Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4

Abstract

Protocadherins (Pcdhs) are cell adhesion and signaling proteins used by neurons to develop and maintain neuronal networks, relying on trans homophilic interactions between their extracellular cadherin (EC) repeat domains. We present the structure of the antiparallel EC1-4 homodimer of human PcdhγB3, a member of the γ subfamily of clustered Pcdhs. Structure and sequence comparisons of α, β, and γ clustered Pcdh isoforms illustrate that subfamilies encode specificity in distinct ways through diversification of loop region structure and composition in EC2 and EC3, which contains isoform-specific conservation of primarily polar residues. In contrast, the EC1/EC4 interface comprises hydrophobic interactions that provide non-selective dimerization affinity. Using sequence coevolution analysis, we found evidence for a similar antiparallel EC1-4 interaction in non-clustered Pcdh families. We thus deduce that the EC1-4 antiparallel homodimer is a general interaction strategy that evolved before the divergence of these distinct protocadherin families.DOI: http://dx.doi.org/10.7554/eLife.18449.001

γ-Protocadherin structural diversity and functional implications

“…The γB2 EC1–5 and γB7 EC1–4 trans dimer structures show the same overall arrangement as the previously published γB3 EC1–4   trans dimer structure (Nicoludis et al, 2016). However, closer analysis revealed that the γB3 EC1–4 structure is an outlier among the γB structures, both in terms of its overall structure (Figure 1—source data 3–7), and in the interactions at the recognition interface (Figure 1—figure supplement 3).…”

“…Excluding the structurally diverse γA-Pcdhs and the partially occluded γB3 dimer (Nicoludis et al, 2016), the EC1–4 dimers of isoforms from the same subfamily have similar overall structures (RMSDs ~1.5–3.4 Å; Figure 1—source data 3). This similarity is even more apparent when the two mutually exclusive interaction regions (EC1:EC4 and EC2–3:EC2–3) are compared separately revealing RMSDs of <2 Å (Figure 1—source data 4–5).…”

“…The structures of representative γA- and γB-Pcdh protein isoforms reported here complete a set of representative structures for trans -recognition interfaces from alternate clustered Pcdh isoforms, with structures now available for at least two Pcdhs from each of the α-, β- (Goodman et al, 2016), γB- (Nicoludis et al, 2016; this paper), and γA- (this paper) Pcdh subfamilies. Representative structures of engaged trans dimers of C-type Pcdhs have yet to be obtained.…”

“…Structures of the trans dimer formed through this interface have been reported for two α-Pcdhs and two β-Pcdhs which revealed overall-similar recognition-dimer structures, mediated by interfaces populated with diverse residue compositions that determine homophilic specificity (Goodman et al, 2016). Recently a trans dimer structure of a γB-Pcdh has also been reported (Nicoludis et al, 2016). Unfortunately, this structure contained a HEPES molecule in the EC2:EC3 interface, preventing formation of native specificity-determining intermolecular contacts in this region.…”

Regulation of neural circuit formation by protocadherins

“…Using sequence coevolution analysis and comparison to γ-Pcdh structures, it was suggested that non-clustered Pcdhs likely interact via antiparallel EC1-4 contacts, in a manner similar to the clustered Pcdhs [62]. Recently, Cooper et al [72] reported structural data for EC1-4 of zebrafish Pcdh19, a δ2-Pcdh family member, which indicate a similar architecture to that of clustered Pcdhs.…”