Programmable Protein-DNA Composite Nanostructures: from Nanostructure Construction to Protein-Induced Micro-Scale Material Self-Assembly and Functionalization.

Zhou W, Strmšek Ž, Snoj J, Škarabot M, Jerala R, Small 21(30):e2502060 (2025) Europe PMC

SASDW57 – SSRD-2xDGSt - Coiled-Coil Tetrahedron with Four Functional Domains (2x SpyCatcher, RFP, DCV) and Dual SpyCatcher-SpyTag Linkages with DCV-GFP-St Extension

TET12-2Sc-RFP-DCV
DCV-GFP-St
DCV-GFP-St
MWexperimental 220 kDa
MWexpected 192 kDa
VPorod 580 nm3
log I(s) 5.16×104 5.16×103 5.16×102 5.16×101
TET12-2Sc-RFP-DCV DCV-GFP-St DCV-GFP-St small angle scattering data  s, nm-1
ln I(s)
TET12-2Sc-RFP-DCV DCV-GFP-St DCV-GFP-St Guinier plot ln 5.16×104 Rg: 5.8 nm 0 (5.8 nm)-2 s2
(sRg)2I(s)/I(0)
TET12-2Sc-RFP-DCV DCV-GFP-St DCV-GFP-St Kratky plot 1.104 0 3 sRg
p(r)
TET12-2Sc-RFP-DCV DCV-GFP-St DCV-GFP-St pair distance distribution function Rg: 5.7 nm 0 Dmax: 17.3 nm

Data validation


Fits and models


log I(s)
 s, nm-1
TET12-2Sc-RFP-DCV DCV-GFP-St DCV-GFP-St MODELLER model

Synchrotron SAXS data from solutions of SSRD-2xDGSt - Coiled-Coil Tetrahedron with Four Functional Domains (2x SpyCatcher, RFP, DCV) and Dual SpyCatcher-SpyTag Linkages with DCV-GFP-St Extension in 20 mM Tris, 150 mM NaCL, 3% glycerol, pH 7.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123982 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 40.00 μl sample at 8 mg/ml was injected at a 0.70 ml/min flow rate onto a Cytiva Superdex 200 Increase 10/300 column at 20°C. 3000 successive 1 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.

Note: The experimentally determined protein mass (SEC-MALS) is overestimated due to the presence of a fluorescent protein in the sample. The light scattering laser operates at a wavelength that excites the fluorescent protein, leading to inaccurate signal measurements.

TET12-2Sc-RFP-DCV (SSRD)
Mol. type   Protein
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   109.0 kDa
Sequence   FASTA
 
DCV-GFP-St (DGSt)
Mol. type   Protein
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   41.3 kDa
Sequence   FASTA
 
DCV-GFP-St (DGSt)
Mol. type   Protein
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   41.3 kDa
Sequence   FASTA