3D protein structure lesson

Basic steps for designing 3D protein structure. 

For your information, CADD (Computer Aided Drug Design) is the minor of Bioinformatics. It encompasses the application of computational approaches, in understanding the molecular mechanism of drug activity and in designing new drugs. Before we going into deep about CADD, we first must understand the basic technique of designing the 3D protein structure of organism using certain related software.

1. Go to Google or Yahoo, search for MEROPS. When the windows pop ups, click on MEROPS and it will directly connect you to the MEROPS website.  

2. In the website, click the Organism icon located at the left side of the window.

3. Search for microorganism Burkholderia pseudomallei without strain.

 

4. Since there are so many peptidase organisms, choose only one particular organism with specific peptidase. For this example, we will use Lon-A peptidase organism and ClpP peptidase organism.

5. For Lon-A peptidase organism, find for SJ S16 and click their Merops ID. The window for peptidase unit will appear. Then, copy all the sequence in the notepad. Do for another three merops(MER).
*You can also copy all the sequences in the Microsoft Excel so that you can view them more clearly.

6. For ClpP peptidase, find for SK S14 and click the Merops ID. Do the same procedure with Lon.

7. While in notepad, what you should do is remove all the numbers and spaces between the sequences except the MEROPS ID.

8. Make sure your sequence is correct and no sequence is missing. This is important because when your sequence is incomplete, it will affect your protein structure in the next step.

9. Then, save the Notepad as ClpplonBP.
 
10. Next, search for NCBI website in Google or Yahoo. Click Blast on your right side. Go to protein blast.

 

11. This below window will appear after clicking the protein blast icon. At the Enter Query Sequence, fill in the empty box with the MER sequence from the notepad that you have already saved.

12. When you press enter, the MER ID will appear in the Job Title box.

13. Choose for Protein Databank protein (pdb).

14. Choose PSI-BLAST for Algorithm and click BLAST.

15. The window appears show the sequence of organism. Click the 4th band with red color and it will show the pdb ID of the band which is 1RR9.

16. Do for ClpP sequence and the pdb ID will appear as 1TYF.

17. Open for RCSB Protein Databank website. Type the pdb ID (eg: 1RR9) and click ‘search’. Click for the ID and download for PDB File (gz).

18. To view the 3D structure, we need the RasWin package. Click File and Open for the file of downloaded PDB File (gz). You can change the appearance of the structure. Apply for other organisms.