View source for Jmol-Application/C2/Proteins-and-Macromolecules/English-timed

{| border=1
|'''Time'''
| '''Narration'''

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| 00:01
|Welcome to this tutorial on '''Proteins and Macromolecules.'''

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| 00:06
| In this tutorial, we will learn to

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|00:09
|* Load structures of proteins from '''Protein Data Bank (PDB).'''

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|00:13
|* Download '''.pdb '''files from '''PDB''' database.

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|00:18
|* Display secondary structure of proteins in various formats

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|00:24
|* Highlight '''hydrogen bonds '''and '''disulfide bonds'''. 

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|00:29
| To follow this tutorial you should be familiar with basic operations from '''Jmol Application window.'''

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|00:37
|If not, watch the relevant tutorials available at our website. 

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| 00:42
|To record this tutorial I am using,

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| 00:46
|* '''Ubuntu '''OS version. 12.04

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|00:50
|* '''Jmol''' version 12.2.2

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|00:54
|* '''Java''' version 7 

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|00:57
|* '''Mozilla Firefox '''Browser 22.0

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| 01:02
|Structure Analysis of large '''biomolecules''' such as 

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|01:06
|* '''Proteins''' and '''Macromolecules'''

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|01:10
|* '''Nucleic acids, DNA''' and '''RNA'''

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|01:13
|* '''Crystal structures and polymers''' can be done using '''Jmol Application.'''

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| 01:19
|Here I have opened a new '''Jmol''' window.

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| 01:24
|3D structures of '''biomolecules''' can be viewed, by direct download from database. 

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| 01:29
| To do so, click on '''File '''menu, scroll down to''' Get PDB.''' 

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|  01:36
| An input dialog box appears on screen. 

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| 01:40
|We have to type the four letter '''PDB code''' for the particular '''protein,''' in the input box. 

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| 01:48
| This code can be obtained from the '''Protein Data Bank (PDB) '''website'''.'''

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|  01:53
| This is the web page of '''Protein Data Bank.'''



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|  01:57
|It has information about biomolecules such as '''proteins''' and '''nucleic acids.'''

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| 02:04
| As an example: Let us try to find '''PDB code '''for '''Pancreatic Enzyme Insulin '''from the '''PDB '''website.

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|02:13
| In the search box type name of the protein as '''Human''' '''Insulin.'''
Press Enter key on the keyboard.

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| 02:24
| Now, on the web-page that is displayed, scroll down.

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| 02:28
| A list of known structures of '''Human Insulin''' along with the '''PDB codes '''appear on screen.

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| 02:36
| As an example, let's select''' Human Insulin''' with a code '''4EX1.'''

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|  02:44
|Click on the name of the protein.

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| 02:47
| A window opens with all the details of the structure.

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| 02:52
| Information like 

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| 02:54
|* '''Primary Citation'''

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| 02:56
|* '''Molecular Description '''and

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|02:58
|* '''Structure Validation'''are available on this page.


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| 03:02
| We can save the structures of proteins as '''.pdb '''files and view them in 3D mode in '''Jmol.'''

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|  03:12
| Click on the '''Download Files''' link, located at the top right hand corner of the page. 

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| 03:20
| From the drop down menu, select '''PDB file (gz) '''option'''. '''

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| 03:28
|A dialog box opens on the screen. 

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|  03:32
|Select '''Save file''' option. 

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|03:35
|Click on '''OK''' button.

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| 03:39
| 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 '''.pdb '''files of various proteins and save them in separate files. 

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| 04:02
| Now, lets switch to '''Jmol''' window to view the 3D structure of '''Insulin'''.

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|04:09 
| If you are connected to Internet, you can directly download the protein structure on Jmol panel.

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|  04:15
| Type the 4 letter '''PDB code “4EX1” '''in the text box and click on '''OK''' button. 

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| 04:25
| If you are not connected to Internet, then click on '''Open a File''' icon on the tool bar.

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| 04:34
| A dialog box opens on the panel.

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|  04:38
|Navigate to the location of '''4EX1.pdb.gz''' file i.e. to '''Downloads '''folder.

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|  04:47
|Select '''Downloads''' folder and click on '''open '''button. 

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|  04:52
|Select '''4EX1.pdb.gz''' file and click on '''open''' button.

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| 05:00
| 3D Structure of Insulin opens on screen.

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| 05:05
| The default display of the '''protein''' on the panel, is '''ball and stick.'''

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| 05:12
| The model of protein on the panel is shown without hydrogens atoms.

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| 05:17
| To show the model with hydrogen atoms, open the '''modelkit''' menu.

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|  05:23
|Scroll down to '''add hydrogens''' option and click on it.

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| 05:28
| The model on the panel is now displayed with hydrogen atoms.

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| 05:33
| The '''protein''' structure is also shown with water molecules.

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| 05:38
| To hide the water molecules, follow the steps as shown.

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| 05:43
| First open the pop-up menu and go to '''Select.'''

