Welcome to this tutorial on Proteins and Macromolecules.
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.
If not, watch the relevant tutorials available at our website.
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.
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.
Here, I have opened a new Jmol window.
3D structures of biomolecules can be viewed by direct download from database.
To do so, click on File menu, scroll down to Get PDB.
An Input dialog-box appears on screen.
We have to type the four letter PDB code for the particular protein, in the Input box.
This code can be obtained from the Protein Data Bank (PDB) website.
This is the web-page of Protein Data Bank.
It has information about biomolecules such as proteins and nucleic acids.
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.
Now, on the web-page that is displayed, scroll down.
A list of known structures of Human Insulin along with the PDB codes appears on the screen.
As an example, let's select Human Insulin with a code 4EX1.
Click on the name of the protein.
A window opens with all the details of the structure.
Information like-
Primary Citation
Molecular Description and
Structure Validationare available on this page.
We can save the structures of proteins as '.pdb' files and view them in 3D mode in Jmol.
Click on the Download Files link, located at the top right hand corner of the page.
From the drop-down menu, select PDB file (gz) option.
A dialog-box opens on the screen.
Select Save file option.
Click on OK button.
The structure of protein will be saved as 4EX1.pdb.gz, in the Downloads folder.
Similarly, you can download the required '.pdb' files of various proteins and save them in separate files.
Now, let's 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.
Type the 4 letter PDB code “4EX1” in the text-box and click on OK button.
If you are not connected to internet then click on Open a File icon on the tool-bar.
A dialog-box opens on the panel.
Navigate to the location of 4EX1.pdb.gz file i.e. to Downloads folder.
Select Downloads folder and click on Open button.
Select 4EX1.pdb.gz file and click on Open button.
'3D' Structure of Insulin opens on screen.
The default display of the protein on the panel is ball and stick.
The model of protein on the panel is shown without hydrogen atoms.
To show the model with hydrogen atoms, open the modelkit menu.
Scroll down to add hydrogens option and click on it.
The model on the panel is now displayed with hydrogen atoms.
The protein structure is also shown with water molecules.
To hide the water molecules, follow the steps as shown.
First, open the pop-up menu and go to Select.
From the sub-menu, choose Hetero and click on “All Water option.
Open the pop-up menu again, go to Style >> Scheme and click on CPK spacefill option.
This will convert all the water molecules to CPK Spacefill display.
Open the pop-up menu again and go to Style, scroll down to Atoms and click on Off option.
Now on the panel, we have Insulin structure without any water molecules.
Next, let us learn to display the secondary structure of the protein in various formats.
Open the pop-up menu.
Go to Select option.
Scroll down to Protein and click on All 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, Sticks, Wireframe, cartoon, trace etc.
Click on Cartoon option from the sub-menu.
This display shows the secondary structure of protein as helices, random coils, strands, sheets etc.
For more display options-
Open the pop-up menu and scroll down to Style, then to Structures.
Here, we see many more options to display secondary structure of protein.
For example, click on Strands option.
The protein is now displayed as Strands on the panel.
To change the color of display: Open the Pop-up-menu. Scroll down to Color. select Atoms and click on Blue option.
Observe the change in color 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.
We can also highlight hydrogen bonds and di-sulpfide bonds in the protein model.
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.
Click on Calculate option to show the hydrogen bonds in the model.
The hydrogen bonds are displayed as white and red long dashes.
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.
We can also change the color of hydrogen bonds.
From the Pop-up-menu, scroll down to Color, then Hydrogen Bonds, then click on orange option.
On the panel, we have all the hydrogen bonds in orange color.
Disulfide bonds and sulphur atoms are shown in the model, in yellow colour.
To modify the disulfide bonds, open the option disulfide bonds in the pop-up menu.
Click on the features you may want to change, like size, color etc.
Similarly, try to open '.pdb' files of different enzymes and view their 3D structures.
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.
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.
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