Login

Join for Free!
118351 members


Extracellular domain or intracellular domain?

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

Moderator: BioTeam

Extracellular domain or intracellular domain?

Postby simpleton » Sun Nov 21, 2010 3:24 pm

I spent quite a while thinking how to determine which parts of a protein face outward from the plasma membrane and which parts face inwards?

How can I go about determining the intracellular domain and extracellular domain of a new protein?

Can anyone please help? Many thanks in advance!
simpleton
Garter
Garter
 
Posts: 34
Joined: Thu Mar 18, 2010 3:48 am

Postby JackBean » Tue Nov 23, 2010 1:29 pm

1) you could use some bioinformatic approach

2) you could try some partial hydrolysis of your protein inserted into the membrane and by analysis of released domain/peptides, you should be able to say, which part is intra/extracellular

3) maybe (really not sure, whether this would work!), you could somehow color your protein and see it under microscope (but I don't think you would be able to distinguish extra/intra :( )

4) if you know, whether it binds something, you could try to design some suicide ligand, which would bind covalently after bonding and by analysis of which peptide it contains, you should be able to see, which part is extra/intra

of course for all these approaches you need to work with some system, where you have inserted all proteins in the same way in intact bodies
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
User avatar
JackBean
Inland Taipan
Inland Taipan
 
Posts: 5678
Joined: Mon Sep 14, 2009 7:12 pm

Postby simpleton » Tue Nov 23, 2010 3:19 pm

Hey JackBean! Thanks a lot for your help!

Really appreciate it!

Sadly this is just a theoretical question. I doubt I will be given the opportunity to carry out this experiment :(
simpleton
Garter
Garter
 
Posts: 34
Joined: Thu Mar 18, 2010 3:48 am


Postby JackBean » Wed Nov 24, 2010 8:15 am

aha, well, too bad...

then I would suggest points 1,2 and 4
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
User avatar
JackBean
Inland Taipan
Inland Taipan
 
Posts: 5678
Joined: Mon Sep 14, 2009 7:12 pm


Return to Molecular Biology

Who is online

Users browsing this forum: No registered users and 3 guests