Difference between revisions of "Jmol-Application/C2/Proteins-and-Macromolecules/English-timed"
From Script | Spoken-Tutorial
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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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| This is the web page of '''Protein Data Bank.''' | | This is the web page of '''Protein Data Bank.''' | ||
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|* '''Structure Validation'''are available on this page. | |* '''Structure Validation'''are available on this page. | ||
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| From the sub-menu,choose '''Hetero'''and click on '''“All Water''' option. | | From the sub-menu,choose '''Hetero'''and click on '''“All Water''' option. | ||
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| This display shows the secondary structure of protein as '''helices, random coils, strands, sheets '''etc. | | This display shows the secondary structure of protein as '''helices, random coils, strands, sheets '''etc. | ||
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| Open the pop-up menu, select '''Style''', then '''Scheme''' and click on '''Ball and stick '''option. | | Open the pop-up menu, select '''Style''', then '''Scheme''' and click on '''Ball and stick '''option. | ||
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| '''The Hydrogen Bonds''' option in the Pop-up menu has features such as: | | '''The Hydrogen Bonds''' option in the Pop-up menu has features such as: | ||
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Revision as of 16:05, 14 August 2014
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, lets 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 hydrogens 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 Heteroand 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 Insulinstructure 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 | * To 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. |