Figure 4.

Binding model of DNA–SOD1 complexes. (A) The SL bases directly involved in the DNA–SOD1 interactions fixed by 1% formaldehyde cross-linking were determined by capillary electropherograms following DNase I digestion of 5′-FAM-labelled pentameric SL. Stars represent the sites protected by SOD1. (C) Capillary electropherograms were generated from the SL-SOD1 complexes treated without 1% formaldehyde following DNase I digestion of 5′-FAM-labelled SL. (B and D) Cartoon representation of SL highlights the SOD1 binding DNA sites resulted from DNase I footprinting tests in (A) and (C). (E) The structural docking model for S1-DNA complex. The purple regions in DNA represent the potential SOD1 binding sites in S1 motif. α-helix, red; β-sheet, yellow; random coil and DNA, green; SOD1 binding sites, purple. (F) A final concentration of 100 μM SOD1 and 100 μM of S1 was incubated in 20 mM Tris–HCl (pH 7.4) at 37°C for 24 h. Before data collection, the sample was centrifuged at 10,000 rpm at 4°C for 10 min to remove the potential aggregates. Based on SAXS results, space-filling models of the S1-SOD1 complexes were constructed. Space-filling models of the S1-SOD1 complexes derived from SAXS data are depicted in grey, with HADDOCK model of this complexes docked into mesh envelope.