Difference between revisions of "Jmol-Application/C2/Proteins-and-Macromolecules/English-timed"
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− | | 00:01 | + | |00:01 |
|Welcome to this tutorial on '''Proteins and Macromolecules.''' | |Welcome to this tutorial on '''Proteins and Macromolecules.''' | ||
|- | |- | ||
− | | 00:06 | + | |00:06 |
− | | In this tutorial, we will learn to | + | |In this tutorial, we will learn to: |
|- | |- | ||
|00:09 | |00:09 | ||
− | | | + | |'''Load''' structures of '''protein'''s from '''Protein Data Bank (PDB)''' |
|- | |- | ||
|00:13 | |00:13 | ||
− | | | + | |Download '.pdb' files from '''PDB''' database |
|- | |- | ||
|00:18 | |00:18 | ||
− | | | + | |Display secondary structure of proteins in various formats |
|- | |- | ||
|00:24 | |00:24 | ||
− | | | + | |Highlight '''hydrogen bonds '''and '''disulfide bonds'''. |
|- | |- | ||
|00:29 | |00:29 | ||
− | | To follow this tutorial you should be familiar with basic operations from '''Jmol Application window.''' | + | |To follow this tutorial, you should be familiar with basic operations from '''Jmol Application window.''' |
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− | | 00:42 | + | |00:42 |
− | |To record this tutorial I am using | + | |To record this tutorial, I am using: |
|- | |- | ||
− | | 00:46 | + | |00:46 |
− | | | + | |'''Ubuntu '''OS version '''12.04''' |
|- | |- | ||
|00:50 | |00:50 | ||
− | | | + | |'''Jmol''' version '''12.2.2''' |
|- | |- | ||
|00:54 | |00:54 | ||
− | | | + | |'''Java''' version '''7''' |
|- | |- | ||
|00:57 | |00:57 | ||
− | | | + | |'''Mozilla Firefox Browser''' '''22.0'''. |
|- | |- | ||
− | | 01:02 | + | |01:02 |
− | | | + | |'''Structure Analysis''' of large biomolecules such as- |
|- | |- | ||
|01:06 | |01:06 | ||
− | | | + | |'''Proteins''' and '''Macromolecules''' |
|- | |- | ||
|01:10 | |01:10 | ||
− | | | + | |'''Nucleic acids, DNA''' and '''RNA''' |
|- | |- | ||
|01:13 | |01:13 | ||
− | | | + | |'''Crystal structures''' and '''polymers''' can be done using '''Jmol Application.''' |
|- | |- | ||
− | | 01:19 | + | |01:19 |
− | |Here I have opened a new '''Jmol''' | + | |Here, I have opened a new '''Jmol window'''. |
|- | |- | ||
− | | 01:24 | + | |01:24 |
− | | | + | |'''3D structure'''s of biomolecules can be viewed by direct download from database. |
|- | |- | ||
− | | 01:29 | + | |01:29 |
− | | To do so, click on '''File '''menu, scroll down to''' Get PDB.''' | + | |To do so, click on '''File '''menu, scroll down to''' Get PDB.''' |
|- | |- | ||
− | | | + | |01:36 |
− | | An | + | |An '''Input''' dialog-box appears on '''screen'''. |
|- | |- | ||
− | | 01:40 | + | |01:40 |
− | |We have to type the four letter '''PDB code''' for the particular '''protein,''' in the | + | |We have to type the four letter '''PDB code''' for the particular '''protein,''' in the '''Input''' box. |
|- | |- | ||
− | | 01:48 | + | |01:48 |
− | | This code can be obtained from the '''Protein Data Bank (PDB) '''website | + | |This code can be obtained from the '''Protein Data Bank (PDB) '''website. |
|- | |- | ||
− | | | + | |01:53 |
− | | This is the web page of '''Protein Data Bank.''' | + | |This is the web-page of '''Protein Data Bank.''' |
|- | |- | ||
− | | | + | |01:57 |
|It has information about biomolecules such as '''proteins''' and '''nucleic acids.''' | |It has information about biomolecules such as '''proteins''' and '''nucleic acids.''' | ||
|- | |- | ||
− | | 02:04 | + | |02:04 |
− | | As an example | + | |As an example, let us try to find '''PDB code '''for '''Pancreatic Enzyme Insulin '''from the '''PDB '''website. |
|- | |- | ||
|02:13 | |02:13 | ||
− | | 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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− | | 02:24 | + | |02:24 |
