I am working with the apoptosis inhibition by RNA virus. I could figure out the protein in my virus which decelerate the apoptosis in its host. I have also learnt from the literature that it uses the mitochondrial dependent pathway for apoptosis. Now my problem is how find out which host and viral protein interaction leads to the apoptotic inhibition in host.
You can have the apoptosis inhibitor and run 2D electrophoresis and then staining the gels with silver-staining or if you label the protein extract with DIGE (quite expensive but very Effective) .. Then analyze the result to see what proteins are up / down regulated, and then cut out the spots and run MS identification.
Goodluck :)
Thanks Fuad for your kind suggestion. Can you let me know how can i get the Protein A and Protein B from the virus and host respectively in its AB complex. If A is the Apoptotic inhibitor and B is the protein from the host, complementing the process of apoptosis.
I don't understand your post. Are you saying you have identified the viral protein?
Yes, I have Identified the Viral protein that down regulate the apoptosis. The next step is to find the host protein with which the viral protein interact to inhibit apoptosis. I hope you got my point.
Ok, if you have an antibody to your viral protein, you can do a coimmuno precipitation so any proteins bound to your viral protein will be purified along with your viral protein. Then you can run on a gel and cut out the band and send the band in for protein sequencing on Mass spec. MS/MS.
Otherwise you can clone your viral gene for expression and use some sort of yeast 2 hybrid system to fish out interacting proteins.
If you google "protein-protein interactions", you will find a lot of info and protocols.
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