Cadherin sequence homology and design of peptide antagonists. (A) Analysis of structural and mutational data of classic cadherin family members determined 3 regions likely to be involved in cadherin transdimerization (colored residues). Sequence homology analysis within these residues was used to identify conserved (blue) and nonconserved (red) residues between R-cadherin (green) and other classical cadherin family members above the dotted line, as well as N- and R-cadherin sequences from different species (mouse, rat, human, or chick; below the dotted line). The region corresponding to amino acids 53-59 was found to have the highest percentage of nonconserved residues likely to participate in the formation of the transdimerization interface. (B) Aggregation of R-cadherin-expressing cells was effectively inhibited by cyclic IDS peptides (IC₅₀ ∼ 300 μM). The linear IDSMSGR peptide also inhibited R-cadherin aggregation with lower affinity. Small effects on aggregation were observed for cyclic INP and other control peptides only at high concentrations. (C) Aggregation of N-cadherin-expressing cells was effectively inhibited by cyclic INP peptides (IC₅₀ ∼ 325 μM). Cyclic IDS was relatively ineffective at inhibiting N-cadherin-mediated aggregation, demonstrating that cyclic IDS inhibition was specific to R-cadherin-mediated aggregation. Incubation of the cells in either TC buffer (with Ca⁺) or TE buffer (no Ca⁺, + EDTA) with no inhibitors was done to establish the negative and positive baselines for cadherin-mediated aggregation. Error bars indicate standard deviation.