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

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{| border=1
{| style="border-spacing:0;"
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|| '''Visual Cue'''
! <center>Visual Cue</center>
+
|| '''Narration'''
! <center>Narration</center>
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 1'''
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||'''Slide Number 1
 
+
Title Slide'''
'''Title Slide'''
+
||Hello everyone.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Hello everyone.
+
Welcome to this tutorial on '''3D Models of Enzymes in Jmol '''.  
 
+
Welcome to this tutorial on '''3D Models of Enzymes''' in '''Jmol'''.
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 2'''
+
||'''Slide Number 2
 
+
Learning Objectives'''
'''Learning Objectives'''
+
|| In this tutorial, we will learn to  
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will learn to
+
* Load structure of '''Human Pancreatic Hexokinase''' on '''Jmol panel'''.
 
+
* Load structure of '''Human Pancreatic Hexokinase''' on '''Jmol panel. '''
+
 
* Modify the display of secondary structure .
 
* Modify the display of secondary structure .
* Highlight amino acid residues at the active site.
+
* Highlight amino acid residues at the active site.      
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 3'''
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||'''Slide Number 3
 
+
Learning Objectives'''
'''Learning Objectives'''
+
||  
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * 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              
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 4'''
+
||'''Slide Number 4
 
+
Pre-requisites'''
'''Pre-requisites'''
+
|| To follow this tutorial you should have Knowledge of basic biochemistry.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should have  
+
 
+
And familiar with basic operations from '''Jmol Application window'''.
Knowledge of basic biochemistry.
+
     
 
+
Please view the tutorial '''Proteins and Macromolecules''' in the Jmol Application series.
And familiar with basic operations from '''Jmol Application window.'''
+
     
 
+
It is available at the following link.
Please view the tutorial ''Proteins and Macromolecules' in the Jmol Application series.
+
 
+
Please view the tutorial ''Proteins and Macromolecules' in the Jmol Application series
+
 
+
 
+
 
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 5'''
+
||'''Slide Number 5
 
+
System Requirement'''
'''System Requirement'''
+
||To record this tutorial I am using,
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial, I am using
+
* '''Ubuntu''' Operating System version 12.04 .
 
+
* '''Jmol''' version 12.2.2.
* '''Ubuntu '''OS version. 12.04
+
* '''Java''' version 7. and
* '''Jmol v'''ersion 12.2.2
+
* '''Mozilla Firefox browser''' 22.0
* '''Java''' version 7 and  
+
* Mozilla firefox browser 22.0
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
+
||Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Open the Jmol window and load the structure of Hexokinase enzyme.
+
||Open the Jmol window and load the structure of '''hexokinase'''  enzyme.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
+
|| Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I am connected to internet, so I will load the structure directly from the PDB website.
+
||I am connected to '''internet''', so I will load the structure directly from the '''PDB website'''.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open File menu, Scroll down to Get PDB.
+
||Open '''File''' menu, Scroll down to '''Get PDB'''.  
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To do so,  
+
|| To do so,  
 
+
Open the '''File''' menu, scroll down and click on '''Get PDB''' option.
Open the '''File '''menu, scroll down and click on''' Get PDB option.'''
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on input box.
+
||Cursor on input box.
 
+
 
Type '''3IDH''' in the text box.
 
Type '''3IDH''' in the text box.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| An Input box appears on the screen.  
+
||An Input dialog box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''', that is '''3IDH''' in the text box.  
 
+
 
+
Type the four letter '''PDB code '''for '''hexokinase''', that is '''3IDH”''' in the text box.  
+
 
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the Jmol panel
+
||Cursor on the Jmol panel
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This code was obtained from the '''Protein Data Bank '''website.
+
||This code was obtained from the '''Protein Data Bank''' website.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “open a file option”
+
||Click on '''open a file''' option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| If you do not have a working Internet connection:
+
|| If you do not have a working Internet connection: Open the existing '''pdb''' file using '''open a file''' icon on the tool bar.
 
+
 
+
Open the existing '''pdb''' file using''' open a file '''icon on the tool bar.  
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''OK '''button.
+
||Click on '''OK''' button.
 
+
|| Click on '''OK''' button.
 
