Structural and energetic determinants of adhesive binding specificity in type I cadherins

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 111; no. 40; p. 14322
• Main Authors: Vendome, Jeremie, Felsovalyi, Klara, Song, Hang, Yang, Zhongyu, Jin, Xiangshu, Brasch, Julia, Harrison, Oliver J., Ahlsen, Goran, Bahna, Fabiana, Kaczynska, Anna, Katsamba, Phinikoula S., Edmond, Darwin, Hubbell, Wayne L., Shapiro, Lawrence, Honig, Barry
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 07.10.2014; National Acad Sciences
• Series: PNAS Plus
• Subjects: Amino Acid Sequence; Animals; binding capacity; Binding sites; Binding, Competitive; Biological Sciences; cadherins; Cadherins - chemistry; Cadherins - genetics; Cadherins - metabolism; cell adhesion; Cell adhesion & migration; Crystallography; Crystallography, X-Ray; dimerization; Electron Spin Resonance Spectroscopy; Electrons; Evolution; HEK293 Cells; Heterogeneity; Humans; Hydrophobic and Hydrophilic Interactions; Kinetics; Mice; Models, Molecular; Molecular Sequence Data; Molecular structure; Mutation; PNAS Plus; PNAS PLUS Significance Statements; Protein Binding; Protein Multimerization; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins; Resonance; Sequence Homology, Amino Acid; Static Electricity; Xenopus; Xenopus Proteins - chemistry; Xenopus Proteins - genetics; Xenopus Proteins - metabolism; entropy contribution; protein family design; cadherin dimerization
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1416737111

Type I cadherins comprise a family of cell–cell adhesion proteins that dimerize in a highly specific fashion. There are small differences in dimerization affinities among family members that are evolutionarily conserved and that have profound effects on cell-patterning behavior. There are few examples where the molecular origins of small affinity differences between closely related proteins have been explored in depth. We have brought an unusually broad range of technologies to bear on the problem in a unique integrated approach. Our results reveal how a subtle combination of physical interactions combine to tune binding affinities and, in the course of our analysis, we discover a new conformational entropy-based mechanism that can also be exploited by other multidomain proteins. Type I cadherin cell-adhesion proteins are similar in sequence and structure and yet are different enough to mediate highly specific cell–cell recognition phenomena. It has previously been shown that small differences in the homophilic and heterophilic binding affinities of different type I family members can account for the differential cell-sorting behavior. Here we use a combination of X-ray crystallography, analytical ultracentrifugation, surface plasmon resonance and double electron-electron resonance (DEER) electron paramagnetic resonance spectroscopy to identify the molecular determinants of type I cadherin dimerization affinities. Small changes in sequence are found to produce subtle structural and dynamical changes that impact relative affinities, in part via electrostatic and hydrophobic interactions, and in part through entropic effects because of increased conformational heterogeneity in the bound states as revealed by DEER distance mapping in the dimers. These findings highlight the remarkable ability of evolution to exploit a wide range of molecular properties to produce closely related members of the same protein family that have affinity differences finely tuned to mediate their biological roles.