Difference between revisions of "Jmol-Application/C2/Proteins-and-Macromolecules/English-timed"
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| − | |* Download | + | |* Download '.pdb' files from '''PDB''' database. |
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| − | |* '''Ubuntu '''OS version. 12.04 | + | |* '''Ubuntu '''OS version. '''12.04''' |
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| − | |* '''Jmol''' version 12.2.2 | + | |* '''Jmol''' version '''12.2.2''' |
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|00:54 | |00:54 | ||
| − | |* '''Java''' version 7 | + | |* '''Java''' version '''7''' |
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|00:57 | |00:57 | ||
| − | |* '''Mozilla Firefox '''Browser 22.0 | + | |* '''Mozilla Firefox '''Browser '''22.0'''. |
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| − | | To do so, click on '''File '''menu, scroll down to''' Get PDB.''' | + | | To do so, click on '''File '''menu, scroll-down to''' Get PDB.''' |
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| − | | An ''' | + | | An '''Input''' dialog-box appears on '''screen'''. |
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| − | | In the '''search box''' type name of the protein as | + | | In the '''search box''', type name of the protein as "Human Insulin". Press '''Enter''' key on the keyboard. |
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Revision as of 18:10, 8 February 2016
| 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 appear on 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 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 disulfide bonds, open the option disulfide bonds in pop menu. |
| 09:38 | Click on the features you may want to change, like size and 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. |
| 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. |
| 11:31 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |