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| 05:48
| From the sub-menu,choose '''Hetero'''and click on '''“All Water''' option.



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| 05:55
| Open the pop-up menu again, go to '''Style''', '''Scheme '''and click on '''CPK spacefill '''option.

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| 06:05
|This will convert all the water molecules to '''CPK Spacefill '''display.

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| 06:11 
| Open the pop-up menu again and go to '''Style''' scroll down to '''Atoms '''and click on '''Off '''option.

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| 06:22
| Now on panel we have '''Insulin'''structure without any water molecules.

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| 06:27
| Next, let us learn to display the secondary structure of the '''protein''' in various formats.

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|  06:35
|Open the pop-up menu. 

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| 06:37
| Go to '''Select '''option. 

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| 06:39
| Scroll down to '''Protein '''and click on''' All '''option.

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| 06:44
|Open the pop-up menu again and scroll down to '''Style, '''then''' Scheme. '''

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|  06:50
|A sub-menu opens with options like '''CPK Spacefill''', '''Ball and Stick, Sticks, Wireframe, cartoon, trace, etc. '''

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|07:02  
|Click on''' Cartoon '''option from the sub-menu.

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|07:07
| This display shows the secondary structure of protein as '''helices, random coils, strands, sheets '''etc.


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| 07:17
| For more display options,

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| 07:19
| Open the pop-up menu and scroll down to '''Style,''' then to''' Structures'''.

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| 07:25
| Here we see many more options to display secondary structure of protein.

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| 07:31
| For example click on '''Strands''' option.

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| 07:35
| The protein is now displayed as '''Strands''' on the panel.

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| 07:40
| To change the color of display, open the Pop-up-menu. Scroll down to '''Color''' select '''Atoms''' and click on '''Blue''' option.

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| 07:52
| Observe the change in color on the panel.

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| 07:56
| To convert the structure back to '''Ball-and-stick''' display,

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| 07:59
| Open the pop-up menu, select '''Style''', then '''Scheme''' and click on '''Ball and stick '''option.


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| 08:08
| We can also highlight '''hydrogen bonds '''and''' di-sulpfide bonds '''in the protein model.

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| 08:14
| To display '''hydrogen bonds''': Open the pop-up menu and scroll down to '''Style''' and then to '''Hydrogen Bonds''' option.

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|08:25 
| '''The Hydrogen Bonds''' option in the Pop-up menu has features such as:


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|08:30
|'''Calculate''', '''Set Hydrogen Bonds Side Chain.'''

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|08:35
|'''Set Hydrogen Bonds in the Backbone.'''
And also has options to change the thickness of the bonds.

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| 08:42
| Click on '''Calculate''' option to show the '''hydrogen bonds''' in the model.

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|  08:47
|The '''hydrogen bonds''' are displayed as white and red long dashes.

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| 08:53
| To change the thickness of '''hydrogen bonds''', Click on''' 0.10 A '''option from the''' pop-up-menu'''.

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|  09:02
|Now on the panel we can see thicker''' hydrogen bonds'''. 

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|09:06
| We can also change the color of hydrogen bonds. 

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| 09:11
| From the Pop-up-menu scroll down to '''Color''' then '''Hydrogen Bonds''' then click on '''orange''' option.

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| 09:20
| On the panel, we have all the '''hydrogen bonds''' in orange color.

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| 09:25
|   '''Disulfide''' bonds, and sulphur atoms are shown in the model in yellow colour.

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|09:31
| To modify disulfide bonds open the option disulfide bonds in pop menu


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| 09:38
| Click on the features you may want to change like size and color etc.

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| 09:44
| Similarly try to open '''.pdb '''files of different '''enzymes '''and view their 3D structures.

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|09:51
| Let us summarize, in this tutorial we have learnt to:

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|09:57
|* To Load structures of protein from Protein Data Bank (PDB).

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|10:00
|* Download '''.pdb''' files from the database.

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|10:05
|* View 3D structure of Insulin using '''PDB code.''' 

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|10:10
|* View '''Protein''' structure without water molecules.

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|10:14
|* Display secondary structure in various formats.

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|10:17
|* Highlight '''hydrogen bonds '''and '''disulfide bonds.'''

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|10:22
| Here is an assignment for you.

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|10:24
|* Download the '''.pdb''' file of '''Human Hemoglobin''' from '''PDB '''database.

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|10:31
|* Show secondary structure in '''cartoon '''display.

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|10:35
|* Highlight the “'''porphyrin'''” units of the '''protein'''. 

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|10:39
|* Refer the following link for the '''PDB code.'''

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| 10:42
| Watch the video available at this URL.
[http://spoken-tutorial.org/What 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: 

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|10:57
|Conducts workshops using spoken tutorials

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|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

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|11:25
|More information on this Mission is available at this link [http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.org/NMEICT-Intro] ] 

|-
|11:31
|This is Snehalatha from IIT Bombay signing off. Thank you for joining. 

|}