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

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This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
 
This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
  
 
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Latest revision as of 11:33, 8 August 2014

Title of script: Proteins and Macromolecules

Author: Snehalatha Kaliappan

Keywords: Protein structures from PDB, Cartoons of proteins, Jmol Video tutorial

Visual Cue
Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Proteins and Macromolecules.
Slide Number 2

Learning Objectives

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.
Slide Number 3

Pre-requisites

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

If not, watch the relevant tutorials available at our website.

Slide Number 4

System Requirement

To record this tutorial I am using,
  • Ubuntu OS version. 12.04
  • Jmol version 12.2.2
  • Java version 7
  • Mozilla Firefox Browser 22.0
Slide Number 5

Jmol for Biomolecules

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.

Open a new Jmol window.

Cursor on the Jmol panel.

Here I have opened a new Jmol window.

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

Click on File menu, Scroll down to Get PDB. To do so, click on File menu, scroll down to Get PDB.
Cursor on input box An input dialog box appears on screen.

We have to type the four letter PDB code for the particular protein, in the input box.

Cursor on the Jmol panel This code can be obtained from the Protein Data Bank (PDB) website.
Open PDB web site

http://www.rcsb.org/pdb/home/home.do

This is the web page of Protein Data Bank.

It has information about biomolecules such as proteins and nucleic acids.

Cursor on the Jmol panel As an example:

Let us try to find PDB code for Pancreatic Enzyme Insulin from the PDB website.

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

Press Enter key on the keyboard.

Visual Cue? Now, on the web-page that is displayed, scroll down.
Scroll down the list. A list of known structures of Human Insulin along with the PDB codes appear on screen.
Click on the name of the protein. As an example, let's select Human Insulin with a code 4EX1.

Click on the name of the protein.

Cursor on the webpage>> scroll down A window opens with all the details of the structure.
Scroll down the page. Information like
  • Primary Citation
  • Molecular Description and
  • Structure Validation

are available on this page.

Cursor on the webpage. We can save the structures of proteins as .pdb files and view them in 3D mode in Jmol.
Click on Download Files. Click on the Download Files link, located at the top right hand corner of the page.
Select PDB file (gz). From the drop down menu, select PDB file (gz) option.
Select Save file. A dialog box opens on the screen.

Select Save file option.

Click on OK button Click on OK button.
Cursor on the webpage. The structure of protein will be saved as 4EX1.pdb.gz, in the Downloads folder.
Cursor on the webpage. Similarly, you can download the required .pdb files of various proteins and save them in separate files.
Cursor on Jmol panel. With Get PDB input box open. Now, lets switch to Jmol window to view the 3D structure of Insulin.
Cursor on Jmol panel. If you are connected to Internet, you can directly download the protein structure on Jmol panel.
Type 4EX1 in the input text box.

Click on OK button.

Type the 4 letter PDB code “4EX1” in the text box and click on OK button.
Click on Open a File icon. If you are not connected to Internet, then click on Open a File icon on the tool bar.
Select Downloads folder >> click on Open.

Select 4EX1.pdb.gz.>> click on open.

A dialog box opens on the panel.

Navigate to the location of 4EX1.pdb.gz file i.e. to the Downloads folder.

Select Downloads folder and click on open button.

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

Cursor on the panel. 3D Structure of Insulin opens on screen.
Cursor on the panel. The default display of the protein on the panel, is ball and stick.
Cursor on the panel. The model of protein on the panel is shown without hydrogens atoms.
Click on modelkit icon,

Scroll down and click on add hydrogens option.

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

Scroll down to add hydrogens option and click on it.

Cursor on the panel. The model on the panel is now displayed with hydrogen atoms.
Cursor on the panel. The protein structure is also shown with water molecules.
Cursor on the panel. To hide the water molecules, follow the steps as shown.
Open the Pop-up menu, go to Select,

from the submenu choose Hetero.

