Hi,if you add the TM segment, I would expect that the protein will then get targeted to the membrane and hopefully inserted correctly. My guess is that you will have to treat your protein as a membrane protein or a membrane-anchored protein...which means prepare a membrane fraction, use detergent and look for your protein in there. Is your ectodomain N or C-terminal (I assume it is N from your message)? Have you looked at the targeting sequences present in the protein (signal sequence, reverse anchoring motifs)?
Hope this helps Pascal F. Egea, PhD
