Abstract
E-cadherin is a transmembrane glycoprotein that facilitates inter-cellular adhesion in the epithelium. The ectodomain of the native structure is comprised of five repeated immunoglobulin-like domains. All E-cadherin crystal structures show the protein in one of three alternative conformations: a monomer, a strand-swapped trans homodimer and the so-called X-dimer, which is proposed to be a kinetic intermediate to forming the strand-swapped trans homodimer. However, previous studies have indicated that even once the trans strand-swapped dimer is formed, the complex is highly dynamic and the E-cadherin monomers may reorient relative to each other. Here, molecular dynamics simulations have been used to investigate the stability and conformational flexibility of the human E-cadherin trans strand-swapped dimer. In four independent, 100 ns simulations, the dimer moved away from the starting structure and converged to a previously unreported structure, which we call the Y-dimer. The Y-dimer was present for over 90% of the combined simulation time, suggesting that it represents a stable conformation of the E-cadherin dimer in solution. The Y-dimer conformation is stabilised by interactions present in both the trans strand-swapped dimer and X-dimer crystal structures, as well as additional interactions not found in any E-cadherin dimer crystal structures. The Y-dimer represents a previously unreported, stable conformation of the human E-cadherin trans strand-swapped dimer and suggests that the available crystal structures do not fully capture the conformations that the human E-cadherin trans homodimer adopts in solution.
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Abbreviations
- DEER:
-
Double electron–electron resonance
- EC:
-
Extracellular cadherin
- GROMACS:
-
GROningen MAchine for Chemical Simulation
- MD:
-
Molecular dynamics
- PDB:
-
Protein Data Bank
- RMSD:
-
Root-mean-square deviation
- SPC:
-
Simple point charge
References
Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410. doi:10.1006/jmbi.1990.9999
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. In: Pullman B (ed) Intermolecular forces. Springer, Netherlands, pp 331–342
Berendsen HJC, Postma JPM, van Gunsteren WF et al (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684. doi:10.1063/1.448118
Boggon TJ, Murray J, Chappuis-Flament S et al (2002) C-cadherin ectodomain structure and implications for cell adhesion mechanisms. Science 296(80):1308–1313. doi:10.1126/science.1071559
Brasch J, Harrison OJ, Ahlsen G et al (2011) Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin. J Mol Biol 408:57–73. doi:10.1016/j.jmb.2011.01.031
Cailliez F, Lavery R (2005) Cadherin mechanics and complexation: the importance of calcium binding. Biophys J 89:3895–3903. doi:10.1529/biophysj.105.067322
Cailliez F, Lavery R (2006) Dynamics and stability of E-cadherin dimers. Biophys J 91:3964–3971. doi:10.1529/biophysj.106.087213
Dalle Vedove A, Lucarelli AP, Nardone V et al (2015) The X-ray structure of human P-cadherin EC1-EC2 in a closed conformation provides insight into the type I cadherin dimerization pathway. Acta Crystallogr Sect F Struct Biol Commun 71:371–380. doi:10.1107/S2053230x15003878
Daura X, Gademann K, Jaun B et al (1999a) Peptide folding: when simulation meets experiment. Angew Chem Int Ed 38:236–240. doi:10.1002/(Sici)1521-3773(19990115)38:1/2<236:Aid-Anie236>3.0.Co;2-M
Daura X, van Gunsteren WF, Mark AE (1999b) Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations. Proteins 34:269–280. doi:10.1002/(SICI)1097-0134(19990215)34:3
Feenstra KA, Hess B, Berendsen HJC (1999) Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J Comput Chem 20:786–798. doi:10.1002/(SICI)1096-987X(199906)20:8<786:AID-JCC5>3.0.CO;2-B
Harrison OJ, Corps EM, Kilshaw PJ (2005) Cadherin adhesion depends on a salt bridge at the N terminus. J Cell Sci 118:4123–4130. doi:10.1242/jcs.02539
Harrison OJ, Bahna F, Katsamba PS et al (2010) Two-step adhesive binding by classical cadherins. Nat Struct Mol Biol 17:348–357. doi:10.1038/nsmb.1784
Harrison OJ, Jin X, Hong S et al (2011) The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure 19:244–256. doi:10.1016/j.str.2010.11.016
Häussinger D, Ahrens T, Aberle T et al (2004) Proteolytic E-cadherin activation followed by solution NMR and X-ray crystallography. EMBO J 23:1699–1708. doi:10.1038/sj.emboj.7600192
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463–1472. doi:10.1002/(Sici)1096-987x(199709)18:12<1463:Aid-Jcc4>3.0.Co;2-H
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:27–38. doi:10.1016/0263-7855(96)00018-5
Kabsch W (1976) A solution for the best rotation to relate two sets of vectors. Acta Crystallogr Sect A 32:922–923. doi:10.1107/S0567739476001873
