Modeling the ComD/ComE/comcde interaction network using small angle X-ray scattering.

Sanchez D, Boudes M, van Tilbeurgh H, Durand D, Quevillon-Cheruel S, FEBS J 2015 Apr;282(8):1538-53 PubMed

SASDAC7 – Complex LytTR-comcde

comcde
Response regulator
MWexperimental 56 kDa
MWexpected 52 kDa
VPorod 74 nm3
log I(s) 2.36×10-2 2.36×10-3 2.36×10-4 2.36×10-5
comcde Response regulator small angle scattering data  s, nm-1
ln I(s)
comcde Response regulator Guinier plot ln 2.36×10-2 Rg: 3.6 nm 0 (3.6 nm)-2 s2
(sRg)2I(s)/I(0)
comcde Response regulator Kratky plot 1.104 0 3 sRg
p(r)
comcde Response regulator pair distance distribution function Rg: 3.6 nm 0 Dmax: 12.5 nm

Experimental data validation


Fits and models


log I(s)
 s, nm-1
comcde Response regulator SASREF model
X-ray synchrotron radiation scattering data from solutions of complex LytTR-comcde in 50 mM MES 200 mM NaCl, 2% (vol/vol) glycerol, 5 mM β-mercaptoethanol were collected on the SWING beamline on the storage ring SOLEIL (Saint-Aubin, France) using a CCD AVIEX detector (s = 4π sin θ/λ, where 2θ is the scattering angle). The sample was loaded on a SE-HPLC column on line with the SAXS measuring cell. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The scattered intensities were displayed on an absolute scale (cm-1) using the scattering by water. Frames were examined individually and 16 identical frames were averaged and further processed. The corresponding concentration was 0.4 g/L.

Use of SAXS to describe the interaction between the LytTR domain of the response regulator ComE from S. pneumonia and the promoter region comcde. The complex is constituted of two monomers of LytTR and one molecule of comcde. The SAXS data were collected directly after elution through an on-line size-exclusion high-performance liquid chromatography (SEC-HPLC) column. The molecular weight is not estimated from I(0) because the concentration of the complex cannot be accurately determined. It is obtained from the macromolecule volume using the method developed by Craievich’s team (the SAXS Mow program).

comcde
Mol. type   DNA
Organism   Streptococcus pneumoniae
Olig. state   Other
Mon. MW   23.5 kDa
Sequence   FASTA
 
Response regulator (LytTR)
Mol. type   Protein
Organism   Streptococcus pneumoniae
Olig. state   Monomers
Mon. MW   14.4 kDa
 
UniProt   Q8DMW5 (138-250)
Sequence   FASTA