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Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins

Nature Structural & Molecular Biology volume 18, pages 693–700 (2011)Cite this article

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Abstract

Cell adhesion by classical cadherins is mediated by dimerization of their EC1 domains through the 'swapping' of N-terminal β-strands. We use molecular simulations, measurements of binding affinities and X-ray crystallography to provide a detailed picture of the structural and energetic factors that control the adhesive dimerization of cadherins. We show that strand swapping in EC1 is driven by conformational strain in cadherin monomers that arises from the anchoring of their short N-terminal strand at one end by the conserved Trp2 and at the other by ligation to Ca2+ ions. We also demonstrate that a conserved proline-proline motif functions to avoid the formation of an overly tight interface where affinity differences between different cadherins, crucial at the cellular level, are lost. We use these findings to design site-directed mutations that transform a monomeric EC2-EC3 domain cadherin construct into a strand-swapped dimer.

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Figure 1: Dimerization by strand swapping in classical cadherins.
Figure 2: R.m.s. fluctuations (r.m.s.f., a measure of the average atomic mobility) of backbone atoms (N, Cα and C atoms) during the molecular dynamics (MD) simulations.
Figure 3: Distance between the N- and C-terminal anchorage points of the A*/A strand during the simulations of the closed E-cadherin monomer and T-cadherin.
Figure 4: Modulation of the effect of Ca2+ on the A*/A strand mobility by the W2F mutation.
Figure 5: Comparison of E-cadherin EC1 and EC2 domains.
Figure 6: Structure of the E-cadherin P5A P6A mutant swapped dimer and comparison with the wild-type (WT) swapped dimer.

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References

  1. Nollet, F., Kools, P. & van Roy, F. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. J. Mol. Biol. 299, 551–572 (2000).

    Article  CAS  PubMed  Google Scholar 

  2. Hulpiau, P. & van Roy, F. Molecular evolution of the cadherin superfamily. Int. J. Biochem. Cell Biol. 41, 349–369 (2009).

    Article  CAS  PubMed  Google Scholar 

  3. Boggon, T.J. et al. C-cadherin ectodomain structure and implications for cell adhesion mechanisms. Science 296, 1308–1313 (2002).

    Article  CAS  PubMed  Google Scholar 

  4. Parisini, E., Higgins, J.M., Liu, J.H., Brenner, M.B. & Wang, J.H. The crystal structure of human E-cadherin domains 1 and 2, and comparison with other cadherins in the context of adhesion mechanism. J. Mol. Biol. 373, 401–411 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Patel, S.D. et al. Type II cadherin ectodomain structures: implications for classical cadherin specificity. Cell 124, 1255–1268 (2006).

    Article  CAS  PubMed  Google Scholar 

  6. Harrison, O.J. et al. The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure 19, 244–256 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Posy, S., Shapiro, L. & Honig, B. Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface? J. Mol. Biol. 378, 954–968 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  8. Nose, A., Tsuji, K. & Takeichi, M. Localization of specificity determining sites in cadherin cell adhesion molecules. Cell 61, 147–155 (1990).

    Article  CAS  PubMed  Google Scholar 

  9. Price, S.R., De Marco Garcia, N.V., Ranscht, B. & Jessell, T.M. Regulation of motor neuron pool sorting by differential expression of type II cadherins. Cell 109, 205–216 (2002).

    Article  CAS  PubMed  Google Scholar 

  10. Shan, W.S., Koch, A., Murray, J., Colman, D.R. & Shapiro, L. The adhesive binding site of cadherins revisited. Biophys. Chem. 82, 157–163 (1999).

    Article  CAS  PubMed  Google Scholar 

  11. Shan, W. et al. The minimal essential unit for cadherin-mediated intercellular adhesion comprises extracellular domains 1 and 2. J. Biol. Chem. 279, 55914–55923 (2004).

    Article  CAS  PubMed  Google Scholar 

  12. Katsamba, P. et al. Linking molecular affinity and cellular specificity in cadherin-mediated adhesion. Proc. Natl. Acad. Sci. USA 106, 11594–11599 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Chen, C.P., Posy, S., Ben-Shaul, A., Shapiro, L. & Honig, B.H. Specificity of cell-cell adhesion by classical cadherins: critical role for low-affinity dimerization through β-strand swapping. Proc. Natl. Acad. Sci. USA 102, 8531–8536 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Ciatto, C. et al. T-cadherin structures reveal a novel adhesive binding mechanism. Nat. Struct. Mol. Biol. 17, 339–347 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Harrison, O.J. et al. Two-step adhesive binding by classical cadherins. Nat. Struct. Mol. Biol. 17, 348–357 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Sotomayor, M. & Schulten, K. The allosteric role of the Ca2+ switch in adhesion and elasticity of C-cadherin. Biophys. J. 94, 4621–4633 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Miloushev, V.Z. et al. Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins. Structure 16, 1195–1205 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Prasad, A., Housley, N.A. & Pedigo, S. Thermodynamic stability of domain 2 of epithelial cadherin. Biochemistry 43, 8055–8066 (2004).

    Article  CAS  PubMed  Google Scholar 

  19. Tamura, K., Shan, W.S., Hendrickson, W.A., Colman, D.R. & Shapiro, L. Structure-function analysis of cell adhesion by neural (N-) cadherin. Neuron 20, 1153–1163 (1998).

