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

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

|| 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.       

|| Highlight substrate and cofactors of the enzyme.

|| And view '''Ramachandran plot''' for protein  

|| 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.

||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

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

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

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

||An Input dialogue box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''',  that is '''3IDH'''  in the text box.  

|| 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.

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

|| Open the console window using the '''File''' menu.

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

||On the panel we have the ball and stick model of '''hexokinase'''.

||Remove the '''water molecules''' from the '''protein model''' on the panel.  

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

||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.

|| 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.

||Now let us go back to the Jmol panel.

||We can select and highlight the components  of  enzymes like :  Substrate, Cofactors or Amino acid residues at the active site.

||To select a particular component Open the pop-up menu using the right click.  

||We have individual amino acid residues listed here.

||Also amino acids are  grouped under headings like: '''Polar''', '''Non-polar''', '''Basic''', '''Acidic''', '''Uncharged''' etc.

||We can modify the display of enzyme to easily locate the substrate binding site.`

||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'''.

And click on '''Sticks''' option.  

||Now we have on the panel the protein in '''sticks''' display  

|Now to change the color, open the pop-up menu again, go to '''Color''', '''Atoms''', and click on '''Blue''' option.

||We have on the screen the model of '''hexokinase''' in blue color and in sticks display

||Observe the substrate, '''Alfa-D-Glucose''' in ball and stick display in the cleft.

||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 again , scroll down to '''Style''', '''Scheme''' and  click on '''Sticks''' option.

||To change the color, Open the pop-up menu again, go down to '''Color''', '''Atoms''' and click on '''White''' option.  

||On panel is the model of '''hexokinase''' with position of the substrate clearly highlighted.

||As mentioned earlier the amino acids involved at the active-site are '''Aspergine''' at position 204,  

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

||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.

||Observe that the atoms of  '''aspargine''' residue now in orange color.

||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.

||Press Enter

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

||Color of atoms to green and Press Enter .  

|| We have on the panel a 3D model of '''hexokinase''' with substrate and the active site highlighted.

||Also highlighted in the model is the '''potassium''' atom shown here in purple color.  

||On the console, at the $ prompt type  '''plot ramachandran'''  

||Press Enter .  

||On the screen we have a '''ramachandran plot''' for '''hexokinase'''.

||Try to load different enzymes using '''pdb files''' from the database.

||Change the display of secondary structure

||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.

||* Highlight substrate and cofactors of the enzyme.  

||And View '''ramachandran''' plot for  proteins.

||As an Assignment:  Load the dot pdb file of enzyme '''Lysozyme''' on Jmol panel.

||It summarizes the Spoken Tutorial project.

|| The Spoken Tutorial Project Team:

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|| Spoken Tutorial Project is a part of the Talk to a Teacher project.  

||More information on this Mission is available at this link  

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