+
 
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''OK '''button.
+
 
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
+
||Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''3D Structure of hexokinase also known as glucokinase opens on the screen.'''
+
|| 3D Structure of '''hexokinase''' also known as '''glucokinase''' opens on the screen.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open File menu and click on Console option.
+
||Open File menu and click on Console option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Open the console window using the file menu.
+
|| Open the console window using the '''File''' menu.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the console window from the file menu.
+
||Cursor on the Console.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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.
 
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel
+
||Cursor on the panel
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| On the panel we have the ball and stick model of '''hexokinase'''.
+
||On the panel we have the ball and stick model of '''hexokinase'''.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
+
||Cursor on the panel.
 
+
||Remove the '''water molecules''' from the '''protein model''' on the panel.  
 
+
To remove water molecules:
+
 
+
Open the pop-up menu by right clicking on the panel.
+
 
+
Move the cursor on Select then Scroll down and select “Hetero” from the drop down select “All water” option.
+
 
+
Open the pop-up menu again and scroll down to '''Style,''' then '''Scheme, '''from the drop down select '''CPK''' option.
+
 
+
Open the pop-up menu again , scroll down to “Style”, then to “Atoms” from the drop down, select “Off” option.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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'''.
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 6'''
+
||'''Slide Number 6'''
 
+
 
+
 
'''Hexokinase'''
 
'''Hexokinase'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''About Hexokinase Enzyme.'''
+
||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.
* Hexokinase is a monomeric protein of 465 amino acids.<br/>
+
 
+
* 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.
+
 
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 7'''
+
||'''Slide Number 7
 
+
Hexokinase'''
'''Hexokinase'''
+
|| Active-site for '''hexokinase''' has 3 amino acid residues:
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Active-site for hexokinase has 3 amino acid residues:
+
* '''Aspergine''' at 204,
 
+
* '''Aspergine''' at position 231 and
* Aspergine at 204,  
+
* '''Glutamic acid''' at 256.
* Aspergine at position 231 and  
+
* Glutamic acid at 256.
+
  
 
'''Alpha-D-Glucose''' is the substrate for this enzyme.
 
'''Alpha-D-Glucose''' is the substrate for this enzyme.
 
 
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol panel.
+
||Cursor on Jmol panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now Let us now go back to the Jmol panel.
+
||Now let us go back to the Jmol panel.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol panel with the model of Hexokinase.
+
||Cursor on Jmol panel with the model of '''hexokinase'''
 
+
||We can select and highlight the components of enzymes like :
 
+
Display the model with “spin on”
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can select and highlight the components of enzymes like :
+
 
+
 
* Substrate
 
* Substrate
* Cofactors or  
+
* Cofactors or
* Amino acid residues at the active site.<br/>
+
* Amino acid residues at the active site.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Right-click to open the pop-up menu.
+
|| Right-click to open the pop-up menu.
 
+
Go to '''Select''' option.
Go to 'Select' option.  
+
||To select a particular component
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To select a particular component:
+
Open the pop-up menu using the right click.  
 
+
Scroll down to '''Select''' option.
* Open the '''pop-up '''menu using the right click.  
+
* Scroll down to '''Select''' option.
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| From the drop down select''' Proteins''' option.  
+
||From the drop down select '''Proteins''' option.  
 
+
From the submenu select '''By Residue name''' option.
From the submenu '''select “By Residue name” '''option.
+
 
+
 
Point to the amino acid residues in the list.  
 
Point to the amino acid residues in the list.  
 
+
||From the sub-menu, '''Proteins''', select '''By Residue name'''.
For the reviewers
+
We have individual amino acid residues listed here.
 
+
Click on the name of the amino acid to select it.
Only show and do not click on the name of the “'''amino acid'''”
+
 
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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.
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the submenu for the '''Protein''' option.
+
||Scroll down the submenu for the '''Protein''' option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Also amino acids are grouped under headings like:
+
||Also amino acids are grouped under headings like:
 
+
'''Polar''', '''Non-polar''', '''Basic''', '''Acidic''', '''Uncharged''' etc.
 
+
'''Polar, Non-polar, Basic, Acidic, Uncharged''' etc.
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| From the “select menu”
+
||From the '''Select''' menu
 
+
Go to '''Hetero''' menu, select By '''HETATM''' option. Show '''K-Potassium and GLU-Alfa-D-glucose'''.
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'''.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Listed in the '''Hetero''' menu, are the metal ion '''potassium''' and '''substrate glucose'''.
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Exit the pop-up menu.
+
||Exit the pop-up menu.
 
