Allergen-induced structural rearrangements in IgE: insights from SAXS and molecular dynamics.

Gómez-Velasco H, García-Ramírez B, Siliqi D, Graewert MA, Quintero-Martinez A, Ortega E, Rodríguez-Romero A, Int J Biol Macromol :147658 (2025) Europe PMC

SASDXJ4 – Allergen Hev b 8 protein, Profilin-2

Profilin-2
MWI(0) 12 kDa
MWexpected 18 kDa
VPorod 21 nm3
log I(s) 6.74×10-2 6.74×10-3 6.74×10-4 6.74×10-5
Profilin-2 small angle scattering data  s, nm-1
ln I(s)
Profilin-2 Guinier plot ln 6.74×10-2 Rg: 1.7 nm 0 (1.7 nm)-2 s2
(sRg)2I(s)/I(0)
Profilin-2 Kratky plot 1.104 0 √3 sRg
p(r)
Profilin-2 pair distance distribution function Rg: 1.5 nm 0 Dmax: 4.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Profilin-2 GASBOR model
log I(s)
 s, nm-1
Profilin-2 PDB (PROTEIN DATA BANK) model
A low-resolution dummy residue model was generated by using GASBOR. In this SAXS model the crystallographic model (PDB entry 7SBD, chain C), confirms the good quality of sample preparation before running the experiments for its complex with IgE antibody.

Synchrotron SAXS data from solutions of allergen Hev b 8 protein, Profilin-2 in 20 mM Tris, 50 mM NaCl, pH 8.4 were collected on the P12 beamline at DESY (Hamburg, Germany) using a Pilatus 6m detector at a sample-detector distance of 3.0 m and a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). A solute concentration of 0.6 mg/ml was measured at 20°C. 20 successive 0.51 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged and brought into the absolute scale with respect to the intensity of the empty capillary and the water; the scattering of the solvent-blank was subtracted.

Profilin-2 (PRF)
Mol. type   Protein
Organism   Hevea brasiliensis
Olig. state   Monomer
Mon. MW   18.3 kDa
 
UniProt   Q9STB6 (1-131)
Sequence   FASTA
 
PDB ID   7SDB