Programmed −1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes

Fig. 1. The −1 PRF signal from HIV-1. This signal consists of a slippery sequence (underlined), a stimulatory hairpin, and an 8-nucleotide spacer in between. Schematic presentation of the ribosome indicates relative positions between functional sites of the ribosome and mRNA during −1 PRF.

Fig. 2. Conformational changes of the bacterial ribosome during translation elongation. (A) Cycle of elongation. For clarity, only the aa-tRNA (red; instead of the ternary complex) is shown in step 1, and the swiveling of the 30S head is not shown in steps 5–7. See the text for details. (B) 30S subunit rotation during translocation. Calculated by superimposing the 50S subunit (not shown). (C) 30S head rotation (swiveling). Calculated by superimposing the 30S body. Rotational axes are calculated by pseudo-angular momentum, and the non-rotated and rotated states of the ribosome are modeled as described [38]. (D) 30S subunit rolling during pseudoknot-induced −1 PRF [38]. The 50S subunit (not shown) is superimposed. The rolling axis lies approximately along helix 44 (green ribbon). (B)–(D) are viewed from the solvent side. (E) mRNA entrance site of the 30S subunit (PDB ID: 6BY1) [67]. uS3 is on the 30S head, while uS4 and uS5 are on the 30S body. R131, R132, and K135 of uS3, as well as K44 and R46 of uS4, are highlighted in blue. The relative movement of the 30S head and body described in (C) are indicated with black arrows. The codons at positions +13 to +15, +10 to +12, and +7 to +9 are…

Fig. 3. Mechanical unfolding of RNA structures by optical tweezers. (A) One type of optical tweezers. The RNA structure of interest is held between two micron-sized polystyrene beads by flanking the handles of RNA/DNA hybrids. One bead is placed in an optical trap for manipulation and force measurements. The figure is schematic and not to scale. (B) DU177 pseudoknot. The structure contains two stems (S1 and S2) and two loops (L1 and L2). Red dotted lines indicate five base triples and one noncanonical base pair. (C) Bimolecular design to mimic the DU177 pseudoknot. Pseudoknot is split into a hairpin (black) and an oligomer (blue) at the junction of S1 and L2. Expected direction of pulling force when the structure is placed on optical tweezers is indicated by arrows. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 4. Hypothetical models for conformational changes of the ribosome and mRNA stimulatory structure during −1 PRF. Refolding of the downstream RNA intermediate structure occurs when the ribosome translocates to (A) the first half of the slippery sequence (step a1) or (B) the second half of the slippery sequence (step b2). The slippery sequence and the sequence under tension are shown in yellow and red, respectively. The partially-unwound downstream RNA structures before refolding are shown in red. See the text for details. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)