Wednesday, March 3, 2010

protein data bank

Tyrpsin is a serine protease found in digestive system of many vertebrates. Tyrpsin is produced in the pancreas as the inactive proenzyme trypsinogen. trypsin cleaves peptide chains mainly at the carboxyl side of the amino acid lysine or arginine,except when either is followed by proline. It is used for numerous biotechnological processes.  
Molecular Description
Molecule: Chymotrypsin inhibitor 3
Classifucation: Hydrolase Inhibitor
Structure Weight: 41630.11
Polymer 1 with polypeptide (L) type, 187 in length
Chains: A and B

Molecular Function
- Endopeptidase inhibitor activity
- Serine-type endopeptidase inhibitor activity
- Peptidase inhibitor activity

DSSP secondary structure
- 3% helical (2 helices; 7 residues)
- 37% beta sheet (20 strands; 70 residues)


Subtilisin a.k.a serine endopeptidase is protease (a protein-digesting enzyme) initially obtained from Bacillus subtilis. They are physically and chemically well characterized enzymes. They can obtained from soil bacteria, for example Bacillus amyloliguefaciens. Subtilisin are secreted in large amounts from many Bacillus species.

Molecular Description

Classification: Hydrolase
Structure Weight: 142388.37
Molecule: Subtilisin-like protease
Polymer 1 with polypeptide (L) type, 649 in length
Chains: A and B
Fragment: UNP residues 113-761

Molecular Function
- Serine-type endopeptidase activity
- Peptidase activity
- Serine-type peptidase activity
- Hydrolase activity
- Identical protein binding

Biological process
- Proteolysis
- Negative regulation of catalytic activity

DSSP secondary structure
- 22% helical (20 helices;146 residues)
- 29% beta sheet (44 strands; 190 residues)


Classification: Hydrolase
Structure Weight: 35432.25
Molecule: Termolysin
Polymer 1 with polypeptide (L) type, 316 in length
Chains: A and B
Fragment: UNP residues 233-548

Molecular Function
- Metalloendopeptidase activity
- Calcium Ion binding
- Peptidase activity
- Metallopeptidase activity
- Zinc Ion binding
- Hydrolase activity
- Metral Ion binding

Biological Process
- Proteolysis

Cellular Component
- Extracellular region

Monday, February 1, 2010 and science..

I was late to class today,class start at 2pm,i woke up at 2.05pm..I reached the com lab at 2.30pm..luckly it was Madam Linda first class..she will teach us about HTML and other related stuff which is I'm not familiar with..nothing much to learn today, just an introduction about html.  So the first task that Madam ask us to do is creating a blog and write about "Journey of Life" in our post. Thanks God, I already have my own blog which has been used in my CADD,I just using the same blog for KOS1110..and fortunately I had created my post for "Journey of Life" task for today's class is already done..and this is my first post for my KOS1110..actually this subject must be taken when i was in my 1st year..but i took it in my final year with the other's fun actually cause i get to know other junior,sharing experience about how's life in classmates are very nice and they're really helpful especially during Dr.Salihin class..they helped me a lot!!thanks friends!!this some of my friends name:-

No Friend's Name Course
1 Atikah Bsms
2 Amina Bsms
3 Daila Bsms

What I expect from this class is to get as much knowledge about computers related with we are going to apply all the skills and knowledge in our study and when we're working soon.  I really hope that Madam Linda will teach us everything about computer in science till the end of this semester..Insyaallah

Wednesday, January 13, 2010

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.