Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface?

Cadherins are cell surface adhesion proteins important for tissue development and integrity. Type I and type II, or classical, cadherins form adhesive dimers via an interface formed through the exchange, or "swapping", of the N-terminal beta-strands from their membrane-distal EC1 domains. Here, we ask which sequence and structural features in EC1 domains are responsible for beta-strand swapping and whether members of other cadherin families form similar strand-swapped binding interfaces. We created a comprehensive database of multiple alignments of each type of cadherin domain. We used the known three-dimensional structures of classical cadherins to identify conserved positions in multiple sequence alignments that appear to be crucial determinants of the cadherin domain structure. We identified features that are unique to EC1 domains. On the basis of our analysis, we conclude that all cadherin domains have very similar overall folds but, with the exception of classical and desmosomal cadherin EC1 domains, most of them do not appear to bind through a strand-swapping mechanism. Thus, non-classical cadherins that function in adhesion are likely to use different protein-protein interaction interfaces. Our results have implications for the evolution of molecular mechanisms of cadherin-mediated adhesion in vertebrates.