Jmol-Application/C2/Proteins-and-Macromolecules/English-timed

Time	Narration
00:01	Welcome to this tutorial on Proteins and Macromolecules.
00:06	In this tutorial, we will learn to:
00:09	* Load structures of proteins from Protein Data Bank (PDB)
00:13	* Download '.pdb' files from PDB database
00:18	* Display secondary structure of proteins in various formats
00:24	* Highlight hydrogen bonds and disulfide bonds.
00:29	To follow this tutorial, you should be familiar with basic operations from Jmol Application window.
00:37	If not, watch the relevant tutorials available at our website.
00:42	To record this tutorial, I am using:
00:46	* Ubuntu OS version 12.04
00:50	* Jmol version 12.2.2
00:54	* Java version 7
00:57	* Mozilla Firefox Browser 22.0.
01:02	Structure Analysis of large biomolecules such as-
01:06	* Proteins and Macromolecules
01:10	* Nucleic acids, DNA and RNA
01:13	* Crystal structures and polymers can be done using Jmol Application.
01:19	Here, I have opened a new Jmol window.
01:24	3D structures of biomolecules can be viewed by direct download from database.
01:29	To do so, click on File menu, scroll down to Get PDB.
01:36	An Input dialog-box appears on screen.
01:40	We have to type the four letter PDB code for the particular protein, in the Input box.
01:48	This code can be obtained from the Protein Data Bank (PDB) website.
01:53	This is the web-page of Protein Data Bank.
01:57	It has information about biomolecules such as proteins and nucleic acids.
02:04	As an example, let us try to find PDB code for Pancreatic Enzyme Insulin from the PDB website.
02:13	In the search box, type name of the protein as "human insulin". Press Enter key on the keyboard.
02:24	Now, on the web-page that is displayed, scroll down.
02:28	A list of known structures of Human Insulin along with the PDB codes appears on the screen.
02:36	As an example, let's select Human Insulin with a code 4EX1.
02:44	Click on the name of the protein.
02:47	A window opens with all the details of the structure.
02:52	Information like-
02:54	* Primary Citation
02:56	* Molecular Description and
02:58	* Structure Validationare available on this page.
03:02	We can save the structures of proteins as '.pdb' files and view them in 3D mode in Jmol.
03:12	Click on the Download Files link, located at the top right hand corner of the page.
03:20	From the drop-down menu, select PDB file (gz) option.
03:28	A dialog-box opens on the screen.
03:32	Select Save file option.
03:35	Click on OK button.
03:39	The structure of protein will be saved as 4EX1.pdb.gz, in the Downloads folder.
03:51	Similarly, you can download the required '.pdb' files of various proteins and save them in separate files.
04:02	Now, let's switch to Jmol window to view the 3D structure of Insulin.
04:09	If you are connected to internet, you can directly download the protein structure on Jmol panel.
04:15	Type the 4 letter PDB code “4EX1” in the text-box and click on OK button.
04:25	If you are not connected to internet then click on Open a File icon on the tool-bar.
04:34	A dialog-box opens on the panel.
04:38	Navigate to the location of 4EX1.pdb.gz file i.e. to Downloads folder.
04:47	Select Downloads folder and click on Open button.
04:52	Select 4EX1.pdb.gz file and click on Open button.
05:00	'3D' Structure of Insulin opens on screen.
05:05	The default display of the protein on the panel is ball and stick.
05:12	The model of protein on the panel is shown without hydrogen atoms.
05:17	To show the model with hydrogen atoms, open the modelkit menu.
05:23	Scroll down to add hydrogens option and click on it.
05:28	The model on the panel is now displayed with hydrogen atoms.
05:33	The protein structure is also shown with water molecules.
05:38	To hide the water molecules, follow the steps as shown.
05:43	First, open the pop-up menu and go to Select.
05:48	From the sub-menu, choose Hetero and click on “All Water option.
05:55	Open the pop-up menu again, go to Style >> Scheme and click on CPK spacefill option.
06:05	This will convert all the water molecules to CPK Spacefill display.