− | | Now, on the web-page that is displayed, scroll down. | + | |Now, on the web-page that is displayed, scroll down. |
|- | |- | ||
− | | 02:28 | + | |02:28 |
− | | A list of known structures of '''Human Insulin''' along with the '''PDB codes ''' | + | |A list of known structures of '''Human Insulin''' along with the '''PDB codes '''appears on the screen. |
|- | |- | ||
− | | 02:36 | + | |02:36 |
− | | As an example, let's select''' Human Insulin''' with a code '''4EX1.''' | + | |As an example, let's select''' Human Insulin''' with a code '''4EX1.''' |
|- | |- | ||
− | | | + | |02:44 |
|Click on the name of the protein. | |Click on the name of the protein. | ||
|- | |- | ||
− | | 02:47 | + | |02:47 |
− | | A window opens with all the details of the structure. | + | |A '''window''' opens with all the details of the structure. |
|- | |- | ||
− | | 02:52 | + | |02:52 |
− | | Information like | + | |Information like- |
|- | |- | ||
− | | 02:54 | + | |02:54 |
− | | | + | |'''Primary Citation''' |
|- | |- | ||
− | | 02:56 | + | |02:56 |
− | | | + | |'''Molecular Description '''and |
|- | |- | ||
|02:58 | |02:58 | ||
− | | | + | |'''Structure Validation'''are available on this page. |
|- | |- | ||
− | | 03:02 | + | |03:02 |
− | | We can save the structures of proteins as | + | |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. | + | |Click on the '''Download Files''' link, located at the top right hand corner of the '''page'''. |
|- | |- | ||
− | | 03:20 | + | |03:20 |
− | | From the drop down menu, select '''PDB file (gz) '''option | + | |From the drop-down menu, select '''PDB file (gz) '''option. |
|- | |- | ||
− | | 03:28 | + | |03:28 |
− | |A dialog box opens on the screen. | + | |A dialog-box opens on the screen. |
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− | | | + | |03:32 |
|Select '''Save file''' option. | |Select '''Save file''' option. | ||
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− | | 03:39 | + | |03:39 |
− | | The structure of protein will be saved as '''4EX1.pdb.gz | + | |The structure of '''protein''' will be saved as '''4EX1.pdb.gz''', in the '''Downloads '''folder. |
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− | | | + | |03:51 |
− | | Similarly, you can download the required | + | |Similarly, you can download the required '.pdb' files of various proteins and '''save''' them in separate files. |
|- | |- | ||
− | | 04:02 | + | |04:02 |
− | | Now, | + | |Now, let's switch to '''Jmol''' window to view the '''3D''' structure of '''Insulin'''. |
|- | |- | ||
|04:09 | |04:09 | ||
− | | If you are connected to | + | |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. | + | |Type the 4 letter '''PDB code “4EX1” '''in the text-box and click on '''OK''' button. |
|- | |- | ||
− | | 04:25 | + | |04:25 |
− | | If you are not connected to | + | |If you are not connected to internet then click on '''Open a File''' icon on the tool-bar. |
|- | |- | ||
− | | 04:34 | + | |04:34 |
− | | A dialog box opens on the panel. | + | |A dialog-box opens on the panel. |
|- | |- | ||
− | | | + | |04:38 |
|Navigate to the location of '''4EX1.pdb.gz''' file i.e. to '''Downloads '''folder. | |Navigate to the location of '''4EX1.pdb.gz''' file i.e. to '''Downloads '''folder. | ||
|- | |- | ||
− | | | + | |04:47 |
− | |Select '''Downloads''' folder and click on ''' | + | |Select '''Downloads''' folder and click on '''Open '''button. |
|- | |- | ||
− | | | + | |04:52 |
− | |Select '''4EX1.pdb.gz''' file and click on ''' | + | |Select '''4EX1.pdb.gz''' file and click on '''Open''' button. |
|- | |- | ||
− | | 05:00 | + | |05:00 |
− | | 3D Structure of Insulin opens on screen. | + | |'3D' Structure of Insulin opens on screen. |
