Extracellular domain or intracellular domain?

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    • #14160
      simpleton
      Participant

      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!

    • #102407
      JackBean
      Participant

      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

    • #102408
      simpleton
      Participant

      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 🙁

    • #102426
      JackBean
      Participant

      aha, well, too bad…

      then I would suggest points 1,2 and 4

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