Extended Data Fig. 8: Design and characterization of sensors for anti-SARS-CoV-2 antibodies.

a, b, Experimental screening of de novo sensors for antibodies against the SARS-CoV-2 membrane protein (a) and the nucleocapsid protein (b). Selected epitopes of the membrane protein (M1, M3 and M4) and the nucleocapsid protein (N6 and N62) were computationally grafted into lucCage at different positions of the latch. Each design comprised two tandem copies of each epitope, separated by a flexible linker, to take advantage of the bivalent binding of antibodies. All designs were experimentally screened for an increase in luminescence at 20 nM of each lucCage design and 20 nM of lucKey in the presence of anti-M rabbit polyclonal antibodies (a) or anti-N mouse monoclonal antibody at 100 nM (clone 18F629.1) (b). These experiments were performed in duplicate (a) or single replicates (b) in two independent instances, and representative data are shown. The luminescence values were normalized to 100 in the absence of antibodies. Designs M3_1-17_334 and N62_369-382_340 were selected as the best candidates owing to high sensitivity and stability, and were named lucCageSARS2-M and ucCageSARS2-N, respectively. c, Left, structural model of lucCageSARS2-M, showing a close-up view of the predicted interface between the M3 epitope (red) and lucCage (blue). Middle, determination of lucCageSARS2-M sensitivity to anti-M polyclonal antibody. Bioluminescence was measured over 4,000 s in the presence of serially diluted anti-M polyclonal antibody. The lucCageSARS2-M:lucKey concentrations (in nM) were 50:50 (top) and 5:5 (bottom). Right, LOD calculations for the sensor at different concentrations. d, Left, structural model of lucCageSARS2-N, showing a close-up view of the predicted interface between the N62 epitope (purple) and lucCage (blue). Middle,determination of lucCageSARS2-N sensitivity to anti-N monoclonal antibody. Bioluminescence was measured over 4,000 s for lucCageSARS2-N plus lucKey at 50 nM in the presence of serially diluted anti-N antibody. Right, LOD calculations for the sensor. All experiments were performed in triplicate unless specifically indicated, representative data are shown, and data are mean ± s.d.