Fig. 3: Molecular details of the NET1ΔC - SOS interaction. | Nature Communications

Fig. 3: Molecular details of the NET1ΔC - SOS interaction.

From: The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation

Fig. 3

a SOSab (silver) and SOScd (yellow) binding motifs from our X-ray crystal structure. Individual loop segments are labelled a–d, accordingly. Amino acid residues studied in mutagenesis experiments are underlined and depicted as loop ab (RRXRXN), loop cd (RH-KHRK) mutant versions. b ELISA-based GAG-binding studies of wild type NET1ΔC and mutant versions of NET1ΔC. The coordinates of the mutated residues at the GAG binding sites are shown at the bottom of the panel. c Molecular dynamics cluster analysis of NET1ΔC-dp10 and (d) NET1ΔC-dp24 with SOS moieties shown in yellow. RMSD analysis shows a minimal change in the NET1-HO conformation (red) throughout the simulation, whereas the conformations of both HO-dp10 and HO-dp24 (blue) experienced some degree of flexibility. This is expected due to the flexible nature of the GAG molecule.

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