Li Y, Altorelli NL, Bahna F et al (2013) Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion. Proc Natl Acad Sci USA 110:16462–16467. doi:10.1073/pnas.1314303110
Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306–317. doi:10.1007/s008940100045
Lindorff-Larsen K, Piana S, Palmo K et al (2010) Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78:1950–1958. doi:10.1002/prot.22711
Maiorov VN, Crippen GM (1995) Size-independent comparison of protein three-dimensional structures. Proteins 22:273–283. doi:10.1002/prot.340220308
Miyamoto S, Kollman PA (1992) Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem 13:952–962. doi:10.1002/jcc.540130805
Mohamet L, Hawkins K, Ward CM (2011) Loss of function of E-cadherin in embryonic stem cells and the relevance to models of tumorigenesis. J Oncol 2011:352616. doi:10.1155/2011/352616
Nagar B, Overduin M, Ikura M, Rini JM (1996) Structural basis of calcium-induced E-cadherin rigidification and dimerization. Nature 380:360–364. doi:10.1038/380360a0
Ozawa M (2002) Lateral dimerization of the E-cadherin extracellular domain is necessary but not sufficient for adhesive activity. J Biol Chem 277:19600–19608. doi:10.1074/jbc.M202029200
Parisini E, Higgins JM, Liu JH et al (2007) 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. doi:10.1016/j.jmb.2007.08.011
Patel SD, Chen CP, Bahna F et al (2003) Cadherin-mediated cell–cell adhesion: sticking together as a family. Curr Opin Struct Biol 13:690–698. doi:10.1016/j.sbi.2003.10.007
Pertz O, Bozic D, Koch AW et al (1999) A new crystal structure, Ca2+ dependence and mutational analysis reveal molecular details of E-cadherin homoassociation. EMBO J 18:1738–1747. doi:10.1093/emboj/18.7.1738
Schmid N, Eichenberger AP, Choutko A et al (2011) Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J with Biophys Lett 40:843–856. doi:10.1007/s00249-011-0700-9
Shapiro L, Fannon AM, Kwong PD et al (1995) Structural basis of cell–cell adhesion by cadherins. Nature 374:327–337. doi:10.1038/374327a0
Sivasankar S, Zhang Y, Nelson WJ, Chu S (2009) Characterizing the initial encounter complex in cadherin adhesion. Structure 17:1075–1081. doi:10.1016/j.str.2009.06.012
Takeichi M (1988) The cadherins: cell–cell adhesion molecules controlling animal morphogenesis. Development 102:639–655
Takeichi M (1990) Cadherins: a molecular family important in selective cell–cell adhesion. Annu Rev Biochem 59:237–252. doi:10.1146/annurev.bi.59.070190.001321
Tamura K, Shan WS, Hendrickson WA et al (1998) Structure–function analysis of cell adhesion by neural (N-) cadherin. Neuron 20:1153–1163. doi:10.1016/S0896-6273(00)80496-1
Tironi IG, Sperb R, Smith PE, van Gunsteren WF (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102:5451–5459. doi:10.1063/1.469273
Troyanovsky RB, Sokolov E, Troyanovsky SM (2003) Adhesive and lateral E-cadherin dimers are mediated by the same interface. Mol Cell Biol 23:7965–7972. doi:10.1128/MCB.23.22.7965-7972.2003
van der Spoel D, Lindahl E, Hess B et al (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718. doi:10.1002/jcc.20291
van Roy F (2014) Beyond E-cadherin: roles of other cadherin superfamily members in cancer. Nat Rev Cancer 14:121–134. doi:10.1038/nrc3647
Vendome J, Posy S, Jin X et al (2011) Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins. Nat Struct Mol Biol 18:693–700. doi:10.1038/nsmb.2051
Vendome J, Felsovalyi K, Song H et al (2014) Structural and energetic determinants of adhesive binding specificity in type I cadherins. Proc Natl Acad Sci USA 111:E4175–E4184. doi:10.1073/pnas.1416737111
Zhang YX, Sivasankar S, Nelson WJ, Chu S (2009) Resolving cadherin interactions and binding cooperativity at the single-molecule level. Proc Natl Acad Sci USA 106:109–114. doi:10.1073/pnas.0811350106
Acknowledgements
This work was supported by grants from the Australian Research Council (ARC) to AEM and MLO (DP130102153), and the Medical Advances Without Animals Trust (MAWA) to MLO, ED and ASG. ED is a NHMRC Early Career Research Fellow. This research was undertaken with the assistance of resources provided at the National Computational Infrastructure National Facility systems, housed at the Australian National University, through the National Computational Merit Allocation Scheme supported by the Australian Government.
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Schumann-Gillett, A., Mark, A.E., Deplazes, E. et al. A potential new, stable state of the E-cadherin strand-swapped dimer in solution. Eur Biophys J 47, 59–67 (2018). https://doi.org/10.1007/s00249-017-1229-3
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DOI: https://doi.org/10.1007/s00249-017-1229-3