Fig. 4. Binding site mapping of RRE-TR-0/rev complexes by CAD MS.

a Site-specific occupancies (O) of c (left axis) and y (right axis) fragments with rev ARM peptide from CAD of 1:1 complex ions, (RRE-TR-0 + 1·rev - 14H)¹⁴⁻, at 137.2 eV and the corresponding binding region (blue) mapped onto the predicted secondary structure of RRE-TR-0 (b) show poor agreement with binding sites in the NMR structure (e). c Occupancies of fragments from CAD of 1:2 complex ions, (RRE-TR-0 + 2·rev - 14H)¹⁴⁻, at 175.5 eV and corresponding binding sites (violet) mapped onto the RRE-TR-0 structure (d) show good agreement with binding sites in the NMR structure (e). Darker and lighter colors in b, d, and e stand for stronger and weaker binding, respectively.