Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro.

Yadav R, Courouble VV, Dey SK, Harrison JJEK, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E, Sci Adv 8(49):eadd2191 (2022) Europe PMC

SASDPY2 – SARS-CoV-2 non-structural protein 7-8 (nsp7-8) polyprotein monomer

Replicase polyprotein 1ab
MWI(0) 34 kDa
MWexpected 31 kDa
VPorod 50 nm3
log I(s) 7.92×10-1 7.92×10-2 7.92×10-3 7.92×10-4
Replicase polyprotein 1ab small angle scattering data  s, nm-1
ln I(s)
Replicase polyprotein 1ab Guinier plot ln 7.93×10-1 Rg: 2.5 nm 0 (2.5 nm)-2 s2
(sRg)2I(s)/I(0)
Replicase polyprotein 1ab Kratky plot 1.104 0 3 sRg
p(r)
Replicase polyprotein 1ab pair distance distribution function Rg: 2.5 nm 0 Dmax: 8.8 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Replicase polyprotein 1ab DAMMIF model

Synchrotron SAXS data from solutions of SARS-CoV-2 non-structural protein 7-8 (nsp7-8) polyprotein monomer in 50 mM Tris, 500 mM NaCl, 5% glycerol, and 1 mM TCEP, pH 8 were collected on the BioCAT 18ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA) using a Pilatus3 X 1M detector at a sample-detector distance of 3.6 m and at a wavelength of λ = 0.1033 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line co-flow (sheath cell) size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A sample at 8 mg/ml was injected onto a GE Superdex 200 Increase 10/300 column at 22°C. 1300 successive 0.500 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.

SEC-MALS-SAXS. Size separation used a 1260 Infinity II HPLC (Agilent Technologies). UV data was measured in the Agilent, and MALS-DLS-RI data by DAWN HELEOS-II (17 MALS + 1 DLS channels) and Optilab T-rEX (RI) instruments (Wyatt Technology).

Replicase polyprotein 1ab (nsp7-8)
Mol. type   Protein
Organism   Severe acute respiratory syndrome coronavirus 2
Olig. state   Monomer
Mon. MW   31.3 kDa
 
UniProt   P0DTD1 (3860-4140)
Sequence   FASTA