Fig. 3: Molecular dynamic simulations reproduce the molecular reach obtained by bivalent SPR highlighting the contribution of the antigen to reach.
From: The molecular reach of antibodies crucially underpins their viral neutralisation capacity
A Coarse-grained structure of IgG1 FD-11A bound to two RBD antigens indicating the Lys15 biotinylation site (within an N-terminus AviTag), which anchors RBD to the SPR surface. The anchor point of RBD forming interface 1 was fixed while the one forming interface 2 was moved at a constant velocity. B The fraction of native contacts at the indicated interface (normalised to the number of contacts in the native structure) and C the force in the pulling direction exerted by the steering restraint (i.e., constant velocity over time). D Snapshots from the simulations at the indicated time points indicating the distance between Lys15 on each RBD. The maximum distance in this trajectory was 34.4 nm. E The maximum Lys15-Lys15 distance from N = 50 independent trajectories over the interface binding strength (η). The molecular reach is defined as the largest distance (horizontal dashed line). Mean values are shown, error bars are 95% confidence intervals computed from bootstrapping with 106 independent samples. F The molecular reach for the indicated antibody estimated by simulation or experiment (left) and the difference between these estimates (right). Reach values measured by SPR are shown as mean values ± SD determined from N ≥ 2 independent experiments for each antibody (EY6A: N = 6, FD-5D: N = 6, FD11A: N = 8, CR3022: N = 5, FI-3A: N = 2, REGN10987: N = 3). A one-sample t-test is used to determine the p-value for the null hypothesis that the mean is 0 (N = 6). Source data are provided as a Source Data file.
