The crystal structure of EC1 domain of N-cadherin was determined by Shapiro et al. in 1995. In that structure he observed cis dimers. Although many biochemical methods have provided evidence of E-cadherin dimers, but none of the biophysical methods which tried to directly measure the E-cadherin dimerization were successful. Does anyone know the reason for that?
Assuming that dimers occur as indicated by the structural and biochemical data the reason why biophysical assays do not detect them may be multiple but one of the first to check is to place donor/acceptor proteins (Rluc/YFP….) in the right position/orientation. Otherwise they may be too far to allow energy transfer. Of course it may be the opposite that dimers do not occur and then the biophysical results are the "good" ones. In any case I would think first on the orientation of the donor/acceptors within the fusion proteins. Also take into account if (as I understand for what you describe) the dimers in the structure are just of a given domain. I suggest to place the donor/acceptor in just this domain and/or to know where are located the other domains in the receptor (again the other domains of the protein may difficult the finding of donor/acceptor when using the whole protein to design the fusion proteins)
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