Jmol-Application/C2/Proteins-and-Macromolecules/English-timed
From Script | Spoken-Tutorial
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. |
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. |
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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: |
11:31 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |