Difference between revisions of "Jmol-Application/C2/Proteins-and-Macromolecules/English-timed"

From Script | Spoken-Tutorial
Jump to: navigation, search
 
Line 4: Line 4:
  
 
|-
 
|-
−
| 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)'''
+
|'''Load''' structures of '''protein'''s from '''Protein Data Bank (PDB)'''
  
 
|-
 
|-
 
|00:13
 
|00:13
−
|* Download '.pdb' files from '''PDB''' database
+
|Download '.pdb' files from '''PDB''' database
  
 
|-
 
|-
 
|00:18
 
|00:18
−
|* Display secondary structure of proteins in various formats
+
|Display secondary structure of proteins in various formats
  
 
|-
 
|-
 
|00:24
 
|00:24
−
|* Highlight '''hydrogen bonds '''and '''disulfide bonds'''.  
+
|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.'''
  
 
|-
 
|-
Line 36: Line 36:
  
 
|-
 
|-
−
| 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'''
+
|'''Ubuntu '''OS version '''12.04'''
  
 
|-
 
|-
 
|00:50
 
|00:50
−
|* '''Jmol''' version '''12.2.2'''
+
|'''Jmol''' version '''12.2.2'''
  
 
|-
 
|-
 
|00:54
 
|00:54
−
|* '''Java''' version '''7'''  
+
|'''Java''' version '''7'''  
  
 
|-
 
|-
 
|00:57
 
|00:57
−
|* '''Mozilla Firefox Browser''' '''22.0'''.
+
|'''Mozilla Firefox Browser''' '''22.0'''.
  
 
|-
 
|-
−
| 01:02
+
|01:02
 
|'''Structure Analysis''' of large biomolecules such as-  
 
|'''Structure Analysis''' of large biomolecules such as-  
  
 
|-
 
|-
 
|01:06
 
|01:06
−
|* '''Proteins''' and '''Macromolecules'''
+
|'''Proteins''' and '''Macromolecules'''
  
 
|-
 
|-
 
|01:10
 
|01:10
−
|* '''Nucleic acids, DNA''' and '''RNA'''
+
|'''Nucleic acids, DNA''' and '''RNA'''
  
 
|-
 
|-
 
|01:13
 
|01:13
−
|* '''Crystal structures''' and '''polymers''' can be done using '''Jmol Application.'''
+
|'''Crystal structures''' and '''polymers''' can be done using '''Jmol Application.'''
  
 
|-
 
|-
−
| 01:19
+
|01:19
 
|Here, I have opened a new '''Jmol window'''.
 
|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.  
 
|'''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
+
|01:36
−
| An '''Input''' dialog-box appears on '''screen'''.  
+
|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 '''Input''' box.  
 
|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
+
|01:53
−
| This is the web-page of '''Protein Data Bank.'''
+
|This is the web-page of '''Protein Data Bank.'''
  
 
|-
 
|-
−
| 01:57
+
|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, let us try to find '''PDB code '''for '''Pancreatic Enzyme Insulin '''from the '''PDB '''website.
+
|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 "human insulin". Press '''Enter''' key on the keyboard.
+
|In the '''search box''', type name of the protein as "human insulin". Press '''Enter''' key on the keyboard.
  
 
|-
 
|-
−
| 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 '''appears on the screen.
+
|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
+
|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'''
+
|'''Primary Citation'''
  
 
|-
 
|-
−
| 02:56
+
|02:56
−
|* '''Molecular Description '''and
+
|'''Molecular Description '''and
  
 
|-
 
|-
 
|02:58
 
|02:58
−
|* '''Structure Validation'''are available on this page.
+
|'''Structure Validation'''are available on this page.
  
 
|-
 
|-
−
| 03:02
+
|03:02
−
| We can '''save''' the structures of proteins as '.pdb' files and view them in '''3D mode''' in '''Jmol.'''
+
|We can '''save''' the structures of proteins as '.pdb' files and view them in '''3D mode''' in '''Jmol.'''
  
 
|-
 
|-
−
| 03:12
+
|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.  
  
 
|-
 
|-
−
| 03:32
+
|03:32
 
|Select '''Save file''' option.  
 
|Select '''Save file''' option.  
  
Line 172: Line 172:
  
 
|-
 
|-
−
| 03:39
+
|03:39
−
| The structure of '''protein''' will be saved as '''4EX1.pdb.gz''', in the '''Downloads '''folder.
+
|The structure of '''protein''' will be saved as '''4EX1.pdb.gz''', in the '''Downloads '''folder.
  
 
|-
 
|-
−
| 03:51
+
|03:51
−
| Similarly, you can download the required '.pdb' files of various proteins and '''save''' them in separate files.  
+
|Similarly, you can download the required '.pdb' files of various proteins and '''save''' them in separate files.  
  
 
|-
 
|-
−
| 04:02
+
|04:02
−
| Now, let's switch to '''Jmol''' window to view the '''3D''' structure of '''Insulin'''.
+
|Now, let's switch to '''Jmol''' window to view the '''3D''' structure of '''Insulin'''.
  
 
|-
 
|-
 
|04:09  
 
|04:09  
−
| If you are connected to internet, you can directly download the protein structure on '''Jmol panel'''.
+
|If you are connected to internet, you can directly download the protein structure on '''Jmol panel'''.
  
 
|-
 
|-
−
| 04:15
+
|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 internet then click on '''Open a File''' icon on the tool-bar.
+
|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
+
|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
+
|04:47
 
|Select '''Downloads''' folder and click on '''Open '''button.  
 
|Select '''Downloads''' folder and click on '''Open '''button.  
  
 
|-
 
|-
−
| 04:52
+
|04:52
 
|Select '''4EX1.pdb.gz''' file and click on '''Open''' button.
 
|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 protein on the panel is '''ball and stick.'''
+
|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 hydrogen atoms.
+
|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
+
|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''' >> '''Scheme '''and click on '''CPK spacefill '''option.
+
|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 the 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
+
|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
+
|06:50
 
|A sub-menu opens with options like '''CPK Spacefill''', '''Ball and Stick, Sticks, Wireframe, cartoon, trace''' etc.  
 
|A sub-menu opens with options like '''CPK Spacefill''', '''Ball and Stick, Sticks, Wireframe, cartoon, trace''' etc.  
  
Line 297: Line 297:
 
|-
 
|-
 
|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: Open the Pop-up-menu. Scroll down to '''Color'''. select '''Atoms''' and click on '''Blue''' option.
+
|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.
  
 
|-
 
|-
Line 356: Line 356:
  
 
|-
 
|-
−
| 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
+
|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''', click on''' 0.10 A '''option from the''' pop-up-menu'''.
+
|To change the thickness of '''hydrogen bonds''', click on''' 0.10 A '''option from the''' pop-up-menu'''.
  
 
|-
 
|-
−
| 09:02
+
|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.
+
|'''Disulfide bonds''' and '''sulphur''' atoms are shown in the model, in yellow colour.
  
 
|-
 
|-
 
|09:31
 
|09:31
−
| To modify the disulfide bonds, open the option '''disulfide bonds''' in the pop-up 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''', '''color''' etc.
+
|Click on the features you may want to change, like '''size''', '''color''' etc.
  
 
|-
 
|-
−
| 09:44
+
|09:44
−
| Similarly, try to open '.pdb' files of different '''enzymes '''and view their '''3D''' structures.
+
|Similarly, try to open '.pdb' files of different '''enzymes '''and view their '''3D''' structures.
  
 
|-
 
|-
 
|09:51
 
|09:51
−
| Let us summarize. In this tutorial, we have learnt to:
+
|Let us summarize. In this tutorial, we have learnt to:
  
 
|-
 
|-
 
|09:57
 
|09:57
−
|* '''Load''' structures of protein from '''Protein Data Bank''' (PDB).
+
|'''Load''' structures of protein from '''Protein Data Bank''' (PDB).
  
 
|-
 
|-
 
|10:00
 
|10:00
−
|* Download '.pdb' files from the database.
+
|Download '.pdb' files from the database.
  
 
|-
 
|-
 
|10:05
 
|10:05
−
|* View '''3D structure''' of Insulin using '''PDB code.'''  
+
|View '''3D structure''' of Insulin using '''PDB code.'''  
  
 
|-
 
|-
 
|10:10
 
|10:10
−
|* View '''Protein''' structure without water molecules.
+
|View '''Protein''' structure without water molecules.
  
 
|-
 
|-
 
|10:14
 
|10:14
−
|* Display secondary structure in various formats.
+
|Display secondary structure in various formats.
  
 
|-
 
|-
 
|10:17
 
|10:17
−
|* Highlight '''hydrogen bonds '''and '''disulfide bonds.'''
+
|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.
+
|Download the '.pdb' file of '''Human Hemoglobin''' from '''PDB '''database.
  
 
|-
 
|-
 
|10:31
 
|10:31
−
|* Show secondary structure in '''cartoon '''display.
+
|Show secondary structure in '''cartoon '''display.
  
 
|-
 
|-
 
|10:35
 
|10:35
−
|* Highlight the “'''porphyrin'''” units of the protein.  
+
|Highlight the “'''porphyrin'''” units of the protein.  
  
 
|-
 
|-
 
|10:39
 
|10:39
−
|* Refer the following link for the '''PDB code.'''
+
|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
 
http://spoken-tutorial.org/What_is_a_Spoken_Tutorial
  
Line 461: Line 461:
  
 
|-
 
|-
−
| 10:55
+
|10:55
−
| The Spoken Tutorial Project team:  
+
|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.  
  
 
|-
 
|-
Line 478: Line 478:
  
 
|-
 
|-
−
| 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.  
  
 
|-
 
|-
Line 493: Line 493:
 
|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.

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

Retrieved from "https://script.spoken-tutorial.org/index.php?title=Jmol-Application/C2/Proteins-and-Macromolecules/English-timed&oldid=34558"