Dynamics of Forward and Backward Translocation of mRNA in the Ribosome

<div><p>Translocation of the mRNA-tRNA complex in the ribosome, which is catalyzed by elongation factor EF-G, is one of critical steps in the elongation cycle of protein synthesis. Besides this conventional forward translocation, the backward translocation can also occur, which can be catalyzed by elongation factor LepA. However, the molecular mechanism of the translocation remains elusive. To understand the mechanism, here we study theoretically the dynamics of the forward translocation under various nucleotide states of EF-G and the backward translocation in the absence of and in the presence of LepA. We present a consistent explanation of spontaneous forward translocations in the absence of EF-G, the EF-G-catalyzed forward translocations in the presence of a non-hydrolysable GTP analogue and in the presence of GTP, and the spontaneous and LepA-catalyzed backward translocation. The theoretical results provide quantitative explanations of a lot of different, independent experimental data, and also provide testable predictions.</p></div

Summary of energy barriers during forward translocation.

<p>Summary of energy barriers during forward translocation.</p

Backward translocation.

<p>(a) Schematic of transition from post- (State POST) to pre-translocation state, including the classical non-ratchet state (State NR) and hybrid state (State hybrid). (b) Potential <i>V</i>(<i>x</i>) that characterizes the transition from the pre- to post-translocation state.</p

Results of forward mRNA translocation time <i>T</i>₁ as a function of energy barrier <i>E_POST</i>, which are calculated by using Eq. (5), with <i>E_NR</i> = 23.87 <i>k_BT</i> and <i>E_H</i> = 24.24 <i>k_BT</i> (corresponding to the case in the absence of EF-G).

<p>Results of forward mRNA translocation time <i>T</i>₁ as a function of energy barrier <i>E_POST</i>, which are calculated by using Eq. (5), with <i>E_NR</i> = 23.87 <i>k_BT</i> and <i>E_H</i> = 24.24 <i>k_BT</i> (corresponding to the case in the absence of EF-G).</p

Forward translocation.

<p>(a) Schematic of transition from pre-translocation state, including the classical non-ratchet state (State NR) and hybrid state (State hybrid), to post-translocation state (State POST). (b) Potential <i>V</i>(<i>x</i>) that characterizes the transition from the pre- to post-translocation state.</p

Results of backward mRNA translocation time <i>T</i>₀ as a function of energy barrier <i>E</i>₀, which are calculated by Eq. (3) but with <i>E_NR</i> and <i>E_H</i> being replaced by <i>E</i>₀ and <i>E_POST</i>, respectively. <i>E_POST</i> = 33.91<i>k_BT</i>.

<p>Results of backward mRNA translocation time <i>T</i>₀ as a function of energy barrier <i>E</i>₀, which are calculated by Eq. (3) but with <i>E_NR</i> and <i>E_H</i> being replaced by <i>E</i>₀ and <i>E_POST</i>, respectively. <i>E_POST</i> = 33.91<i>k_BT</i>.</p

Schematic of the 30S subunit complexed mRNA containing one (a), two (b) and three (c) base pairs in the codon which is immediately adjacent to the mRNA entry channel in the 30S subunit.

<p>Schematic of the 30S subunit complexed mRNA containing one (a), two (b) and three (c) base pairs in the codon which is immediately adjacent to the mRNA entry channel in the 30S subunit.</p

Results of forward mRNA translocation time <i>T</i>₂ as a function of energy barrier <i>E_POST</i>, which are calculated by using Eq. (7), with <i>E_NR</i> = 23.02 <i>k_BT</i> and <i>E_H</i> = 26.54 <i>k_BT</i> (corresponding to the case with binding of EF-G.GDPNP).

<p>Results of forward mRNA translocation time <i>T</i>₂ as a function of energy barrier <i>E_POST</i>, which are calculated by using Eq. (7), with <i>E_NR</i> = 23.02 <i>k_BT</i> and <i>E_H</i> = 26.54 <i>k_BT</i> (corresponding to the case with binding of EF-G.GDPNP).</p

The labile state of ribosome with deacylated tRNA bound to the 30S P site and peptidyl-tRNA bound to the 30S A site.

<p>(a) Schematic of transition from the classical non-ratchet state (State NR) to hybrid state (State hybrid) and vice versa. (b) Potential <i>V</i>(<i>x</i>) that characterizes the transition between the classical non-ratchet and hybrid states.</p

Summary of energy barriers in posttranslocation state.

<p>Summary of energy barriers in posttranslocation state.</p