop-up menu.
−
||We can modify the display of the enzyme to easily locate the substrate binding site.`
+
||We can modify the display of enzyme to easily locate the substrate binding site.`
 
|-
 
|-
 
||Cursor on the panel.
 
||Cursor on the panel.
 
||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.
 
|-
 
|-
−
||Open the Pop-up menu.
+
||Open the pop-up menu.
 
Scroll down the '''Protein''' option.
 
Scroll down the '''Protein''' option.
 
Click on '''All''' option.
 
Click on '''All''' option.
 +
||Open the pop-up menu, go to '''Select''', and scroll down to '''Protein''' option.
 +
Click on '''All'''.
 +
|- 
 +
||Open the Pop-up menu again, scroll down to '''Style''', then to '''Scheme'''.
 +
Click on '''Sticks''' option.
 
||Open the pop-up menu again, scroll down to '''Style''', then to '''Scheme'''.
 
||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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|-
 
|-
 
||Open pop-up menu, Scroll down to '''Color''', go to '''Atoms''', click on '''Blue''' option.
 
||Open pop-up menu, Scroll down to '''Color''', go to '''Atoms''', click on '''Blue''' option.
−
||Open the pop-up menu again, go to '''Color''', '''Atoms''', click on '''Blue''' option.
+
||Open the pop-up menu again, go to '''Color''', '''Atoms''', and click on '''Blue''' option.
 
|-
 
|-
 
||Cursor on the panel
 
||Cursor on the panel
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||Cursor on the panel.
 
||Cursor on the panel.
 
||As mentioned earlier the amino acids involved at the active-site are  
 
||As mentioned earlier the amino acids involved at the active-site are  
−
'''Aspergine''' at position 204
+
 
−
'''Aspergine''' at position 231 and
+
'''Aspergine''' at position 204  
−
'''Glutamic acid''' at 256  
+
 
 +
'''Aspergine''' at position 231 and  
 +
 
 +
'''Glutamic acid''' at 256.
 
|-
 
|-
 
||Open the file menu, scroll down to '''Console''' and click on it.  
 
||Open the file menu, scroll down to '''Console''' and click on it.  
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Press enter key on the keyboard.
 
Press enter key on the keyboard.
 
||At the $ prompt type:
 
||At the $ prompt type:
−
select within square brackets Asn for '''aspergine'' close the bracket, 204 i.e the position semicolon color atoms orange.
+
'''select within square brackets Asn for aspergine close the bracket, 204 i.e the position semicolon color atoms orange'''.
 
Press enter.
 
Press enter.
 
|-
 
|-
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||'''Slide Number 9
 
||'''Slide Number 9
 
Summary'''  
 
Summary'''  
−
||* Highlight substrate and cofactors of the enzyme.  
+
||
 +
* Highlight substrate and cofactors of the enzyme.  
 
* And View '''ramachandran''' plot for  proteins.
 
* And View '''ramachandran''' plot for  proteins.
 
|-
 
|-
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||As an Assignment:  
 
||As an Assignment:  
 
* Load the dot pdb file of enzyme '''Lysozyme''' on  Jmol panel.
 
* Load the dot pdb file of enzyme '''Lysozyme''' on  Jmol panel.
 +
 
* Highlight the substrate bound to the enzyme.
 
* Highlight the substrate bound to the enzyme.
 +
 
* Highlight the amino acids at the active site.
 
* Highlight the amino acids at the active site.
−
Hint: Get the '''pdb file''' of ''Lysozyme'''  from  '''PDB database'''.  
+
 
 +
Hint: Get the '''pdb''' file of '''Lysozyme'''  from  '''PDB database'''.  
 
|-   
 
|-   
 
||'''Slide Number11
 
||'''Slide Number11
 +
 
Acknowledgement'''
 
Acknowledgement'''
 
||Watch the video available at this URL.
 
||Watch the video available at this URL.
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||'''Slide Number 12'''
 
||'''Slide Number 12'''
 
|| The Spoken Tutorial Project Team:  
 
|| The Spoken Tutorial Project Team:  
 +
 
Conducts workshops and distributes certificates.
 
