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

Vendome J, Posy S, Jin X, Bahna F, Ahlsen G, Shapiro L, Honig B - Nat. Struct. Mol. Biol. (2011)

Bottom Line: 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 Ca(2+) 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA. Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA. Howard Hughes Medical Institute, Columbia University, New York, New York, USA.

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 Ca(2+) 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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Dimerization by strand swapping in classical cadherins. (a) Ribbon representation of the strand swapped dimer of the entire type I C-cadherin ectodomain 3. The three Ca2+ bound at each interdomain region are indicated by red arrows. The dashed box indicates the region of the adhesive contact, which is encompassed entirely within the EC1 domain. (b) Cartoon representation of the strand swapped adhesive interface between EC1 domains of the type I E-cadherin 4. The A* and A strands are labeled, the hinge region is indicated (Hn) and the side chains of the swapped Trp2 are represented. (c) Schematic diagram of the strand swapping process. Two monomers are schematically represented in their closed conformation on the left and as a strand swapped dimer on the right. Only EC1 and EC2 domains are represented, and the three yellow stars between the domains denote bound calcium ions. The A* strand is colored in light green, the A strand in dark green and the hinge region in dashed dark blue. Trp2 and Glu11 (red line) are also indicated. (d) Superposed ribbon representations of the E-cadherin EC1 domain in its closed (in yellow) and swapped (in blue) conformations. The hinge region and the two prolines it contains are indicated. (e) Alignment of the N-terminal sequence of type I cadherins. Conserved residues Trp2, Glu11, Pro5 and Pro6 are colored. Secondary structure elements and the hinge region are indicated above the alignment. Xenla is an abbreviation for Xenopus laevis.
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Figure 1: Dimerization by strand swapping in classical cadherins. (a) Ribbon representation of the strand swapped dimer of the entire type I C-cadherin ectodomain 3. The three Ca2+ bound at each interdomain region are indicated by red arrows. The dashed box indicates the region of the adhesive contact, which is encompassed entirely within the EC1 domain. (b) Cartoon representation of the strand swapped adhesive interface between EC1 domains of the type I E-cadherin 4. The A* and A strands are labeled, the hinge region is indicated (Hn) and the side chains of the swapped Trp2 are represented. (c) Schematic diagram of the strand swapping process. Two monomers are schematically represented in their closed conformation on the left and as a strand swapped dimer on the right. Only EC1 and EC2 domains are represented, and the three yellow stars between the domains denote bound calcium ions. The A* strand is colored in light green, the A strand in dark green and the hinge region in dashed dark blue. Trp2 and Glu11 (red line) are also indicated. (d) Superposed ribbon representations of the E-cadherin EC1 domain in its closed (in yellow) and swapped (in blue) conformations. The hinge region and the two prolines it contains are indicated. (e) Alignment of the N-terminal sequence of type I cadherins. Conserved residues Trp2, Glu11, Pro5 and Pro6 are colored. Secondary structure elements and the hinge region are indicated above the alignment. Xenla is an abbreviation for Xenopus laevis.

Mentions: Cadherins constitute a large family of cell-cell adhesion proteins that are represented in both vertebrates and invertebrates 1,2. The “classical” type I and type II cadherins are found only in vertebrates and contain an extracellular region consisting of a tandem repeat of five extracellular cadherin immunoglobulin-like domains (EC1-EC5), that extend from the cell surface (Fig. 1A). Cadherin ectodomains bind between cells through the interaction of their EC1 domains which exchange, or swap, their N-terminal β-strand (the A* strand). Conserved anchor residues – Trp2 in type I cadherins or Trp2 and Trp4 in type II – dock into a complementary pocket in the partner molecule 3-6. The A* strand, which comprises residues 1-3, represents the N-terminal segment of a strand that, in type I cadherins spans residues 1-10 and includes a break at residues 4-6 due to the presence of prolines at positions 5 and 6, which provides a hinge that mediates conformational changes necessary for strand swapping (Fig. 1). Following our previous analysis we denote residues 7-10 as the A strand and residues 110 as the A*/A strand (Fig. 1b) 7.


