Dimerization mechanism and structural features of human LI-cadherin

Abstract

LI-cadherin is a member of cadherin superfamily which is a Ca2+-dependent cell adhesion protein. Its expression is observed on various types of cells in the human body such as normal small intestine and colon cells, and gastric cancer cells. Because its expression is not observed on normal gastric cells, LI-cadherin is a promising target for gastric cancer imaging. However, since the cell adhesion mechanism of LI-cadherin has remained unknown, rational design of therapeutics targeting this cadherin has been complicated. Here, we have studied the homodimerization mechanism of LI-cadherin. We report the crystal structure of the LI-cadherin EC1-4 homodimer. The EC1-4 homodimer exhibited a unique architecture different from that of other cadherins reported so far. The crystal structure also revealed that LI-cadherin possesses a noncanonical calcium ion-free linker between EC2 and EC3. We also show that LI-cadherin EC1-2 and EC3-4 have different characteristics to that of the EC1-2 domains of classical cadherins despite the sequence similarity among them. Various biochemical techniques, molecular dynamics (MD) simulations and small angle X-ray scattering (SAXS) were employed to elucidate the mechanism of homodimerization. We expect these findings will advance the generation of therapeutic molecules targeting LI-cadherin and to establish the specific role of LI-cadherin on cancer cells.

Crystal structure of the nonclassical cadherin-17 N-terminus and implications for its adhesive binding mechanism

“…A mutation at Phe224, at the proposed interface, abolished dimerization and cell aggregation, but also compromised protein stability. Additionally, the EC1-5 and EC3-7 protein fragments did not facilitate cell aggregation (Yui et al, 2020). This is consistent with our own bead-aggregation assays suggesting that EC7 is required for adhesion (Gray, 2020).…”

“…Recent work presented a structure of CDH17 EC1-4 (PDB entry 7cym) forming an antiparallel complex in which the EC2 repeat of one monomer interacts with EC4 from the other, and EC3 is not directly involved in the binding interface (Yui et al, 2020). Features observed in the EC1-2 structure presented here are also found in the EC1-4 structure.…”

“…Intriguingly, the EC1-4 protein fragment produced by Yui and coworkers was mostly monomeric in SEC multi-angle light-scattering experiments at low protein concentration and dimeric in analytical ultracentrifugation experiments at higher concentrations (Yui et al, 2020). A mutation at Phe224, at the proposed interface, abolished dimerization and cell aggregation, but also compromised protein stability.…”

“…These glycans are likely to interfere with the interfaces observed in our structure of CDH17 EC1-2. Glycosylation can modify the biophysical properties of various cadherins (Pinho et al, 2011;Langer et al, 2012), and several glycosylation sites have been experimentally identified for CDH17 (Bernhard et al, 2013;Yui et al, 2020), yet the role of glycosylation in altering CDH17 function remains to be determined.…”

Molecular mechanism underlying the increased risk of colorectal cancer metastasis caused by single nucleotide polymorphisms in LI-cadherin gene

“…Interaction of this domain with catenins is necessary for efficient cell-cell adhesion via classical cadherins (15,16). Although LI-cadherin exhibits structural features distinct from classical cadherins, sequence analysis comparing LI-cadherin with E-, N-, and P-cadherins revealed sequence homology between EC1-2 of these proteins as well as between EC3-7 of LI-cadherin and EC1-5 of E-, N-, and P-cadherins (9,17). The number of EC repeats and the existence of a calcium-free linker in LI-cadherin differentiate both types of cadherins.…”