+
||We can modify the display of enzyme to easily locate the substrate binding site.`
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can modify the display of the '''enzyme''' to easily locate the '''substrate''' binding site.
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
+
||Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| 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.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Open the pop-up menu, go to''' Select''', and scroll down to '''Protein''' option.  
+
||Open the pop-up menu, go to '''Select''', and scroll down to '''Protein''' option.
 
+
 
+
 
Click on '''All'''.
 
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.
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the pop-up menu again,go to Style, then to Scheme.
+
||Cursor on the panel.
 
+
||Now we have on the panel the protein in '''sticks''' display
Click on Sticks option.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Open the pop-up menu again, scroll down to '''Style, '''then to '''Scheme'''.
+
 
+
 
+
And click on '''Sticks''' option.
+
 
+
|-
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now we have on the panel the protein in sticks display
+
 
+
 
Now to change the color.
 
Now to change the color.
 
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| 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.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
+
||Cursor on the panel
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Point out to glucose molecule.
+
||Point out to glucose molecule
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the pop-up menu, go to Select option and scroll down to Hetero.
+
||Open the pop-up menu, go to '''Select''' option and scroll down to '''Hetero'''.
 
+
Click on '''GLC-Alfa-D-glucose'''.
Click on GLC-Alfa-D-glucose
+
||To highlight the substrate.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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, go to '''Select,''' then''' Hetero and '''click on '''GLC-ALFA-D-GLUCOSE'''.
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the pop-up menu, scroll down to '''Style''', select '''Sticks''' option.
+
||Open the pop-up menu, scroll down to '''Style''', select '''Sticks''' option.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Open the pop-up menu again , scroll down to '''Style''', '''Scheme and '''click on '''Sticks''' option.
+
||Open the pop-up menu again , scroll down to '''Style''', '''Scheme''' and  click on '''Sticks''' option.
  
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the pop-up menu, scroll down to''' Color''', then '''Atoms''' and click on '''White''' option.  
+
||Open the pop-up menu, scroll down to Color, then Atoms and click on White option.  
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To change the color:
+
||To change the color:
 
+
Open the pop-up menu again, go down to '''Color''', '''Atoms''' and click on '''White''' option.  
Open the pop-up menu again, go down to''' Color''',, '''Atoms''' and click on '''White''' option.  
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Set the model to spin.
+
||Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| On panel is the model of '''hexokinase''' with position of the substrate clearly highlighted.
+
||On panel is the model of '''hexokinase''' with position of the substrate clearly highlighted.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel
+
||Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can change the color of the amino acids at the active site to highlight them.
+
||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.
To do so, we have to type commands in the console window.
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
+
||Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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 204  
  
Aspergine at position 231 and
+
'''Aspergine''' at position 231 and  
 
+
Glutamic acid at 256
+
  
 +
'''Glutamic acid''' at 256.
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the file menu, scroll down to console and click on it.  
+
||Open the file menu, scroll down to '''Console''' and click on it.  
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Open the console window using file menu. Click on C'''onsole.'''
+
|| Open the console window using '''File menu'''. Click on '''Console'''.
 
+
I am using '''Kmag''' Screen magnifier to magnify the console window.
I am using Kmag Screen magnifier to magnify the console window.
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| At the $ prompt type “select [Asn]204; color atoms orange
+
||At the $ prompt type “select [Asn]204; color atoms orange
 
+
 
+
 
Press enter key on the keyboard.
 
Press enter key on the keyboard.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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.
 
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
+
||Cursor on the panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe that the atoms of Aspargine residue now in orange color.
+
||Observe that the atoms of '''aspargine''' residue now in orange color.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press the up arrow button on the key board.
+
||Press the up arrow button on the key board.
 
+
 
+
 
Delete 204 and type 231
 
Delete 204 and type 231
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Press up arrow button on the key board.
+
||Press up arrow button on the key board.
 
+
 
And edit the command.
 
And edit the command.
 
 
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.
 
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Delete orange and type red.
+
||Delete orange and type red.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Press '''Enter .'''
+
||Press Enter
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press up arrow key .
+
||Press up arrow key .
 
