Model of ribosomal translocation coupled with intra- and inter-subunit rotations

Abstract

The ribosomal translocation involves both intersubunit rotations between the small 30S and large 50S subunits and the intrasubunit rotations of the 30S head relative to the 30S body. However, the detailed molecular mechanism on how the intersubunit and intrasubunit rotations are related to the translocation remains unclear. Here, based on available structural data a model is proposed for the ribosomal translocation, into which both the intersubunit and intrasubunit rotations are incorporated. With the model, we provide quantitative explanations of in vitro experimental data showing the biphasic character in the fluorescence change associated with the mRNA translocation and the character of a rapid increase that is followed by a slow single-exponential decrease in the fluorescence change associated with the 30S head rotation. The calculated translation rate is also consistent with the in vitro single-molecule experimental data.

Keywords: Hybrid state; Intersubunit rotation; Intrasubunit rotation; Ribosome; Translation; Translocation.

Fig. 1

The simplified model of mRNA translocation in the ribosome with the consideration of only intersubunit rotations (see text for detailed description).

Fig. 2

The model of mRNA translocation in the ribosome with the inclusion of both intersubunit rotations and intrasubunit rotations of the 30S head (see text for detailed description). The panel on the right hand of State H1 shows the 30S subunit viewed from the 50S subunit, where the ribosomal complex is in the hybrid state with two tRNAs bound to the 30S P and A sites. Green arrows indicate the direction of the forward rotation of the 30S head relative to the 30S body and red arrows indicate the direction of the forward rotation of the 30S subunit relative to the 50S subunit.

Fig. 3

Pathway of translation elongation. Here we draw that the dissociation of the deacylated tRNA from the ribosome occurs after the codon recognition. In fact, before the binding of the ternary complex, the dissociation of the deacylated tRNA can also occurs , .

Fig. 4

Temporal evolutions of P₃(t) (open circles) and $1-P_4(t)$ (open squares) for the case of fixed k₂=0. P₃(t) corresponds to the fluorescence change associated with the rotation of the 30S head and $1-P_4(t)$ to the fluorescence change associated with the mRNA translocation. The data of P₃(t) as a function of t are fit to the function, $P_3(t)=C_1\exp \left(-{\lambda }_{3}t\right)-C_2\exp \left(-{\lambda }_{4}t\right)+C_3$, where C₁=0.66, C₂=0.65, C₃=0.02, ${\lambda }_3$=6.6 ${\text{s}}^{-1}$ and ${\lambda }_4$=80 ${\text{s}}^{-1}$ (black line). The data on the slow phase of P₃(t) as a function of t are fit to the single exponential, $P_3(t)=B_1\exp \left(-\lambda t\right)+B_2$, where B₁=0.66, B₂=0.02 and $\lambda$= 6.6 ${\text{s}}^{-1}$ (blue line). The data of $1-P_4(t)$ are fit to the two-exponential function, $1-P_4(t)=A_1{e}^{-{\lambda }_{1}t}+A_2{e}^{-{\lambda }_{2}t}$, with A₁+A₂=1, A₁=0.57, ${\lambda }_1$=6.6 ${\text{s}}^{-1}$ and ${\lambda }_2$=0.7 ${\text{s}}^{-1}$ (red line).