06:11	Open the pop-up menu again and go to Style, scroll down to Atoms and click on Off option.
06:22	Now on the panel, we have Insulin structure without any water molecules.
06:27	Next, let us learn to display the secondary structure of the protein in various formats.
06:35	Open the pop-up menu.
06:37	Go to Select option.
06:39	Scroll down to Protein and click on All option.
06:44	Open the pop-up menu again and scroll down to Style, then Scheme.
06:50	A sub-menu opens with options like CPK Spacefill, Ball and Stick, Sticks, Wireframe, cartoon, trace etc.
07:02	Click on Cartoon option from the sub-menu.
07:07	This display shows the secondary structure of protein as helices, random coils, strands, sheets etc.
07:17	For more display options-
07:19	Open the pop-up menu and scroll down to Style, then to Structures.
07:25	Here, we see many more options to display secondary structure of protein.
07:31	For example, click on Strands option.
07:35	The protein is now displayed as Strands on the panel.
07:40	To change the color of display: Open the Pop-up-menu. Scroll down to Color. select Atoms and click on Blue option.
07:52	Observe the change in color on the panel.
07:56	To convert the structure back to Ball-and-stick display:
07:59	Open the pop-up menu, select Style, then Scheme and click on Ball and stick option.
08:08	We can also highlight hydrogen bonds and di-sulpfide bonds in the protein model.
08:14	To display hydrogen bonds: Open the pop-up menu and scroll down to Style and then to Hydrogen Bonds option.
08:25	The Hydrogen Bonds option in the pop-up menu has features such as:
08:30	Calculate, Set Hydrogen Bonds Side Chain,
08:35	Set Hydrogen Bonds in the Backbone and also has options to change the thickness of the bonds.
08:42	Click on Calculate option to show the hydrogen bonds in the model.
08:47	The hydrogen bonds are displayed as white and red long dashes.
08:53	To change the thickness of hydrogen bonds, click on 0.10 A option from the pop-up-menu.
09:02	Now, on the panel, we can see thicker hydrogen bonds.
09:06	We can also change the color of hydrogen bonds.
09:11	From the Pop-up-menu, scroll down to Color, then Hydrogen Bonds, then click on orange option.
09:20	On the panel, we have all the hydrogen bonds in orange color.
09:25	Disulfide bonds and sulphur atoms are shown in the model, in yellow colour.
09:31	To modify the disulfide bonds, open the option disulfide bonds in the pop-up menu.
09:38	Click on the features you may want to change, like size, color etc.
09:44	Similarly, try to open '.pdb' files of different enzymes and view their 3D structures.
09:51	Let us summarize. In this tutorial, we have learnt to:
09:57	* Load structures of protein from Protein Data Bank (PDB).
10:00	* Download '.pdb' files from the database.
10:05	* View 3D structure of Insulin using PDB code.
10:10	* View Protein structure without water molecules.
10:14	* Display secondary structure in various formats.
10:17	* Highlight hydrogen bonds and disulfide bonds.
10:22	Here is an assignment for you-
10:24	* Download the '.pdb' file of Human Hemoglobin from PDB database.
10:31	* Show secondary structure in cartoon display.
10:35	* Highlight the “porphyrin” units of the protein.
10:39	* Refer the following link for the PDB code.
10:42	Watch the video available at this URL. http://spoken-tutorial.org/What_is_a_Spoken_Tutorial
10:46	It summarizes the Spoken Tutorial project.
10:50	If you do not have good bandwidth, you can download and watch it.
10:55	The Spoken Tutorial Project team:
10:57	* Conducts workshops using spoken tutorials.
11:01	* Gives certificates to those who pass an on-line test.
11:06	For more details, please write to: contact@spoken-tutorial.org
11:13	Spoken Tutorial Project is a part of the Talk to a Teacher project.
11:18	It is supported by the National Mission on Education through ICT, MHRD, Government of India.
11:25	More information on this mission is available at this link: http://spoken-tutorial.org/NMEICT-Intro.
11:31	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

Gaurav, PoojaMoolya, Pratik kamble, Sandhya.np14