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

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| 00:06

| In this tutorial, we will learn to

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

|* Download '''.pdb '''files from '''PDB''' database.

|* Display secondary structure of proteins in various formats

|* Highlight '''hydrogen bonds '''and '''disulfide bonds'''.  

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

| 00:42

|To record this tutorial I am using,

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|* '''Ubuntu '''OS version. 12.04

|

|* '''Jmol''' version 12.2.2

|* '''Java''' version 7  

|* '''Mozilla Firefox '''Browser 22.0

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|Structure Analysis of large '''biomolecules''' such as  

|* '''Proteins''' and '''Macromolecules'''

|* '''Nucleic acids, DNA''' and '''RNA'''

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

| 01:19

|Here I have opened a new '''Jmol''' window.

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

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

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| 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.  

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

| 01:53

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

 

 

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| 02:04

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

| In the search box type name of the protein as '''Human''' '''Insulin.'''

Press Enter key on the keyboard.

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

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

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

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| A window opens with all the details of the structure.

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| Information like  

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|* '''Primary Citation'''

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|* '''Molecular Description '''and

|* '''Structure Validation'''are available on this page.

 

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

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

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

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|A dialog box opens on the screen.  

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| The structure of protein will be saved as '''4EX1.pdb.gz,''' in the '''Downloads '''folder.

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| Similarly, you can download the required '''.pdb '''files of various proteins and save them in separate files.  

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

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

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

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

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| A dialog box opens on the panel.

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|Select '''Downloads''' folder and click on '''open '''button.  

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

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| 3D Structure of Insulin opens on screen.

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

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

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

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

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

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

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

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

 

 

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

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

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

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|Open the pop-up menu.  

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| Go to '''Select '''option.  

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

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

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

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

 

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| For more display options,

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

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

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| For example click on '''Strands''' option.

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

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| 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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| Observe the change in color on the panel.

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

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

 

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

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

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

 

|'''Calculate''', '''Set Hydrogen Bonds Side Chain.'''

|'''Set Hydrogen Bonds in the Backbone.'''

And also has options to change the thickness of the bonds.

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

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

| We can also change the color of hydrogen bonds.  

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

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

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

| To modify disulfide bonds open the option disulfide bonds in pop menu

 

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

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

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

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

|* Download '''.pdb''' files from the database.

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

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

|* Display secondary structure in various formats.

|* Highlight '''hydrogen bonds '''and '''disulfide bonds.'''

| Here is an assignment for you.

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

|* Show secondary structure in '''cartoon '''display.

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

|* Refer the following link for the '''PDB code.'''

| 10:42

| Watch the video available at this URL.

[http://spoken-tutorial.org/What http://spoken-tutorial.org/What]_is_a_Spoken_ Tutorial

|It summarizes the Spoken Tutorial project

|If you do not have good bandwidth, you can download and watch it  

| 10:55

| The Spoken Tutorial Project Team:  

|Conducts workshops using spoken tutorials

|Gives certificates to those who pass an on-line test  

|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  

|It is supported by the National Mission on Education through ICT, MHRD, Government of India

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

|This is Snehalatha from IIT Bombay signing off. Thank you for joining.