Lateral access mechanism of LPA receptor probed by molecular dynamics simulation

G-protein-coupled receptors (GPCR) are a family of membrane receptors that play important roles in the regulation of various physiological phenomena. LPA receptors (LPA(1-6)) are members of the class A GPCRs, which transduce a lysophosphatidic acid (LPA) signal across the cell membrane and evoke various responses, including cellular survival, proliferation, differentiation, and migration. The crystal structure of LPA(6) revealed a gap between its transmembrane helices (TMs), which is opened toward the membrane side. This led to the proposal of the lateral access model, in which its lipophilic ligand directly enters the binding pocket through the gap structure at the membrane. In this study, we performed molecular dynamics (MD) simulations and Markov state model (MSM) analyses of LPA(6) and LPA, to elucidate the long timescale dynamics of the ligand binding process. The results from the 71.4-mu s MD simulation suggested that the flexibility of the TMs constituting the gap structure enables the lateral entrance of the ligand, and the key interactions between the receptor and ligand facilitate the transition state of the ligand binding process.

Automated summary

The crystal structure of LPA(6) revealed a lateral gap structure that allows the lipophilic ligand to directly enter the binding pocket through the membrane. The flexibility of the gap structure on the membrane enables the lateral entrance of the ligand, facilitating the transition state of the ligand binding process.