Conducts workshops and distributes certificates.
  
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||'''Slide number 13'''
 
||'''Slide number 13'''
 
|| Spoken Tutorial Project is a part of the Talk to a Teacher project.  
 
|| Spoken Tutorial Project is a part of the Talk to a Teacher project.  
 +
 
It is supported by the National Mission on Education through ICT, MHRD, Government of India.
 
It is supported by the National Mission on Education through ICT, MHRD, Government of India.
 
   
 
   

Latest revision as of 15:23, 28 October 2020

Visual Cue Narration
Slide Number 1

Title Slide

Hello everyone.

Welcome to this tutorial on 3D Models of Enzymes in Jmol .

Slide Number 2

Learning Objectives

In this tutorial, we will learn to
  • Load structure of Human Pancreatic Hexokinase on Jmol panel.
  • Modify the display of secondary structure .
  • Highlight amino acid residues at the active site.
Slide Number 3

Learning Objectives

  • Highlight substrate and cofactors of the enzyme.
  • And view Ramachandran plot for protein
Slide Number 4

Pre-requisites

To follow this tutorial you should have Knowledge of basic biochemistry.

And familiar with basic operations from Jmol Application window.

Please view the tutorial Proteins and Macromolecules in the Jmol Application series.

It is available at the following link.

Slide Number 5

System Requirement

To record this tutorial I am using,
  • Ubuntu Operating System version 12.04 .
  • Jmol version 12.2.2.
  • Java version 7. and
  • Mozilla Firefox browser 22.0
Cursor on the panel. Open the Jmol window and load the structure of hexokinase enzyme.
Cursor on the panel. I am connected to internet, so I will load the structure directly from the PDB website.
Open File menu, Scroll down to Get PDB. To do so,

Open the File menu, scroll down and click on Get PDB option.

Cursor on input box.

Type 3IDH in the text box.

An Input dialog box appears on the screen. Type the four letter PDB code for hexokinase, that is 3IDH in the text box.
Cursor on the Jmol panel This code was obtained from the Protein Data Bank website.
Click on open a file option. If you do not have a working Internet connection: Open the existing pdb file using open a file icon on the tool bar.
Click on OK button. Click on OK button.
Cursor on the panel. 3D Structure of hexokinase also known as glucokinase opens on the screen.
Open File menu and click on Console option. Open the console window using the File menu.
Cursor on the Console. As shown on the Console:

The structure on the panel is for Human Pancreatic Glucokinase along with substrate Glucose. Close the Console.

Cursor on the panel On the panel we have the ball and stick model of hexokinase.
Cursor on the panel. Remove the water molecules from the protein model on the panel.

This process is explained in detail in the Jmol tutorial Proteins and macromolecules.

Slide Number 6

Hexokinase

About hexokinase Enzyme.
  • Hexokinase is a monomeric protein of 465 amino acids.
  • It has two domains, a large domain and a small domain.
  • The active-site for this enzyme is located in the cleft between the two domains.
Slide Number 7

Hexokinase

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

Alpha-D-Glucose is the substrate for this enzyme.

Cursor on Jmol panel. Now let us go back to the Jmol panel.
Cursor on Jmol panel with the model of hexokinase We can select and highlight the components of enzymes like :
  • Substrate
  • Cofactors or
  • Amino acid residues at the active site.
Right-click to open the pop-up menu.

Go to Select option.

To select a particular component

Open the pop-up menu using the right click. Scroll down to Select option.

From the drop down select Proteins option.

From the submenu select By Residue name option. Point to the amino acid residues in the list.

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

We have individual amino acid residues listed here. Click on the name of the amino acid to select it.

Scroll down the submenu for the Protein option. Also amino acids are grouped under headings like:

Polar, Non-polar, Basic, Acidic, Uncharged etc.

From the Select menu

Go to Hetero menu, select By HETATM option. Show K-Potassium and GLU-Alfa-D-glucose.

Listed in the Hetero menu, are the metal ion potassium and substrate glucose.
Exit the pop-up menu. We can modify the display of enzyme to easily locate the substrate binding site.`
Cursor on the panel. Let us change the display and color of the atoms of the protein.
Open the pop-up menu.