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

Vendome J, Posy S, Jin X, Bahna F, Ahlsen G, Shapiro L, Honig B - Nat. Struct. Mol. Biol. (2011)

Dimerization by strand swapping in classical cadherins. (a) Ribbon representation of the strand swapped dimer of the entire type I C-cadherin ectodomain 3. The three Ca2+ bound at each interdomain region are indicated by red arrows. The dashed box indicates the region of the adhesive contact, which is encompassed entirely within the EC1 domain. (b) Cartoon representation of the strand swapped adhesive interface between EC1 domains of the type I E-cadherin 4. The A* and A strands are labeled, the hinge region is indicated (Hn) and the side chains of the swapped Trp2 are represented. (c) Schematic diagram of the strand swapping process. Two monomers are schematically represented in their closed conformation on the left and as a strand swapped dimer on the right. Only EC1 and EC2 domains are represented, and the three yellow stars between the domains denote bound calcium ions. The A* strand is colored in light green, the A strand in dark green and the hinge region in dashed dark blue. Trp2 and Glu11 (red line) are also indicated. (d) Superposed ribbon representations of the E-cadherin EC1 domain in its closed (in yellow) and swapped (in blue) conformations. The hinge region and the two prolines it contains are indicated. (e) Alignment of the N-terminal sequence of type I cadherins. Conserved residues Trp2, Glu11, Pro5 and Pro6 are colored. Secondary structure elements and the hinge region are indicated above the alignment. Xenla is an abbreviation for Xenopus laevis.
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Related In: Results  -  Collection

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Figure 1: Dimerization by strand swapping in classical cadherins. (a) Ribbon representation of the strand swapped dimer of the entire type I C-cadherin ectodomain 3. The three Ca2+ bound at each interdomain region are indicated by red arrows. The dashed box indicates the region of the adhesive contact, which is encompassed entirely within the EC1 domain. (b) Cartoon representation of the strand swapped adhesive interface between EC1 domains of the type I E-cadherin 4. The A* and A strands are labeled, the hinge region is indicated (Hn) and the side chains of the swapped Trp2 are represented. (c) Schematic diagram of the strand swapping process. Two monomers are schematically represented in their closed conformation on the left and as a strand swapped dimer on the right. Only EC1 and EC2 domains are represented, and the three yellow stars between the domains denote bound calcium ions. The A* strand is colored in light green, the A strand in dark green and the hinge region in dashed dark blue. Trp2 and Glu11 (red line) are also indicated. (d) Superposed ribbon representations of the E-cadherin EC1 domain in its closed (in yellow) and swapped (in blue) conformations. The hinge region and the two prolines it contains are indicated. (e) Alignment of the N-terminal sequence of type I cadherins. Conserved residues Trp2, Glu11, Pro5 and Pro6 are colored. Secondary structure elements and the hinge region are indicated above the alignment. Xenla is an abbreviation for Xenopus laevis.
Mentions: Cadherins constitute a large family of cell-cell adhesion proteins that are represented in both vertebrates and invertebrates 1,2. The “classical” type I and type II cadherins are found only in vertebrates and contain an extracellular region consisting of a tandem repeat of five extracellular cadherin immunoglobulin-like domains (EC1-EC5), that extend from the cell surface (Fig. 1A). Cadherin ectodomains bind between cells through the interaction of their EC1 domains which exchange, or swap, their N-terminal β-strand (the A* strand). Conserved anchor residues – Trp2 in type I cadherins or Trp2 and Trp4 in type II – dock into a complementary pocket in the partner molecule 3-6. The A* strand, which comprises residues 1-3, represents the N-terminal segment of a strand that, in type I cadherins spans residues 1-10 and includes a break at residues 4-6 due to the presence of prolines at positions 5 and 6, which provides a hinge that mediates conformational changes necessary for strand swapping (Fig. 1). Following our previous analysis we denote residues 7-10 as the A strand and residues 110 as the A*/A strand (Fig. 1b) 7.

Bottom Line: 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 Ca(2+) 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA. Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA. Howard Hughes Medical Institute, Columbia University, New York, New York, USA.

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 Ca(2+) 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.

Show MeSH
Related in: MedlinePlus