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

Time	Narration
00:01	Hello everyone. Welcome to this tutorial on 3D Models of Enzymes in Jmol .
00:08	In this tutorial, we will learn to: * Load structure of Human Pancreatic Hexokinase on Jmol panel.
00:16	* Modify the display of secondary structure .
00:20	* Highlight amino acid residues at the active site.
00:25	* Highlight substrate and cofactors of the enzyme.
00:30	* And view Ramachandran plot for protein.
00:35	To follow this tutorial, you should have knowledge of basic biochemistry
00:41	and familiar with basic operations from Jmol Application window.
00:46	Please view the tutorial Proteins and Macromolecules in the Jmol Application series.
00:53	It is available at the following link.
00:57	To record this tutorial, I am using: * Ubuntu Operating System version 12.04
01:05	* Jmol version 12.2.2.
01:08	* Java version 7. and * Mozilla Firefox browser 22.0.
01:16	Open the Jmol window and load the structure of hexokinase enzyme.
01:22	I am connected to internet. So, I will load the structure directly from the PDB website.
01:28	To do so, open the File menu, scroll down and click on Get PDB option.
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.
01:50	This code was obtained from the Protein Data Bank website.
01:55	If you do not have a working internet connection: Open the existing pdb file using Open a file icon on the tool bar.
02:06	Click on OK button.
02:09	3D structure of hexokinase also known as glucokinase opens on the screen.
02:16	Open the Console window using the File menu.
02:21	As shown on the Console, the structure on the panel is for Human Pancreatic Glucokinase along with substrate Glucose.
02:31	Close the Console.
02:34	On the panel, we have the ball and stick model of hexokinase.
02:40	Remove the water molecules from the protein model on the panel.
02:44	This process is explained in detail in the Jmol tutorial Proteins and macromolecules.
02:53	About hexokinase Enzyme-
02:56	Hexokinase is a monomeric protein of 465 amino acids.
03:02	It has two domains, a large domain and a small domain.
03:07	The active-site for this enzyme is located in the cleft between the two domains.
03:14	Active-site for hexokinase has 3 amino acid residues: Aspergine at 204, Aspergine at position 231 and Glutamic acid at 256.
03:30	Alpha-D-Glucose is the substrate for this enzyme.
03:34	Now, let us go back to the Jmol panel.
03:38	We can select and highlight the components of enzymes like : Substrate, Cofactors or Amino acid residues at the active site.
03:49	To select a particular component- Open the pop-up menu using the right-click.
03:55	Scroll down to Select option.
03:57	From the sub-menu, Proteins, select By Residue name.
04:04	We have individual amino acid residues listed here.
04:10	Click on the name of the amino acid to select it.
04:14	Also, amino acids are grouped under headings like: Polar, Non-polar, Basic, Acidic, Uncharged etc.
04:26	Listed in the Hetero menu, are the metal ion potassium and substrate glucose.
04:34	We can modify the display of enzyme to easily locate the substrate binding site.`
04:41	Let us change the display and color of the atoms of the protein.
04:46	Open the pop-up menu, go to Select and scroll down to Protein option. Click on All.
04:55	Open the pop-up menu again, scroll down to Style, then to Scheme. And click on Sticks option.
05:05	Now we have, on the panel, the protein in sticks display.
05:11	Now, to change the color- open the pop-up menu again, go to Color, Atoms and click on Blue option.
05:23	We have, on the screen, the model of hexokinase in blue color and in sticks display.
05:30	Observe the substrate Alfa-D-Glucose in ball and stick display in the cleft.
05:38	To highlight the substrate- open the pop-up menu, go to Select, then Hetero and click on GLC-ALFA-D-GLUCOSE.
05:52	Open the pop-up menu again, scroll down to Style, Scheme and click on Sticks option.
06:00	To change the color- open the pop-up menu again, go down to Color, Atoms and click on White option.
06:12	On panel is the model of hexokinase with position of the substrate clearly highlighted.
06:20	We can change the color of the amino acids at the active site to highlight them.
06:26	To do so, we have to type commands in the Console window.
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.
06:50	Open the console window using File menu. Click on Console.
06:57	I am using Kmag Screen magnifier to magnify the console window.
07:03	At the $ (dollar) prompt, type: "select" within square brackets "Asn" for aspergine close the bracket, "204" i.e the position semicolon "color atoms orange".
07:25	Press Enter.
07:27	Observe that the atoms of aspargine residue now in orange color.
07:33	Press up-arrow button on the key board and edit the command.
07:39	Edit the amino acid position to 231 and color of atoms to red.
07:48	Press Enter.
07:51	Press up-arrow key again and edit the name of the amino acid to GLU, that is, glutamic acid and position to 256.
08:06	Color of atoms to green and press Enter.
08:13	We have, on the panel, a 3D model of hexokinase with substrate and the active site highlighted.
08:23	Also highlighted in the model is the potassium atom shown here, in purple color.
08:30	We can also show ramachandran plots for a particular protein in jmol.
08:36	On the console, at the dollar($) prompt, type: plot ramachandran
08:45	press Enter.
08:47	On the screen, we have a ramachandran plot for hexokinase.
08:54	Try to load different enzymes using pdb files from the database.
09:00	Change the display of secondary structure.
09:04	Let's summarize. In this tutorial we learnt to: * Load structure of Human Pancreatic Hexokinase using PDB code.
09:14	* Modify the display of secondary structure.
09:17	* Highlight amino acid residues at the active site.
09:21	* Highlight substrate and cofactors of the enzyme.
09:25	And view ramachandran plot for proteins.
09:30	As an assignment: Load the dot pdb file of enzyme Lysozyme on Jmol panel.
09:38	Highlight the substrate bound to the enzyme.
09:42	Highlight the amino acids at the active site.
09:46	Hint: Get the pdb file of Lysozyme from PDB database.
09:52	Watch the video available at this URL.
09:56	It summarizes the Spoken Tutorial project.
10:00	If you do not have a good bandwidth, you can download and watch it.
10:04	The Spoken Tutorial Project team
10:07	conducts workshops and distributes certificates.
10:10	For more details, please write to us.
10:14	Spoken Tutorial project is a part of the Talk to a Teacher project.
10:19	It is supported by the National Mission on Education through ICT, MHRD, Government of India.
10:25	More information on this mission is available at this link.
10:30	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14