Click on “All Water'

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

From the sub-menu,Heteroand click on “All Water option.

Open the pop-up menu, go to 'Style' then to Schemes. Click on CPK spacefill option. Open the pop-up menu again and go to Style, Scheme and click on CPK spacefill option.
Cursor on the panel. This will convert all the water molecules to CPK Spacefill display.
Open the pop-up menu and go to Style and then to Atoms.

Click on Off option.

Open the pop-up menu again and go to Style scroll down to Atoms and click on Off option.
Cursor on the panel. Now on panel we have Insulin structure without any water molecules.
Cursor on the panel.

Right click to open the Pop-up menu

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

Open the pop-up menu.

Go to Select option. Go to Select option.
Scroll down to Protein and click on All option Scroll down to Protein and click on All option.
Open the pop-up menu again and scroll down to Style, then Scheme.

Click on Cartoon option.

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

A sub-menu opens with options like CPK Spacefill, ball and stick, wireframe, cartoon, trace, etc.

Click on Cartoon option from the sub-menu.

Cursor on the panel. This display shows the secondary structure of protein as helices, random coils, strands, sheets etc.
Cursor on the panel For more display options,
Open the pop-up menu and scroll down to Structures. Open the pop-up menu and scroll down to Style, then to Structures.
Scroll down and show the options. Here we see many more options to display secondary structure of protein.
click on Strands option. For example click on Strands option.
Cursor on the panel. The protein is now displayed as Strands on the panel.
Open the pop-up menu and scroll down to color option. To change the color of display, open the Pop-up-menu. Scroll down to Color select Atoms and click on Blue option.
Click on Blue option. Observe the change in color on the panel.
Cursor on the panel. To convert the structure back to Ball-and-stick display,
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.
Open the Pop-up menu, and scroll down to hydrogen bonds, disulfide bonds. We can also highlight hydrogen bonds and di-sulpfide bonds in the protein model.
Open the pop-up menu, go to Style and then to Hydrogen bonds. To display hydrogen bonds:

Open the pop-up menu and scroll down to Style and then to Hydrogen Bonds option.

Scroll down the sub-menu under Hydrogen Bonds option in the Pop-up menu. The Hydrogen Bonds option in the Pop-up menu has features such as:

Set Hydrogen Bonds in the Side Chain.

Set Hydrogen Bonds in the Backbone.

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

Click on Calculate option.

Zoom the display and point on the hydrogen bonds (white and red long dashes)

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

The hydrogen bonds are displayed as white and red long dashes.

Click on 0.15 A . To change the thickness of hydrogen bonds,

Click on 0.10 A option from the pop-up-menu.

Now on the panel we can see thicker hydrogen bonds.

Cursor on the panel. We can also change the color of hydrogen bonds.
Open Pop-up menu, scroll down to Color, then to Hydrogen Bonds.

Click on White option.

From the Pop-up-menu scroll down to Color then Hydrogen Bonds then click on orange option.
Cursor on the panel. On the panel, we have all the hydrogen bonds in orange color.
Point to the Disulfide bonds. Disulfide bonds and sulfur atoms are shown in the model in yellow color.
Open the pop-up menu, go to Style and then to Disulfide Bonds option. To modify the disulfide bonds, open the option Disulfide Bonds in the pop-up menu.
Scroll down the options in the Disulfide Bonds. Click on the features you may want to change like size and color etc.
Cursor on the panel. Similarly try to open .pdb files of different enzymes and view their 3D structures.
Slide Number 6

Summary

Let us summarize, in this tutorial we have learnt 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.
Slide Number 7

Summary

* Display secondary structure in various formats.
  • Highlight hydrogen bonds and disulfide bonds.
Slide Number 8

Assignment

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.
Slide Number 9

Acknowledgement

Watch the video available at this URL.

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

Slide Number 10 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

Slide number 11 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 ]

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

Contributors and Content Editors

Pratik kamble, Snehalathak

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