Structural Insights into the Mechanism of a Nanobody That Stabilizes PAI-1 and Modulates Its Activity

Sillen M, Weeks S, Strelkov S, Declerck P, International Journal of Molecular Sciences 21(16):5859 (2020) DOI

SASDJW5 – Plasminogen activator inhibitor-1 (PAI-1) W175F bound to nanobody Nb93

Plasminogen activator inhibitor 1
VHH-s-a93 (Ig module Nb93)
MWexperimental 58 kDa
MWexpected 56 kDa
VPorod 80 nm3
log I(s) 2.14×10-2 2.14×10-3 2.14×10-4 2.14×10-5
Plasminogen activator inhibitor 1 VHH-s-a93 (Ig module Nb93) small angle scattering data  s, nm-1
ln I(s)
Plasminogen activator inhibitor 1 VHH-s-a93 (Ig module Nb93) Guinier plot ln 2.14×10-2 Rg: 2.9 nm 0 (2.9 nm)-2 s2
(sRg)2I(s)/I(0)
Plasminogen activator inhibitor 1 VHH-s-a93 (Ig module Nb93) Kratky plot 1.104 0 3 sRg
p(r)
Plasminogen activator inhibitor 1 VHH-s-a93 (Ig module Nb93) pair distance distribution function Rg: 3.0 nm 0 Dmax: 9.7 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Plasminogen activator inhibitor 1 VHH-s-a93 (Ig module Nb93) OTHER model

Synchrotron SAXS data from solutions of PAI-1 bound to Nb93 in 30 mM BIS-TRIS pH 5.5, 300 mM sodium chloride, 5% v/v glycerol were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.10332 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 13 mg/ml was injected at a 0.30 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 15°C. 480 successive 0.990 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.

Plasminogen activator inhibitor 1 (PAI-1)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   42.7 kDa
 
UniProt   P05121 (24-402)
Sequence   FASTA
 
VHH-s-a93 (Ig module Nb93) (Nb93)
Mol. type   Protein
Organism   Vicugna pacos
Olig. state   Monomer
Mon. MW   13.2 kDa
Sequence   FASTA