Extended Data Fig. 8: MD simulation study assessing ligand-induced S1PR1 activation.
From: Structural basis of sphingosine-1-phosphate receptor 1 activation and biased agonism
a, Distance distribution matrix of the key residues with S1P (cyan), FTY720-P (green), BAF312 (purple), and ML056 (pink). b, Interaction traces of three replicas (blue, red, and orange) with each ligand. Distance of the nearest non-hydrogen atom pairs is drawn with thick 2-ns moving average traces and thin unsmoothed traces (2-ps interval). c, Plots of averaged distances in Interactions 1-3 from the three replicas (the same color schemes as in b). Bars and error bars represent mean and SEM, respectively. Dotted lines indicate distances in the ML056-bound S1PR1 structure (PDB ID: 3V2Y). d, Fractions of contacts in Interactions 1-3 from the three replicas. Contact thresholds were set as the distances in the ML056-bound S1PR1. Statistical analyses were performed using the ordinary one-way ANOVA followed by the Dunnett’s post hoc test (c, d).
