Anti-CD20 IgG monoclonal antibody (mAb)

Rocco Caliandro.

SASDMX3 – Anti-CD20 IgG antibody

Anti-CD20 IgG antibody (Rituximab heavy chain chimeric)
Anti-CD20 IgG antibody (Rituximab light chain chimeric)
MWexperimental 138 kDa
MWexpected 145 kDa
log I(s) 7.34×10-1 7.34×10-2 7.34×10-3 7.34×10-4
Anti-CD20 IgG antibody (Rituximab heavy chain chimeric) Anti-CD20 IgG antibody (Rituximab light chain chimeric) small angle scattering data  s, nm-1
ln I(s)
Anti-CD20 IgG antibody (Rituximab heavy chain chimeric) Anti-CD20 IgG antibody (Rituximab light chain chimeric) Guinier plot ln 7.34×10-1 Rg: 5.2 nm 0 (5.2 nm)-2 s2
(sRg)2I(s)/I(0)
Anti-CD20 IgG antibody (Rituximab heavy chain chimeric) Anti-CD20 IgG antibody (Rituximab light chain chimeric) Kratky plot 1.104 0 3 sRg
p(r)
Anti-CD20 IgG antibody (Rituximab heavy chain chimeric) Anti-CD20 IgG antibody (Rituximab light chain chimeric) pair distance distribution function Rg: 5.4 nm 0 Dmax: 19.7 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Anti-CD20 IgG antibody Rg histogram Rg, nm

log I(s)
 s, nm-1
Anti-CD20 IgG antibody (Rituximab heavy chain chimeric) Anti-CD20 IgG antibody (Rituximab light chain chimeric) OTHER model

log I(s)
 s, nm-1
Anti-CD20 IgG antibody (Rituximab heavy chain chimeric) Anti-CD20 IgG antibody (Rituximab light chain chimeric) DAMMIN model

Synchrotron SAXS data from solutions of the anti-CD20 IgG monoclonal antibody (mAb) in 0.1 M HEPES, pH 7.7 were collected on the B21 beam line at the Diamond Light Source (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Different solute concentration ranging from 1.00 to 6.00 mg/ml was measured at 5°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. Data from different concentrations were merged to get the final SAXS profile processed for modelling.

Modelling has been performed by using the averaged envelope obtained from 20 runs of DAMMIF, properly clustered, as input of a flexible fitting procedure based on molecular dynamics. The code NAMD with its extension named MDFF (molecular dynamics flexible fitting) was used. This was done to account for the extreme flexibility of the mAb, and its very peculiar shape, which is not easy to model as a molecular envelope. Ensemble analysis was performed using the ensemble optimization method (EOM). The EOM results of the resulting mAb ensemble, including selected model representatives, Rg, and Dmax distributions are located in the full entry zip archive. This study has been carried out in the framework of the AMECRYS project (http://www.amecrys-project.eu/) - Horizon 2020 Future and Emerging Technologies programme FET-OPEN - grant agreement no.712965.

Anti-CD20 IgG antibody (Rituximab heavy chain chimeric) (Anti-CD20 mAb (HC))
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   49.2 kDa
Sequence   FASTA
 
Anti-CD20 IgG antibody (Rituximab light chain chimeric) (Anti-CD20 mAb (LC))
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   23.1 kDa
Sequence   FASTA