|- | |- | ||
− | | 05:05 | + | |05:05 |
− | | The default display of the | + | |The default display of the protein on the panel is '''ball and stick.''' |
|- | |- | ||
− | | 05:12 | + | |05:12 |
− | | The model of protein on the panel is shown without | + | |The model of protein on the panel is shown without hydrogen atoms. |
|- | |- | ||
− | | 05:17 | + | |05:17 |
− | | To show the model with hydrogen atoms, open the '''modelkit''' menu. | + | |To show the model with hydrogen atoms, open the '''modelkit''' menu. |
|- | |- | ||
− | | | + | |05:23 |
|Scroll down to '''add hydrogens''' option and click on it. | |Scroll down to '''add hydrogens''' option and click on it. | ||
|- | |- | ||
− | | 05:28 | + | |05:28 |
− | | The model on the panel is now displayed with hydrogen atoms. | + | |The model on the panel is now displayed with hydrogen atoms. |
|- | |- | ||
− | | 05:33 | + | |05:33 |
− | | The '''protein''' structure is also shown with water molecules. | + | |The '''protein''' structure is also shown with water molecules. |
|- | |- | ||
− | | 05:38 | + | |05:38 |
− | | To hide the water molecules, follow the steps as shown. | + | |To hide the water molecules, follow the steps as shown. |
|- | |- | ||
− | | 05:43 | + | |05:43 |
− | | First open the pop-up menu and go to '''Select.''' | + | |First, open the pop-up menu and go to '''Select.''' |
|- | |- | ||
− | | 05:48 | + | |05:48 |
− | | From the sub-menu,choose '''Hetero'''and click on '''“All Water''' option. | + | |From the sub-menu, choose '''Hetero''' and click on '''“All Water''' option. |
|- | |- | ||
− | | 05:55 | + | |05:55 |
− | | Open the pop-up menu again, go to '''Style''' | + | |Open the pop-up menu again, go to '''Style''' >> '''Scheme '''and click on '''CPK spacefill '''option. |
|- | |- | ||
− | | 06:05 | + | |06:05 |
|This will convert all the water molecules to '''CPK Spacefill '''display. | |This will convert all the water molecules to '''CPK Spacefill '''display. | ||
|- | |- | ||
− | | 06:11 | + | |06:11 |
− | | Open the pop-up menu again and go to '''Style''' scroll down to '''Atoms '''and click on '''Off '''option. | + | |Open the pop-up menu again and go to '''Style''', scroll down to '''Atoms '''and click on '''Off '''option. |
|- | |- | ||
− | | 06:22 | + | |06:22 |
− | | Now on panel we have '''Insulin'''structure without any water molecules. | + | |Now on the panel, we have '''Insulin''' structure without any water molecules. |
|- | |- | ||
− | | 06:27 | + | |06:27 |
− | | Next, let us learn to display the secondary structure of the '''protein''' in various formats. | + | |Next, let us learn to display the secondary structure of the '''protein''' in various formats. |
|- | |- | ||
− | | | + | |06:35 |
− | |Open the pop-up menu. | + | |Open the '''pop-up menu'''. |
|- | |- | ||
− | | 06:37 | + | |06:37 |
− | | Go to '''Select '''option. | + | |Go to '''Select '''option. |
|- | |- | ||
− | | 06:39 | + | |06:39 |
− | | Scroll down to '''Protein '''and click on''' All '''option. | + | |Scroll down to '''Protein '''and click on''' All '''option. |
|- | |- | ||
− | | 06:44 | + | |06:44 |
− | |Open the pop-up menu again and scroll down to '''Style, '''then''' Scheme. ''' | + | |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 | + | |A sub-menu opens with options like '''CPK Spacefill''', '''Ball and Stick, Sticks, Wireframe, cartoon, trace''' etc. |
|- | |- | ||
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|07:07 | |07:07 | ||
− | | 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. |
|- | |- | ||
− | | 07:17 | + | |07:17 |
− | | For more display options | + | |For more display options- |
|- | |- | ||
− | | 07:19 | + | |07:19 |
− | | Open the pop-up menu and scroll down to '''Style,''' then to''' Structures'''. | + | |Open the pop-up menu and scroll down to '''Style,''' then to''' Structures'''. |
|- | |- | ||
− | | 07:25 | + | |07:25 |
− | | Here we see many more options to display secondary structure of protein. | + | |Here, we see many more options to display secondary structure of protein. |
|- | |- | ||
− | | 07:31 | + | |07:31 |
− | | For example click on '''Strands''' option. | + | |For example, click on '''Strands''' option. |
|- | |- | ||
− | | 07:35 | + | |07:35 |
− | | The protein is now displayed as '''Strands''' on the panel. | + | |The protein is now displayed as '''Strands''' on the panel. |
|- | |- | ||
− | | 07:40 | + | |07:40 |
− | | To change the color of display | + | |To change the color of display: Open the Pop-up-menu. Scroll down to '''Color'''. select '''Atoms''' and click on '''Blue''' option. |
|- | |- | ||
− | | 07:52 | + | |07:52 |
− | | Observe the change in color on the panel. | + | |Observe the change in color on the panel. |
|- | |- | ||
− | | 07:56 | + | |07:56 |
− | | To convert the structure back to '''Ball-and-stick''' display | + | |To convert the structure back to '''Ball-and-stick''' display: |
|- | |- | ||
− | | 07:59 | + | |07:59 |
− | | 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. |
|- | |- | ||
− | | 08:08 | + | |08:08 |
− | | We can also highlight '''hydrogen bonds '''and''' di-sulpfide bonds '''in the protein model. | + | |We can also highlight '''hydrogen bonds '''and''' di-sulpfide bonds '''in the '''protein model'''. |
|- | |- | ||
− | | 08:14 | + | |08:14 |
− | | To display '''hydrogen bonds''': Open the pop-up menu and scroll down to '''Style''' and then to '''Hydrogen Bonds''' option. | + | |To display '''hydrogen bonds''': Open the pop-up menu and scroll down to '''Style''' and then to '''Hydrogen Bonds''' option. |
|- | |- | ||
|08:25 | |08:25 | ||
− | | '''The Hydrogen Bonds''' option in the | + | | '''The Hydrogen Bonds''' option in the pop-up menu has features such as: |
|- | |- | ||
|08:30 | |08:30 | ||
− | |'''Calculate''', '''Set Hydrogen Bonds Side Chain | + | |'''Calculate''', '''Set Hydrogen Bonds Side Chain''', |
|- | |- | ||
|08:35 | |08:35 | ||
− | |'''Set Hydrogen Bonds in the Backbone | + | |'''Set Hydrogen Bonds in the Backbone''' and also has options to change the thickness of the bonds. |
− | + | ||
|- | |- | ||
− | | 08:42 | + | |08:42 |
− | | Click on '''Calculate''' option to show the '''hydrogen bonds''' in the model. | + | |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. | |The '''hydrogen bonds''' are displayed as white and red long dashes. | ||
|- | |- | ||
− | | 08:53 | + | |08:53 |
− | | To change the thickness of '''hydrogen bonds''', | + | |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'''. | + | |Now, on the panel, we can see thicker''' hydrogen bonds'''. |
|- | |- | ||
|09:06 | |09:06 | ||
− | | We can also change the color of hydrogen bonds. | + | |We can also change the color of hydrogen bonds. |
|- | |- | ||
− | | 09:11 | + | |09:11 |
− | | From the Pop-up-menu scroll down to '''Color''' then '''Hydrogen Bonds''' then click on '''orange''' option. | + | |From the Pop-up-menu, scroll down to '''Color''', then '''Hydrogen Bonds''', then click on '''orange''' option. |
|- | |- | ||
− | | 09:20 | + | |09:20 |
− | | On the panel, we have all the '''hydrogen bonds''' in orange color. | + | |On the panel, we have all the '''hydrogen bonds''' in orange color. |
|- | |- | ||
− | | 09:25 | + | |09:25 |
− | | | + | |'''Disulfide bonds''' and '''sulphur''' atoms are shown in the model, in yellow colour. |
|- | |- | ||
|09:31 | |09:31 | ||
− | | To modify disulfide bonds open the option disulfide bonds in pop menu | + | |To modify the disulfide bonds, open the option '''disulfide bonds''' in the pop-up menu. |
