Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method

Sagar A, Jeffries C, Petoukhov M, Svergun D, Bernadó P, Journal of Chemical Theory and Computation (2021) DOI

SASDHF8 – Histatin 5 (Histatin 3; His3-(20-43)-peptide) at 4.89 mg/ml in 20 mM Tris 150 mM NaCl pH 7.0, 298 K

Histatin-3, His3-(20-43)-peptide
MWI(0) 3 kDa
MWexpected 3 kDa
VPorod 3 nm3
log I(s) 3.00×10-3 3.00×10-4 3.00×10-5 3.00×10-6
Histatin-3, His3-(20-43)-peptide small angle scattering data  s, nm-1
ln I(s)
Histatin-3, His3-(20-43)-peptide Guinier plot ln 3×10-3 Rg: 1.4 nm 0 (1.4 nm)-2 s2
(sRg)2I(s)/I(0)
Histatin-3, His3-(20-43)-peptide Kratky plot 1.104 0 √3 sRg
p(r)
Histatin-3, His3-(20-43)-peptide pair distance distribution function Rg: 1.5 nm 0 Dmax: 6 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Histatin 5 (Histatin 3; His3-(20-43)-peptide) at 4.89 mg/ml in 20 mM Tris 150 mM NaCl pH 7.0, 298 K Rg histogram Rg, nm
log I(s)
 s, nm-1
Histatin 5 (Histatin 3; His3-(20-43)-peptide) at 4.89 mg/ml in 20 mM Tris 150 mM NaCl pH 7.0, 298 K Rg histogram Rg, nm
log I(s)
 s, nm-1
Histatin 5 (Histatin 3; His3-(20-43)-peptide) at 4.89 mg/ml in 20 mM Tris 150 mM NaCl pH 7.0, 298 K Rg histogram Rg, nm
Synchrotron SAXS data from solutions of Histatin 5 in 20 mM Tris, 150 mM NaCl, pH 7 were collected on the EMBL P12 beam line at PETRA III (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 4.89 mg/ml was measured at 25°C. 30 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.

The data are the combined results from nine replicates and are normalised to protein concentration. The concentration independent MW estimate is 3.5 kDa in the credibility interval 3.0-4.1 kDa. The EOM fits and Rg distributions show the effect of modelling the short histatin 5 peptide (24 amino acids) using a full-atomistic model cohort for EOM refinement (top); the use of a model cohort constructed using a set of dummy-residue (DR) specific form-factors for each individual amino acid in the sequence (middle) and; a model cohort generated using the application of an averaged DR amino acid form factor for each amino acid in the sequence (bottom). The full EOM results, including the atomistic models (generated using Flexible-Meccano) and the effect of fixing the ensemble sizes (20 or 50) during the EOM analysis are included in the full entry zip archive.

Tags: idp
Histatin-3, His3-(20-43)-peptide (Histatin 5)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   3.0 kDa
 
UniProt   P15516 (20-43)
Sequence   FASTA