Fig. 3: Binding site mapping of RRE-IIB-0/rev complexes by CAD MS.
From: Native mass spectrometry reveals the initial binding events of HIV-1 rev to RRE stem II RNA
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-IIB-0 + 1·rev - 15H)15−, at 150 eV laboratory frame collision energy and the corresponding binding region (blue) mapped onto the predicted secondary structure of RRE-IIB-0 (b) show poor agreement with binding sites indicated by chemical interference and mutation analysis (c). d Occupancies of fragments from CAD of 1:2 complex ions, (RRE-IIB-0 + 2·rev - 16H)16−, at 208 eV and corresponding binding sites (violet) mapped onto the RRE-IIB-0 structure (e) show good agreement with chemical interference and mutation analysis data (c). Darker and lighter colors in c–e stand for stronger and weaker binding and interference, respectively, and black circles in c illustrate interference with rev binding by phosphate ethylation.
