Constraints on error rate revealed by computational study of G•U tautomerization in translation

Abstract

Abstract In translation, G•U mismatch in codon-anticodon decoding is an error hotspot likely due to transition of G•U from wobble (wb) to Watson-Crick (WC) geometry, which is governed by keto/enol tautomerization (wb-WC reaction). Yet, effects of the ribosome on the wb-WC reaction and its implications for decoding mechanism remain unclear. Employing quantum-mechanical/molecular-mechanical umbrella sampling simulations using models of the ribosomal decoding site (A site) we determined that the wb-WC reaction is endoergic in the open, but weakly exoergic in the closed A-site state. We extended the classical ‘induced-fit’ model of initial selection by incorporating wb-WC reaction parameters in open and closed states. For predicted parameters, the non-equilibrium exoergic wb-WC reaction is kinetically limited by the decoding rates. The model explains early observations of the WC geometry of G•U from equilibrium structural studies and reveals discrimination capacity for the working ribosome operating at non-equilibrium conditions. The equilibration of the exoergic wb-WC reaction counteracts the equilibration of the open-closed transition of the A site, constraining the decoding accuracy and potentially explaining the persistence of the G•U as an error hotspot. Our results unify structural and mechanistic views of codon-anticodon decoding and generalize the ‘induced-fit’ model for flexible substrates.