When your protein sings to you: “You Know My Name!”
Posted by: Mariam Rizkallah in BioinformaticsMicrobiology, Immunology & Biochemistry Dept.*
Faculty of Pharmacy
Cairo University
Bioinformatics Practical Exam – Winter 2010**
Time allowed: Lab computers will automatically hibernate after 2 hours.***
Target: Assigning the function of the uncharacterized protein O67940_ AQUAE from Aquifex aeolicus ****
A suggested procedure:
1- Get the amino acid sequence of the protein from UniProtKB
— Run it through BLAST to find homologs (related sequences). Do not forget to choose Blastp & PSI-BLAST
— Check the assigned hits (known function & solved crystal structure) which have highest possible similarity (highest score/ highest % id) to your query.
2- Check obtained BLAST alignment of those proteins against your query.
3- Check if the protein belongs to any protein family using PIRSF & COGs
— Check if the protein shares any conserved domain with assigned function using Pfam.
— Using PROSITE the functional site database, check if the protein shares any sequence motifs with other proteins
4- Check if the protein belongs to a superfamily using SCOP database, which provides structural and evolutionary relationships between proteins.
5- As you don’t have the crystal structure of your Aquae protein & you have the structure of the closest assigned protein, use VAST to search & align protein related structures to yours.
6- Extract homologs.
7- Multiple alignment (structure-guided alignment) using Cn3D
— Neighbor-joining (NJ) phylogenetic analysis using CDTree
8- Use PDBSum to obtain an overview of the protein–ligand interactions available for your query.
9- Alignment of homologous sequences to identify conserved functional residues.
10- Evidence-based assignment of biological function of query O67940_Aquefix.
🙂GOOD LUCK 🙂
* What have I got to lose?!
** I have faith.
*** I can provide that; I know a guy who knows a guy!
**** Frankly, I wanted to pick a different protein, but I hesitated.
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sweet dreams, mariam!!!
No..no dreams. It’s a must and it’s happening; soon or later.. biochemistry, microbiology or even pharmaceutical chemistry.
It’s just we don’t have time for a bioinfo course or even for a small “hint”. Plus it’s not suitable to push people to study something they won’t actually use in their career since it’s all about specialties now; what makes bioinfo a postgrad-level course, just for those who are interested….. well, I didn’t get this part totally right; bioinfo is the future now, so we have to know about it, bases will go great with us, like in “drug design” for example.. and much more.
We’re almost in 2010 now!!
Anyway, 2010 may be early, but I promise you that part of this will happen in 2011… I hope one of the Micro Writers will be the Teaching Assistant who will supervise the exam 🙂
Dr. Ramy, it’s so exciting to know that this is actually going to happen. Exciting but not surprising with open-minded members seeking change & searching for the latest in their fields to provide to their students. Good for the upcoming pharmacy students! I hope they get luckier than we do!
Hi Mariam,
I read your nice procedure and was wondering are you a student or a graduate? and to which extent is this strategy applied in Egypt? because this is part of my work here in Germany. I am a Fac. of Pharmacy Cairo Uni. graduate 2000.
Dear Dr. Reham,
I am so glade that you liked the post. The post was just a presentation for the PLoS paper “Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function” by Raja Mazumder & Sona Vasudevan, Biochemistry and Molecular & Cellular Biology Dept., Georgetown University Medical Center, Washington, D.C.
I liked it because it was talking about how to predict protein function guided by a simple approach: for id >80%; BLAST will do, with id >70%; it’s Pfam time, id >50%; 3D-structure and for id <30%; sequence and structural motifs can get them done... I liked that!
I am a 4th year FOPCU student. I knew from AboBakr, another writer who got his bioinformatics diploma from SIRA-Egypt, that it is the exact course and looked like the exam but without the hints 🙂 I want to tell you about the bioinformatics workshops here, but I will be glad to leave this part to Dr. Ramy Aziz, lecturer at Microbiology & Immunology Dept., streptococcal specialist at NMPDR and the one who taught us everything we know about bioinformatics, if he may.
Hi again Mariam,
Thanks for yor reply. I hope u a prospective future.
This is hilarious mariam…
loving the “Good Luck” finale!!
Yeah, I added it to simulate the exams style!!
Glad you liked it. Thank you 🙂