Structural insights into ligand recognition by the lysophosphatidic acid receptor LPA6

Abstract

Lysophosphatidic acid (LPA) is a bioactive lipid composed of a phosphate group, a glycerol backbone, and a single acyl chain that varies in length and saturation. LPA activates six class A G-protein-coupled receptors to provoke various cellular reactions. Because LPA signalling has been implicated in cancer and fibrosis, the LPA receptors are regarded as promising drug targets. The six LPA receptors are subdivided into the endothelial differentiation gene (EDG) family (LPA-LPA) and the phylogenetically distant non-EDG family (LPA-LPA). The structure of LPA has enhanced our understanding of the EDG family of LPA receptors. By contrast, the functional and pharmacological characteristics of the non-EDG family of LPA receptors have remained unknown, owing to the lack of structural information. Although the non-EDG LPA receptors share sequence similarity with the P2Y family of nucleotide receptors, the LPA recognition mechanism cannot be deduced from the P2Y and P2Y structures because of the large differences in the chemical structures of their ligands. Here we determine the 3.2 Å crystal structure of LPA, the gene deletion of which is responsible for congenital hair loss, to clarify the ligand recognition mechanism of the non-EDG family of LPA receptors. Notably, the ligand-binding pocket of LPA is laterally open towards the membrane, and the acyl chain of the lipid used for the crystallization is bound within this pocket, indicating the binding mode of the LPA acyl chain. Docking and mutagenesis analyses also indicated that the conserved positively charged residues within the central cavity recognize the phosphate head group of LPA by inducing an inward shift of transmembrane helices 6 and 7, suggesting that the receptor activation is triggered by this conformational rearrangement.

Quantifying alkyl chain disorder in crystalline models of lipid bilayers using Raman spectroscopy

“…Alkyl chain packing and disorder is of continued interest across a range of fields, including biology where disorder may have an impact on ligand recognition processes in lipid bilayers, self‐assembly of liquid‐crystal materials, crystal engineering, and packing density in multilamellar liposomes . Understanding structural chemistry of biological membrane lipid bilayers is challenged by the difficulty of crystallising such systems, and there is an ongoing demand for spectroscopic approaches, such as solution nuclear magnetic resonance (NMR) and vibrational spectroscopy, for studying bilayer systems that are difficult or impossible to crystallise.…”

Lysophosphatidic acid type 2 receptor agonists in targeted drug development offer broad therapeutic potential

“…Thus, a drug discovery effort aimed at the development of LPA 2 GPCR-specific agonists was launched. Subsequent to the computational modeling of the EDG family GPCRs (6,7,9,10,32), several crystal structures of LPA and S1P GPCRs have been solved (24,(33)(34)(35). The validated computational models and the crystal structures now provide a robust modeling platform for virtual high-throughput-guided LPA GPCR ligand discovery.…”

Uveal Melanoma OncogeneCYSLTR2Encodes a Constitutively Active GPCR Highly Biased Toward Gq Signaling

“…We decided to use the active and inactive state homology models of CysLTR2 from the GPCRdb 34 , which are based on structural templates from the structures of the C-C chemokine receptor 5 (CCR5) for the inactive state 35 and the lysophosphatidic acid receptor 6 (LPA6) for the active state 36 . We introduced the L129Q 3.43 mutation with the Rosetta software to optimize the resulting models by local side-chain repacking and constrained energy minimization, and to predict the difference in free energies ΔΔG of the wild-type and mutant structures 37 .…”