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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.

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10:55 The Spoken Tutorial Project team:
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11:31 This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

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