|- | |- | ||
− | | 09:38 | + | |09:38 |
− | | Click on the features you may want to change like size | + | |Click on the features you may want to change, like '''size''', '''color''' etc. |
|- | |- | ||
− | | 09:44 | + | |09:44 |
− | | Similarly try to open | + | |Similarly, try to open '.pdb' files of different '''enzymes '''and view their '''3D''' structures. |
|- | |- | ||
|09:51 | |09:51 | ||
− | | Let us summarize | + | |Let us summarize. In this tutorial, we have learnt to: |
|- | |- | ||
|09:57 | |09:57 | ||
− | | | + | |'''Load''' structures of protein from '''Protein Data Bank''' (PDB). |
|- | |- | ||
|10:00 | |10:00 | ||
− | | | + | |Download '.pdb' files from the database. |
|- | |- | ||
|10:05 | |10:05 | ||
− | | | + | |View '''3D structure''' of Insulin using '''PDB code.''' |
|- | |- | ||
|10:10 | |10:10 | ||
− | | | + | |View '''Protein''' structure without water molecules. |
|- | |- | ||
|10:14 | |10:14 | ||
− | | | + | |Display secondary structure in various formats. |
|- | |- | ||
|10:17 | |10:17 | ||
− | | | + | |Highlight '''hydrogen bonds '''and '''disulfide bonds.''' |
|- | |- | ||
|10:22 | |10:22 | ||
− | | Here is an assignment for you | + | |Here is an assignment for you- |
|- | |- | ||
|10:24 | |10:24 | ||
− | | | + | |Download the '.pdb' file of '''Human Hemoglobin''' from '''PDB '''database. |
|- | |- | ||
|10:31 | |10:31 | ||
− | | | + | |Show secondary structure in '''cartoon '''display. |
|- | |- | ||
|10:35 | |10:35 | ||
− | | | + | |Highlight the “'''porphyrin'''” units of the protein. |
|- | |- | ||
|10:39 | |10:39 | ||
− | | | + | |Refer the following link for the '''PDB code.''' |
|- | |- | ||
− | | 10:42 | + | |10:42 |
− | | Watch the video available at this URL. | + | |Watch the video available at this URL. |
− | + | http://spoken-tutorial.org/What_is_a_Spoken_Tutorial | |
|- | |- | ||
|10:46 | |10:46 | ||
− | |It summarizes the Spoken Tutorial project | + | |It summarizes the '''Spoken Tutorial''' project. |
|- | |- | ||
|10:50 | |10:50 | ||
− | |If you do not have good bandwidth, you can download and watch it | + | |If you do not have good bandwidth, you can download and watch it. |
|- | |- | ||
− | | 10:55 | + | |10:55 |
− | | The Spoken Tutorial Project | + | |The Spoken Tutorial Project team: |
|- | |- | ||
|10:57 | |10:57 | ||
− | |Conducts workshops using spoken tutorials | + | |Conducts workshops using spoken tutorials. |
|- | |- | ||
|11:01 | |11:01 | ||
− | |Gives certificates to those who pass an on-line test | + | |Gives certificates to those who pass an on-line test. |
|- | |- | ||
|11:06 | |11:06 | ||
− | |For more details, please write to | + | |For more details, please write to: |
+ | '''contact@spoken-tutorial.org''' | ||
|- | |- | ||
− | | 11:13 | + | |11:13 |
− | | Spoken Tutorial Project is a part of the Talk to a Teacher project | + | |'''Spoken Tutorial''' Project is a part of the '''Talk to a Teacher''' project. |
|- | |- | ||
|11:18 | |11:18 | ||
− | |It is supported by the National Mission on Education through ICT, MHRD, Government of India | + | |It is supported by the National Mission on Education through ICT, MHRD, Government of India. |
|- | |- | ||
|11:25 | |11:25 | ||
− | |More information on this | + | |More information on this mission is available at this link: |
+ | '''http://spoken-tutorial.org/NMEICT-Intro'''. | ||
|- | |- | ||
|11:31 | |11:31 | ||
− | |This is Snehalatha from IIT Bombay signing off. Thank you for joining. | + | |This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining. |
− | + | ||
|} | |} |
Latest revision as of 18:22, 28 March 2017
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. |
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. |