The transorientation hypothesis for codon recognition during protein synthesis

Abstract

During decoding, a codon of messenger RNA is matched with its cognate aminoacyl-transfer RNA and the amino acid carried by the tRNA is added to the growing protein chain. Here we propose a molecular mechanism for the decoding phase of translation: the transorientation hypothesis. The model incorporates a newly identified tRNA binding site and utilizes a flip between two tRNA anticodon loop structures, the 5'-stacked and the 3'-stacked conformations. The anticodon loop acts as a three-dimensional hinge permitting rotation of the tRNA about a relatively fixed codon-anticodon pair. This rotation, driven by a conformational change in elongation factor Tu involving GTP hydrolysis, transorients the incoming tRNA into the A site from the D site of initial binding and decoding, where it can be proofread and accommodated. The proposed mechanisms are compatible with the known structures, conformations and functions of the ribosome and its component parts including tRNAs and EF-Tu, in both the GTP and GDP states.

Structural Insights Into Translational Fidelity

“…An unrelated theoretical model of decoding, the transorientation hypothesis, was published recently (139). This model relies on a proposed switch of the anticodon from a 3 to a 5 stack, similar to an earlier proposal for such a switch during translocation (151).…”

“…It has been questioned whether the kirromycin-stalled complex is on the translation pathway (139). However, this objection ignores kinetic data showing that, in the presence and absence of kirromycin, fluorescent signals from both the proflavin and the mant-dGTP reporters are identical prior to GTP hydrolysis (90).…”

Symmetry at the active site of the ribosome: structural and functional implications

“…The non-symmetrical extensions radiating from the SymR interact with regions that carry out central roles in the ribosome function. These include the part of the L1 arm that is involved in the release of E-site tRNA from the ribosome, namely helices H76-8 ( Figure 1B) that extend from helix H75 of the SymR; the extension comprised of helices H81-H88 that reaches 5S rRNA; helix H89 extension ( Figure 1B), whose stemloop nucleotide G2485 interacts with nucleotide C1092 of helix H44, in a region implicated in binding of the ternary complex (Simonson and Lake, 2002) and in GTPase activity (Wimberly et al, 1999;Valle et al, 2002); and H91 extension ( Figure 1B), whose stem loop nucleotides A2531 and G2532 interact with nucleotides A2662 and G2663 of the sarcin-ricin loop of H95, which accommodates EF-Tu and EF-G (Hausner et al, 1987;Moazed et al, 1988;Wilson and Noller, 1998;Wriggers et al, 2000;Mohr et al, 2002;Stark et al, 2002).…”

Testing constraints on rRNA bases that make nonsequence-specific contacts with the codon•anticodon complex in the ribosomal A site

“…Early approaches to address this problem involved docking of static molecular models (VanLoock et al 1999;Lim and Curran 2001;Simonson and Lake 2002). A more powerful approach, molecular dynamics (Karplus and McCammon 2002), uses classical Newtonian mechanics to calculate the movement of atoms in a determined structure under the influence of interatomic forces and heat.…”