Integrating molecular dynamics simulation with small- and wide-angle X-ray scattering to unravel the flexibility, antigen-blocking, and protease-restoring functions in a hindrance-based pro-antibody.

Liao JM, Hong ST, Wang YT, Cheng YA, Ho KW, Toh SI, Shih O, Jeng US, Lyu PC, Hu IC, Huang MY, Chang CY, Cheng TL, Protein Sci 33(9):e5124 (2024) Europe PMC

SASDSN8 – Pro-Nivolumab, Lu02

Pro-Nivolumab, Lu02
MWexperimental 59 kDa
MWexpected 54 kDa
VPorod 69 nm3
log I(s) 6.09×10-2 6.09×10-3 6.09×10-4 6.09×10-5
Pro-Nivolumab, Lu02 small angle scattering data  s, nm-1
ln I(s)
Pro-Nivolumab, Lu02 Guinier plot ln 6.09×10-2 Rg: 3 nm 0 (3 nm)-2 s2
(sRg)2I(s)/I(0)
Pro-Nivolumab, Lu02 Kratky plot 1.104 0 3 sRg
Dmax: 11.5 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Pro-Nivolumab, Lu02 AMBER model

Synchrotron SAXS data from solutions of Pro-Nivolumab, Lu02 in 20 mM Tris, 100 mM NaCl, pH 8 were collected on the TPS13A beam line at the NSRRC storage ring (Hsinchu, Taiwan) using a Eiger X 1M & 9M detector at a sample-detector distance of 2.5 m and at a wavelength of λ = 0.16 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 100.00 μl sample at 10.6 mg/ml was injected at a 0.35 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 10°C. Five successive 2 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.

Pro-Nivolumab, Lu02
Mol. type   Protein
Olig. state   Monomer
Mon. MW   54.4 kDa
Sequence   FASTA