Stretching the chains: the destabilizing impact of Cu(2+) and Zn(2+) ions on K48-linked diubiquitin.

Mangini V, Grasso G, Belviso BD, Sciacca MFM, Lanza V, Caliandro R, Milardi D, Dalton Trans (2023) Europe PMC

SASDSG2 – K48-linked diubiquitin in the presence of zinc ion

Polyubiquitin-C
MWexperimental 10 kDa
MWexpected 17 kDa
VPorod 20 nm3
log I(s) 2.44×10-3 2.44×10-4 2.44×10-5 2.44×10-6
Polyubiquitin-C small angle scattering data  s, nm-1
ln I(s)
Polyubiquitin-C Guinier plot ln 2.44×10-3 Rg: 2.0 nm 0 (2.0 nm)-2 s2
(sRg)2I(s)/I(0)
Polyubiquitin-C Kratky plot 1.104 0 √3 sRg
p(r)
Polyubiquitin-C pair distance distribution function Rg: 2.1 nm 0 Dmax: 7.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
log I(s)
 s, nm-1
Polyubiquitin-C OTHER model
Synchrotron SAXS data from solutions of K48-linked diubiquitin in the presence of zinc ion in 20 mM HEPES, 100 mM NaCl, pH 7 were collected on the B21 beam line at the Diamond Light Source storage ring (Didcot, UK) using a Eiger 4M detector at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 4 mg/ml was injected at a 0.16 ml/min flow rate onto a Shodex KW402.5-4F column at 20°C. One 3 second frame was collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Caution. SAXS data used to calculate P(r) profile are different to the main display data.

Polyubiquitin-C
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   17.1 kDa
 
UniProt   P0CG48 (1-152)
Sequence   FASTA