+
 
Delete ASN. Type GLU.
 
Delete ASN. Type GLU.
 
 
Edit the position number to 256.
 
Edit the position number to 256.
 
 
Press enter key.
 
Press enter key.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Press up arrow key and again and edit name of amino acid to GLU, that is glutamic acid and position to 256.
+
||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.  
 
And color of atoms to green.  
 
+
Press Enter .  
Press '''Enter '''.
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel  
+
||Cursor on the panel  
 
+
|| We have on the panel a 3D model of '''hexokinase''' with substrate and the active site highlighted.
 
+
|-
Set the model to spin.
+
||Point at the Potassium ion.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We have on the panel a 3D model of h'''exokinase''' with substrate and the active site highlighted.
+
 
+
|-
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Point at the Potassium ion.  
+
 
+
 
Select potassium (K) from the Select menu and change the color to yellow.
 
Select potassium (K) from the Select menu and change the color to yellow.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Also highlighted in the model is the '''potassium''' atom.  
+
||Also highlighted in the model is the '''potassium''' atom.  
 
+
 
Shown here in purple color.  
 
Shown here in purple color.  
 
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol.
+
||Cursor on panel.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also show '''Ramachandran plots '''for a particular protein in jmol.  
+
||We can also show '''ramachandran plots''' for a particular protein in jmol.  
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the console, at the $ prompt write “plot ramachandran” .
+
||Open the console, at the $ prompt type '''plot ramachandran''' .
 
+
 
Press Enter key.  
 
Press Enter key.  
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| On the console, at the $ prompt type '''plot ramachandran '''
+
||On the console, at the $ prompt type '''plot ramachandran'''  
 
+
 
+
 
Press Enter .  
 
Press Enter .  
 
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
+
||Cursor on the panel
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| On the screen we have a '''ramachandran plot '''for '''hexokinase'''.
+
||On the screen we have a '''ramachandran plot''' for '''hexokinase'''.
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
+
||Cursor on the panel
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Try to load different enzymes using pdb files from the database.
+
||Try to load different enzymes using '''pdb files''' from the database.
 
+
Change the display of secondary structure
Change the display of secondary structure.
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 8'''
+
||'''Slide Number 8
 
+
Summary'''  
Summary
+
||Lets summarize, In this tutorial we learnt to,
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Lets summarize, In this tutorial we learnt to,
+
 
+
 
+
 
* Load structure of Human Pancreatic Hexokinase using PDB code.
 
* Load structure of Human Pancreatic Hexokinase using PDB code.
 
* Modify the display of secondary structure.
 
* Modify the display of secondary structure.
 
+
* Highlight amino acid residues at the active site.
* Highlight amino acid residues at the active site.<br/>
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 9'''
+
||'''Slide Number 9
 
+
Summary'''  
'''Summary '''
+
||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * 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.<br/>
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 10'''
+
||'''Slide Number 10
 +
Assignment'''
 +
||As an Assignment:
 +
* Load the dot pdb file of enzyme '''Lysozyme''' on  Jmol panel.
  
Assignment
+
* Highlight the substrate bound to the enzyme.
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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.
 
* 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
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 11'''
+
 
+
'''Acknowledgement '''
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Watch the video available at this URL.
+
  
 +
Acknowledgement'''
 +
||Watch the video available at this URL.
  
 
It summarizes the Spoken Tutorial project.
 
It summarizes the Spoken Tutorial project.
  
 
+
If you do not have a good bandwidth, you can download and watch it.
If you do not have a good bandwidth, you can download and watch it.  
+
 
+
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 12'''
+
||'''Slide Number 12'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The Spoken Tutorial Project Team:  
+
|| The Spoken Tutorial Project Team:  
  
 
Conducts workshops and distributes certificates.
 
Conducts workshops and distributes certificates.
  
 
For more details, please write to us.
 
For more details, please write to us.
 
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 13'''
+
||'''Slide number 13'''
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| 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.
 
+
 
More information on this Mission is available at this link  
 
More information on this Mission is available at this link  
  
 +
This is '''Snehalatha''' from '''IIT Bombay''' signing off. Thank you for joining.
 
|-
 
|-
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"|
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This is Snehalatha from IIT Bombay signing off. Thank you for joining.
 
 
 
|}
 
|}

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