What is the easiest way to determine whether a protein belongs to transcription factors? Is there any database available for this kind of query? And if I need to gain some evidence by experiment, what assays are routinely used. Please tell me every possible ways
Good question! I suppose you have cDNA of your protein and know the sequence?
I would first use web-based databases and peroform homology search for the known domains. Good if your protein appears to have homology to DNA-binding domain. I would then go through the hits of predicted "domains" and would try to evaluate and compare with known proteins of similar structure.
The first thing you should do - just as Maria suggested - is to look for known DNA-binding domains. You can do this by Conserved Domain Search at NCBI.
In case your protein does not show up, you have to do the long and laborious way of doing experiments!
A real TF should at least have DNA-binding properties - which is the most crucial thing you need to find out. Thus, you should try, if your protein is capable of binding to a 'random' set of DNA-probes.
- Badges
- Science topic