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

||* Highlight '''amino acid residue'''s at the active site.       

||* Highlight '''substrate''' and '''cofactor'''s of the enzyme.

|| To follow this tutorial, you should have knowledge of basic biochemistry

||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.   

|| '''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'''.

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

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

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

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

||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'''.`

|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.

||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, '''Aspergine''' at position 231 and '''Glutamic acid''' at 256.  

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

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

||Edit the amino acid position to '''231''' and color of atoms to red.

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

|| 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.  

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

||Let's summarize. In this tutorial we learnt to: * '''Load''' structure of '''Human Pancreatic Hexokinase''' using PDB code.

||* Highlight '''amino acid residue'''s at the active site.

||* Highlight '''substrate''' and '''cofactor'''s 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.