Targeting the N-Terminus Domain of the Coronavirus Nucleocapsid Protein Induces Abnormal Oligomerization via Allosteric Modulation

Hsu J, Chen J, Lin S, Hong J, Chen Y, Jeng U, Luo S, Hou M Frontiers in Molecular Biosciences 9 (2022) DOI

SASDNJ6 – full-length MERS CoV N-protein complexed with 5-(2-methoxyethoxy)-1H-indole (P4-4 compound)

Nucleoprotein
5-(2-methoxyethoxy)-1H-indole
MWexperimental 183 kDa
MWexpected 183 kDa
VPorod 500 nm3
log I(s) 1.78×10-2 1.78×10-3 1.78×10-4 1.78×10-5
Nucleoprotein 5-(2-methoxyethoxy)-1H-indole small angle scattering data  s, nm-1
ln I(s)
Nucleoprotein 5-(2-methoxyethoxy)-1H-indole Guinier plot ln 1.79×10-2 Rg: 6.0 nm 0 (6.0 nm)-2 s2
(sRg)2I(s)/I(0)
Nucleoprotein 5-(2-methoxyethoxy)-1H-indole Kratky plot 1.104 0 3 sRg
p(r)
Nucleoprotein 5-(2-methoxyethoxy)-1H-indole pair distance distribution function Rg: 6.1 nm 0 Dmax: 18.5 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Nucleoprotein 5-(2-methoxyethoxy)-1H-indole CORAL model

Synchrotron SAXS data from solutions of full-length MERS CoV N-protein complexed with 5-(2-methoxyethoxy)-1H-indole (P4-4 compound) in 50 mM Tris-HCl, 150 mM NaCl, pH 8.5 were collected on the 23A beam line at the Taiwan Photon Source, NSRRC storage ring (Hsinchu, Taiwan) using a Pilatus 1M-F detector at a sample-detector distance of 2.5 m and at a wavelength of λ = 0.08 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 300.00 μl sample at 2 mg/ml was injected at a 0.02 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 14.9°C. 36 successive 30 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.

Quoted experimental molecular weight (183 kDa) cannot be verified from the data. The Dmax is likely underestimated.

Nucleoprotein
Mol. type   Protein
Organism   Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)
Olig. state   Tetramer
Mon. MW   45.7 kDa
 
UniProt   K9N4V7 (1-411)
Sequence   FASTA
 
5-(2-methoxyethoxy)-1H-indole
Mol. type   Other
Olig. state   Tetramer
Mon. MW   0.2 kDa
Chemical formula