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

SASDVH9 – allergen Hev b 8 protein, Profilin-2 (TAG)

Profilin-2
MWexperimental 20 kDa
MWexpected 18 kDa
VPorod 30 nm3
log I(s) 1.25×10-1 1.25×10-2 1.25×10-3 1.25×10-4
Profilin-2 small angle scattering data  s, nm-1
ln I(s)
Profilin-2 Guinier plot ln 1.25×10-1 Rg: 2 nm 0 (2 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: 2.1 nm 0 Dmax: 7.4 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Profilin-2 CORAL model

log I(s)
 s, nm-1
Profilin-2 GASBOR model

Synchrotron SAXS data from solutions of allergen Hev b 8 protein, Profilin-2 (TAG) in 20 mM Tris, 50 mM NaCl, pH 8.4 were collected on the B21 beam line at the Diamond Light Source storage ring (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.094 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.9 and 6.9 mg/ml were measured at 20°C. 20 successive 1 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.

Synchrotron SAXS data from solutions of Profilin (+TAG) in 20 mM Tris, 50 mM NaCl, pH 8.4 were collected on the B21 beam line at Diamond (Didcot, UK) using an EigerX 4M-Detrics detector at a sample-detector distance of 3.7 m and the wavelength of 0.95 A. The experiment was performed in batch at four dilution, starting at 6.9 mg/ml concentration. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The data didn't presented concentration dependence. Four dilution data were automatically merged by PRIMUS. The molecular weight of a Profilin (+TAG), is 18.4 kDa. In the Ca-model (GASBOR) was possible not only to fit the PDB model (from 7sbd) but to see the TAG (40 dummy CA) as a long tail, which was next reconstructed by using of CORAL program.

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   7SBD