    Article  CAS  PubMed  Google Scholar 

  20. Sivasankar, S., Zhang, Y., Nelson, W.J. & Chu, S. Characterizing the initial encounter complex in cadherin adhesion. Structure 17, 1075–1081 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Zhang, Y., Sivasankar, S., Nelson, W.J. & Chu, S. Resolving cadherin interactions and binding cooperativity at the single-molecule level. Proc. Natl. Acad. Sci. USA 106, 109–114 (2009).

    Article  CAS  PubMed  Google Scholar 

  22. Harrison, O.J., Corps, E.M. & Kilshaw, P.J. Cadherin adhesion depends on a salt bridge at the N-terminus. J. Cell Sci. 118, 4123–4130 (2005).

    Article  CAS  PubMed  Google Scholar 

  23. Nagar, B., Overduin, M., Ikura, M. & Rini, J.M. Structural basis of calcium-induced E-cadherin rigidification and dimerization. Nature 380, 360–364 (1996).

    Article  CAS  PubMed  Google Scholar 

  24. Pokutta, S., Herrenknecht, K., Kemler, R. & Engel, J. Conformational changes of the recombinant extracellular domain of E-cadherin upon calcium binding. Eur. J. Biochem. 223, 1019–1026 (1994).

    Article  CAS  PubMed  Google Scholar 

  25. Pertz, O. et al. A new crystal structure, Ca2+ dependence and mutational analysis reveal molecular details of E-cadherin homoassociation. EMBO J. 18, 1738–1747 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Cailliez, F. & Lavery, R. Cadherin mechanics and complexation: the importance of calcium binding. Biophys. J. 89, 3895–3903 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Shapiro, L. & Weis, W.I. Structure and biochemistry of cadherins and catenins. Cold Spring Harb. Perspect. Biol. 1, a003053 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  28. Häussinger, D. et al. Proteolytic E-cadherin activation followed by solution NMR and X-ray crystallography. EMBO J. 23, 1699–1708 (2004).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Harrison, O.J., Corps, E.M., Berge, T. & Kilshaw, P.J. The mechanism of cell adhesion by classical cadherins: the role of domain 1. J. Cell Sci. 118, 711–721 (2005).

    Article  CAS  PubMed  Google Scholar 

  30. Green, S.M., Gittis, A.G., Meeker, A.K. & Lattman, E.E. One-step evolution of a dimer from a monomeric protein. Nat. Struct. Biol. 2, 746–751 (1995).

    Article  CAS  PubMed  Google Scholar 

  31. Murray, A.J., Head, J.G., Barker, J.J. & Brady, R.L. Engineering an intertwined form of CD2 for stability and assembly. Nat. Struct. Biol. 5, 778–782 (1998).

    Article  CAS  PubMed  Google Scholar 

  32. Kelley, B.S., Chang, L.C. & Bewley, C.A. Engineering an obligate domain-swapped dimer of cyanovirin-N with enhanced anti-HIV activity. J. Am. Chem. Soc. 124, 3210–3211 (2002).

    Article  CAS  PubMed  Google Scholar 

  33. Simeoni, F., Masotti, L. & Neyroz, P. Structural role of the proline residues of the β-hinge region of p13suc1 as revealed by site-directed mutagenesis and fluorescence studies. Biochemistry 40, 8030–8042 (2001).

    Article  CAS  PubMed  Google Scholar 

  34. Barrientos, L.G. & Gronenborn, A.M. The domain-swapped dimer of cyanovirin-N contains two sets of oligosaccharide binding sites in solution. Biochem. Biophys. Res. Commun. 298, 598–602 (2002).

    Article  CAS  PubMed  Google Scholar 

  35. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  PubMed  Google Scholar 

  36. Vagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D Biol. Crystallogr. 66, 22–25 (2010).

    Article  CAS  PubMed  Google Scholar 

  37. Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).

    Article  CAS  PubMed  Google Scholar 

  39. Chen, V.B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).

    Article  CAS  PubMed  Google Scholar 

  40. Lindahl, E., Hess, B. & Van Der Spoel, D. GROMACS: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7, 306–317 (2001).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by US National Science Foundation Grant MCB-0918535 (to B.H.) and National Institutes of Health Grant R01 GM062270–07 (to L.S.).

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Author notes

  1. Shoshana Posy

    Present address: Present address: Computer-Assisted Drug Design, Bristol-Myers Squibb Company, Princeton, New Jersey, USA.,

  2. Jeremie Vendome and Shoshana Posy: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA

    Jeremie Vendome, Shoshana Posy, Xiangshu Jin, Fabiana Bahna, Goran Ahlsen, Lawrence Shapiro & Barry Honig

  2. Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA

    Jeremie Vendome, Shoshana Posy, Goran Ahlsen & Barry Honig

  3. Howard Hughes Medical Institute, Columbia University, New York, New York, USA

    Jeremie Vendome, Shoshana Posy, Xiangshu Jin, Fabiana Bahna & Barry Honig

  4. Edward S. Harkness Eye Institute, Columbia University, New York, New York, USA

    Lawrence Shapiro

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  1. Jeremie Vendome
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Contributions

J.V. performed and analyzed the simulations; J.V. and S.P. designed the mutants; F.B. produced all the wild-type and mutant proteins; G.A. performed and analyzed the AUC experiments; X.J. determined and refined the crystal structures; J.V., L.S. and B.H. designed experiments, analyzed data and wrote the manuscript.

Corresponding authors

Correspondence to Lawrence Shapiro or Barry Honig.

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The authors declare no competing financial interests.

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Vendome, J., Posy, S., Jin, X. et al. Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins. Nat Struct Mol Biol 18, 693–700 (2011). https://doi.org/10.1038/nsmb.2051

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