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

M Johansson, KW Ieong, S Trobro… - Proceedings of the …, 2011 - National Acad Sciences
M Johansson, KW Ieong, S Trobro, P Strazewski, J Åqvist, MY Pavlov, M Ehrenberg
Proceedings of the National Academy of Sciences, 2011National Acad Sciences
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 pK a-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,, at which the rate was half maximal.
The-values were downshifted relative to the intrinsic pK a-value of aa-tRNAs in bulk solution …
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 pK a-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,, at which the rate was half maximal. The-values were downshifted relative to the intrinsic pK a-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 pK a-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.
National Acad Sciences