Liprin-α-Mediated Assemblies and Their Roles in Synapse Formation

Abstract

Brain's functions, such as memory and learning, rely on synapses that are highly specialized cellular junctions connecting neurons. Functional synapses orchestrate the assembly of ion channels, receptors, enzymes, and scaffold proteins in both pre- and post-synapse. Liprin-α proteins are master scaffolds in synapses and coordinate various synaptic proteins to assemble large protein complexes. The functions of liprin-αs in synapse formation have been largely uncovered by genetic studies in diverse model systems. Recently, emerging structural and biochemical studies on liprin-α proteins and their binding partners begin to unveil the molecular basis of the synaptic assembly. This review summarizes the recent structural findings on liprin-αs, proposes the assembly mechanism of liprin-α-mediated complexes, and discusses the liprin-α-organized assemblies in the regulation of synapse formation and function.

Keywords: LLPS; SYD2; coiled coil; presynaptic active zone; protein structure; protein–protein interaction; scaffold protein.

FIGURE 1

Domain organization of liprin-α. The diagram depicts the domains or regions of liprin-α. CC, coiled-coil region; SAH, single alpha helix; SAM, sterile-α-motif domain. Isoform or species-specific regions were shown above the schematic diagram. LCR, a liprinα3 core region in liprin-α3; Insertion, an inserted loop region in liprin-α2/3/4; PBM, a PDZ binding motif in vertebrate liprin-αs. Regions of liprin-α with solved structure were highlighted by pink lines under the diagram. PDB ids were shown under the pink lines (7D2H and 7D2G for liprin-α2_H2, 7D2E for liprin-α2_H3; 6IUH for the liprin-α2_SAH/GIT1_PBD complex; 4UWX for the liprin-α3_LCR/mDia_DID complex; 3TAC, 3TAD, 6KR4, and 6KIP for the SAM123 structures in complex with CASK_CaMK, liprin-β1_SAM123, LAR_D1D2, and PTPδ_D2, respectively; 1N7F for the liprin-α1_PBM/GRIP1_PDZ6 complex). The value curve at the bottom panel indicates sequence conservation of liprin-α proteins. The conservation score for each residue was calculated in Jalview (Waterhouse et al., 2009) using the sequence alignment of liprin-α family members across species, including Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Xenopus tropicalis, Gallus gallus, Mus musculus, and Homo sapiens. The scores from 0 to 11 indicate the most variable to the most conserved state of each residue, colored from cyan to purple gradually.

FIGURE 2

Liprin-α SAM123 mediates supramolecular assemblies. (A) The structure of liprin-α SAM123. The SAM123 structure is derived from the liprin-α2/CASK complex (PDB id: 3TAC). (B) A structure model showing the SAM123-mediated protein assembly. The SAM123 structures in complex with CASK (PDB id: 3TAC), liprin-β1 (3TAD), and LAR (6KR4) are superimposed. (C) A schematic model indicates the target-binding surfaces of the liprin-α SAM123. Some surface patches on SAM2 and SAM3 may be also involved in protein binding. (D) Conformational dynamics of the αN-helix in the SAM1 domain. The rotational change of αN was indicated by a red bidirectional arrow. (E) Allosteric regulation of the binding of the liprin-α SAM123 to liprin-β1 and LAR-RPTPs. The SAM1 residues that are involved in the allosteric regulation were shown as sticks. The conformational propagation of these SAM1 residues upon LAR-RPTP binding leads to the clash (indicated by a red arrow) between the liprin-α SAM1 and liprin-β1 and thus blocks the liprin-α/β interaction.

FIGURE 3

N-terminal coiled coils mediate the self-assembly of liprin-α. (A) The solved structures of liprin-α N-terminus were indicated by black boxes. The H2 (PDB id: 7D2H), H3 (7D2E), and SAH (6IUH) segment structures of liprin-α2 were shown. (B) A model indicating that the dimeric H2 and H3 competitively transit between homo-tetramers and a H23-dimer. (C) A schematic cartoon showing the self-assembly mechanism of liprin-α CC1. The transition between dimers and higher oligomers may be controlled by unknown regulators. (D) A structure model showing the complete N-terminal structure of liprin-α. The H1 segment and CC2 was modeled as coiled coils and shown in gray.

FIGURE 4

Additional regions of liprin-α in protein–protein interactions. (A) The structure of the LCR in complex with mDia (PDB id: 4UWX). Base on another solved structure of mDia (PDB id: 2BAP), the surface on mDia that is involved in the autoinhibition formation was highlighted by a dotted hotpink circle, showing the two binding sites are largely overlapped. (B) The structure of the PBM in complex with the PDZ6 domain of GRIP1 (PDB id: 1N7F). (C) The manually modeled structure of the PP2A-B56/liprin-α_PBBM complex. The sequences of the PBBMs from different proteins in the solved structures were aligned with the PBBMs of liprin-αs. The residues that are involved in B56 binding were highlighted by red boxes.

FIGURE 5

A proposed model for liprin-α assembly in mediating protein accumulation in synapse development. (A) Liprin-α is self-assembled to form a large complex and to mediate protein assemblies. (B) The highly self-assembled liprin-α proteins, indicated by red arrows, organize different receptor clustering and protein condensates (indicated by dotted circles) on both presynaptic and postsynaptic membrane in synapse formation, although no direct evidence showing the involvement of liprin-α in the clustering of Neurexin and the condensation of the GIT1/PIX complex.