Small-angle X-ray scattering structural insights into alternative pathway of actin oligomerization associated with inactivated state

Ryzhykau Y, Povarova O, Dronova E, Kuklina D, Antifeeva I, Ilyinsky N, Okhrimenko I, Semenov Y, Kuklin A, Ivanovich V, Fonin A, Uversky V, Turoverov K, Kuznetsova I, Biochemical and Biophysical Research Communications :149340 (2023) DOI

SASDTY4 – F-actin - Skeletal muscle actin from Oryctolagus cuniculus: fibrillar actin

Actin, alpha skeletal muscle
MWexperimental 3890 kDa
MWexpected 42 kDa
VPorod 4710 nm3
log I(s) 4.18×10-1 4.18×10-2 4.18×10-3 4.18×10-4
Actin, alpha skeletal muscle small angle scattering data  s, nm-1
ln I(s)
Actin, alpha skeletal muscle Guinier plot ln 4.18×10-1 Rg: 15.7 nm 0 (15.7 nm)-2 s2
(sRg)2I(s)/I(0)
Actin, alpha skeletal muscle Kratky plot 1.104 0 √3 sRg
p(r)
Actin, alpha skeletal muscle pair distance distribution function Rg: 18.2 nm 0 Dmax: 60 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Actin, alpha skeletal muscle DAMMIF model
log I(s)
 s, nm-1
Actin, alpha skeletal muscle OTHER [STATIC IMAGE] model
SAXS data from solutions of F-actin from Oryctolagus cuniculus (fibrillar actin) in 5 mM Tris/Tris-HCl, 0.1 mM CaCl2, 1 mM NaN3, 1.0 mM ATP, 50 mM KCl, 2 mM MgCl2, pH 8.1 were collected using a Rigaku MicroMax 007-HF instrument at the Moscow Institute of Physics and Technology (MIPT; Dolgoprudny, Russian Federation) equipped with a multiwire gas-filled ASM DTR Triton 200 detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.15406 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 6.3 mg/ml were measured at 20°C. Five successive 1800 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 best approximation for F-actin SAXS data, based on simple shaped models in SasView program, is achieved by the semi-flexible elliptical cylinder. Major and minor ellipse axes are 8.5 nm and 5.2 nm, which is in good agreement with the dimensions of the known F-actin structure (PDB ID: 3J8I). SAXS data for F-actin are also well-fitted by DAMMIF program, using assumption of “prolate” particle. The transverse dimensions of the ab initio model coincide with those in 3J8I structure.

Actin, alpha skeletal muscle
Mol. type   Protein
Organism   Oryctolagus cuniculus
Olig. state   Monomer
Mon. MW   42.1 kDa
 
UniProt   P68135 (1-377)
Sequence   FASTA
 
PDB ID   3J8I