Figure 1.

Structural details and system setup. (A) The sequences of the HIV-1 RRE RNA and the RSG-1.2 peptide are shown. The key nucleotides and amino acids are highlighted in unique colors. (B) A side-view of the binding pocket is shown in which the peptide is rendered as a cyan tube with the side chains of key residues highlighted in stick representations. Each key nucleotide in the RNA and each key amino acid in the peptide are highlighted in a unique color and labeled. (C) A side-view of the RRE RNA (gray cartoon) and the peptide (cyan cartoon) complex is shown. A transparent gray sphere represents the approximate volume of the peptide binding pocket. Each arrow corresponds to the peptide dissociation coordinate or direction for one of the four pathways (PWs): PW1 (red), PW2 (cyan), PW3 (orange), and PW4 (blue). To see this figure in color, go online.