pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA.

Magnus Johansson (1) , Ka-Weng Ieong (1) , Stefan Trobro (1) , Peter Strazewski (2) , Johan Åqvist (1) , Michael Y. Pavlov (1) , Måns Ehrenberga (1)

1 Department of Cell and Molecular Biology [Uppsala]
2 ICBMS - Institut de Chimie et Biochimie Moléculaires et Supramoléculaires

We studied the pH-dependence of ribosome catalyzed peptidyl transfer from fMet-tRNAfMet to the aa-tRNAs Phe-tRNAPhe, Ala-tRNAAla, Gly-tRNAGly, Pro-tRNAPro, Asn-tRNAAsn, and Ile-tRNAIle, selected to cover a large range of intrinsic pKa-values for the α-amino group of their amino acids. The peptidyl transfer rates were different at pH 7.5 and displayed different pH-dependence, quantified as the pH-value, Graphic, at which the rate was half maximal. The Graphic-values were downshifted relative to the intrinsic pKa-value of aa-tRNAs in bulk solution. Gly-tRNAGly had the smallest downshift, while Ile-tRNAIle and Ala-tRNAAla had the largest downshifts. These downshifts correlate strongly with molecular dynamics (MD) estimates of the downshifts in pKa-values of these aa-tRNAs upon A-site binding. Our data show the chemistry of peptide bond formation to be rate limiting for peptidyl transfer at pH 7.5 in the Gly and Pro cases and indicate rate limiting chemistry for all six aa-tRNAs.

Mots clés: ribosome; kinetics; rate limiting step; accommodation; molecular dynamics

Domaines: Chimie organique

Magnus Johansson, Ka-Weng Ieong, Stefan Trobro, Peter Strazewski, Johan Åqvist, et al.. pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA.. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108 (1), pp.79-84. ⟨hal-01162444⟩