Abstract G○U(T) mismatch has the highest contribution to the error rate of base pair recognition in replication, as well as in codon-anticodon decoding in translation. Recently, this effect was unambiguously linked to keto-enol tautomerization, which enables the Watson-Crick (WC) geometry of the base pair. Structural studies of the ribosome revealing G○U in the WC geometry in the closed state of the A-site challenge the canonical induced-fit model of decoding and currently lack a physicochemical explanation. Using computational and theoretical methods, we address effects of the ribosomal A-site on the wobble↔WC tautomerization reaction in G○U (wb-WC reaction), and the consequent implications for the decoding mechanism in translation. The free energy change of the wb-WC reaction in the middle codon-anticodon position was calculated with quantum-mechanical/molecular-mechanical umbrella sampling simulations. The wb-WC reaction was endoergic in the open A-site, but exoergic in the closed state. This effect can be explained in part by the decreased polarity of the closed A-site. We developed a model of initial selection in translation that incorporates the wb-WC reaction parameters in the open and closed states of the A-site. In the new model, the exoergic wb-WC reaction is kinetically restricted by the decoding rates, which explains the observations of the WC geometry at equilibrium conditions. Moreover, the model reveals constraints imposed by the exoergic wb-WC reaction on the decoding accuracy: its equilibration counteracts the favorable contribution from equilibration of the open-closed transition. The similarity of the base-pair recognition mechanism in DNA polymerases allows extending this model to replication as well. Our model can be a step towards a general recognition model for flexible substrates. Competing Interest Statement The authors have declared no competing interest. Footnotes * E-mail: kazantsev.and{at}gmail.com; zoya.ignatova{at}chemie.uni-hamburg.de * Corrected grammatical errors in all sections and SI; Missing citations added; The choice of experimental rate constants clarified in Methods. * https://doi.org/10.6084/m9.figshare.c.5178074.v1 * https://github.com/and-kaz/wbwc_paper...

Tautomerization constrains the accuracy of codon-anticodon decoding

10.1101/2020.10.19.344408