TM domains and their functions - (Feb/14/2007 )
My cousin got a following assignment and he is pretty lost on how to proceed, any ideas are welcome.
The assignment is write a research proposal, preferably along with the techniques to support the ideas. The lab discovers a protein in some screen with not much information available in public databases. The initial in-silico analysis (like psi-BLAST etc) finds few transmembrane domains with extracellular N-terminus and intracellular C-terminus. My cousin is supposed to build a story out of this information.
I wonder what ideas can be put into such a small information to write a research proposal?? If I realized this question correctly, the course leader expects to roam around those TM domains..and yes, you are free to select cell lines or model organisms.
did you try a homology search?
Its only for writing a research proposal so they do not have any information about this supposed protein as such but the course leader expects them to write a research proposal.
This is exactly I thought too that doing BLAST search would give you the homologs in other species and from their funciton you could find out what this protein could be doing in your system but what next?
getting some information about the function can help drawing a close structure for your protein, its characteristics and its class
basically, you've an unknown protein and you want to find out what it's doing
- label it with GFP and transfect into cells. Then light microscopy, try to colocalize it with organelle markers
- find interaction partners, by pull-down, yeast two hybrid, chemical crosslinking etc.
- find the gene and chromosome region
- find potential post-translational modifications (phosphorylation) from Prosite and validate them experimentally.