Computational protocol: Homodimerization of the Lymph Vessel Endothelial Receptor LYVE-1 through a Redox-labile Disulfide Is Critical for Hyaluronan Binding in Lymphatic Endothelium*

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Protocol publication

[…] Samples of monomeric and dimeric LYVE-1 were produced as outlined above. SAXS data were collected at beamline X-33, DESY, Germany, at concentrations of between 9.2 and 4.6 mg/ml (monomer) and 6.6 and 4.6 mg/ml (dimer). Scattering data from matched buffer solutions were subtracted using the program PRIMUS (), and the radius of gyration, forward scattering intensity, and distance distribution function p(r) were evaluated with the program GNOM (). Particle shapes were generated from the experimental scattering profiles using ab initio modeling with DAMMIF (). Multiple DAMMIF simulations (>20) were performed for both monomer and dimer (with and without p2 symmetry constraints for the dimer), and these generated very similar but not identical shapes in each case. Enforcing p2 symmetry did not appreciably alter the shape or improve the fit to the raw data, so all dimer models presented are those created without p2 symmetry. An averaged filtered shape was generated using DAMAVER and DAMFILT (). […]

Pipeline specifications

Software tools ATSAS, DAMMIF
Application Small-angle scattering
Organisms Dipturus trachyderma
Chemicals Cysteine