Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2

Custódio T, Das H, Sheward D, Hanke L, Pazicky S, Pieprzyk J, Sorgenfrei M, Schroer M, Gruzinov A, Jeffries C, Graewert M, Svergun D, Dobrev N, Remans K, Seeger M, McInerney G, Murrell B, Hällberg B, Löw C, Nature Communications 11(1) (2020) DOI

SASDJF4 – Synthetic nanobody Sybody 23 (Sy23)

Synthetic nanobody Sybody 23
MWI(0) 21 kDa
MWexpected 16 kDa
VPorod 22 nm3
log I(s) 1.91×103 1.91×102 1.91×101 1.91×100
Synthetic nanobody Sybody 23 small angle scattering data  s, nm-1
ln I(s)
Synthetic nanobody Sybody 23 Guinier plot ln 1.92×103 Rg: 2.1 nm 0 (2.1 nm)-2 s2
(sRg)2I(s)/I(0)
Synthetic nanobody Sybody 23 Kratky plot 1.104 0 √3 sRg
p(r)
Synthetic nanobody Sybody 23 pair distance distribution function Rg: 2.2 nm 0 Dmax: 8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Synthetic nanobody Sybody 23 CORAL model
Synchrotron SAXS data from solutions of Synthetic nanobody Sybody 23 (Sy23) in 50 mM Tris 100 mM NaCl, pH 7.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 1.67 mg/ml was measured at 20°C. 10 successive 0.100 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Synthetic nanobody Sybody 23 (Sy23)
Mol. type   Protein
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   15.7 kDa
Sequence   FASTA