Figure 4 | Scientific Reports

Figure 4

From: Nucleic acid recognition and antiviral activity of 1,4-substituted terphenyl compounds mimicking all faces of the HIV-1 Rev protein positively-charged α-helix

Figure 4The alternative text for this image may have been generated using AI.

RRE subdomain IIB recognition by 1,4-terphenyl compounds. (A) Results of fluorescence intensity experiments. Left: comparison between first-site (Kd1) and second-site (Kd2) equilibrium dissociation constants for the interaction between IIBh and 1,4-terphenyl molecules. Right: comparison of the IIBh binding curve of terphenyl 1a (black) with the TARh association curve (magenta), and with IIBh binding curves obtained in the presence of a 10-fold molar excess of unlabelled competitor RNA (tRNALys; red) or unlabelled competitor double-helical DNA (LTRd; blue). Solution conditions: 10 mM sodium phosphate pH 6.6 and 0.1 mM EDTA. (B) Titration of IIBh with terphenyl 1a monitored by NMR spectroscopy. The H5-H6 region of the TOCSY spectrum of unbound IIBh (blue) is superposed on the spectra of complexes with increasing RNA:1a molar ratios, color-coded as indicated in the graph. A map of the 1a binding site in the IIBh hairpin is shown on the right. Nucleotides whose aromatic protons undergo chemical shift variations upon the addition of two equivalents of 1a are highlighted in orange and red (Δδ ≥0.04 and 0.08 ppm, respectively). Nucleotides with overlapped aromatic resonances are black-coloured, and residues whose aromatic signals were not affected by ligand binding are coloured grey. Solution conditions: 10 mM sodium phosphate pH 6.0 and 0.1 mM EDTA. (C) Model of a 1:1 complex between RRE loop IIB and 1a (depicted with yellow carbon atoms), obtained from unrestrained docking calculations with the 4PMI PDB structure12. The image was generated with MOE 2019.0102 (www.chemcomp.com) and shows superimposed the converged docking poses of 1a.

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