Scroll down the Protein option. Click on All option.

Open the pop-up menu, go to Select, and scroll down to Protein option.

Click on All.

Open the Pop-up menu again, scroll down to Style, then to Scheme.

Click on Sticks option.

Open the pop-up menu again, scroll down to Style, then to Scheme.

And click on Sticks option.

Cursor on the panel. Now we have on the panel the protein in sticks display

Now to change the color.

Open pop-up menu, Scroll down to Color, go to Atoms, click on Blue option. Open the pop-up menu again, go to Color, Atoms, and click on Blue option.
Cursor on the panel We have on the screen the model of hexokinase in blue color and in sticks display
Point out to glucose molecule Observe the substrate, Alfa-D-Glucose in ball and stick display in the cleft.
Open the pop-up menu, go to Select option and scroll down to Hetero.

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.

Open the pop-up menu, scroll down to Style, select Sticks option. Open the pop-up menu again , scroll down to Style, Scheme and click on Sticks option.
Open the pop-up menu, scroll down to Color, then 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.

Cursor on the panel. On panel is the model of hexokinase with position of the substrate clearly highlighted.
Cursor on the panel. We can change the color of the amino acids at the active site to highlight them.

To do so, we have to type commands in the Console window.

Cursor on the panel. 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.

Open the file menu, scroll down to Console and click on it. Open the console window using File menu. Click on Console.

I am using Kmag Screen magnifier to magnify the console window.

At the $ prompt type “select [Asn]204; color atoms orange

Press enter key on the keyboard.

At the $ prompt type:

select within square brackets Asn for aspergine close the bracket, 204 i.e the position semicolon color atoms orange. Press enter.

Cursor on the panel. Observe that the atoms of aspargine residue now in orange color.
Press the up arrow button on the key board.

Delete 204 and type 231

Press up arrow button on the key board.

And edit the command. Edit the amino acid position to 231 and color of atoms to red.

Delete orange and type red. Press Enter
Press up arrow key .

Delete ASN. Type GLU. Edit the position number to 256. Press enter key.

Press up arrow key and again and edit name of amino acid to GLU, that is glutamic acid and position to 256.

And color of atoms to green. Press Enter .

Cursor on the panel We have on the panel a 3D model of hexokinase with substrate and the active site highlighted.
Point at the Potassium ion.

Select potassium (K) from the Select menu and change the color to yellow.

Also highlighted in the model is the potassium atom.

Shown here in purple color.

Cursor on panel. We can also show ramachandran plots for a particular protein in jmol.
Open the console, at the $ prompt type plot ramachandran .

Press Enter key.

On the console, at the $ prompt type plot ramachandran

Press Enter .

Cursor on the panel On the screen we have a ramachandran plot for hexokinase.
Cursor on the panel Try to load different enzymes using pdb files from the database.

Change the display of secondary structure

Slide Number 8

Summary

Lets summarize, In this tutorial we learnt to,
  • Load structure of Human Pancreatic Hexokinase using PDB code.
  • Modify the display of secondary structure.
  • Highlight amino acid residues at the active site.
Slide Number 9

Summary

  • Highlight substrate and cofactors of the enzyme.
  • And View ramachandran plot for proteins.
Slide Number 10

Assignment

As an Assignment:
  • Load the dot pdb file of enzyme Lysozyme on Jmol panel.
  • Highlight the substrate bound to the enzyme.
  • Highlight the amino acids at the active site.

Hint: Get the pdb file of Lysozyme from PDB database.

Slide Number11

Acknowledgement

Watch the video available at this URL.

It summarizes the Spoken Tutorial project.

If you do not have a good bandwidth, you can download and watch it.

Slide Number 12 The Spoken Tutorial Project Team:

Conducts workshops and distributes certificates.

For more details, please write to us.

Slide number 13 Spoken Tutorial Project is a part of the Talk to a Teacher project.

It is supported by the National Mission on Education through ICT, MHRD, Government of India.

More information on this Mission is available at this link

This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Snehalathak

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