Kinetics of d-Amino Acid Incorporation in Translation

ACS Chem Biol. 2019 Feb 15;14(2):204-213. doi: 10.1021/acschembio.8b00952. Epub 2019 Jan 16.

Abstract

Despite the stereospecificity of translation for l-amino acids (l-AAs) in vivo, synthetic biologists have enabled ribosomal incorporation of d-AAs in vitro toward encoding polypeptides with pharmacologically desirable properties. However, the steps in translation limiting d-AA incorporation need clarification. In this work, we compared d- and l-Phe incorporation in translation by quench-flow kinetics, measuring 250-fold slower incorporation into the dipeptide for the d isomer from a tRNAPhe-based adaptor (tRNAPheB). Incorporation was moderately hastened by tRNA body swaps and higher EF-Tu concentrations, indicating that binding by EF-Tu can be rate-limiting. However, from tRNAAlaB with a saturating concentration of EF-Tu, the slow d-Phe incorporation was unexpectedly very efficient in competition with incorporation of the l isomer, indicating fast binding to EF-Tu, fast binding of the resulting complex to the ribosome, and rate-limiting accommodation/peptide bond formation. Subsequent elongation with an l-AA was confirmed to be very slow and inefficient. This understanding helps rationalize incorporation efficiencies in vitro and stereospecific mechanisms in vivo and suggests approaches for improving incorporation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry
  • Amino Acids / metabolism*
  • Guanosine Triphosphate / metabolism
  • Hydrolysis
  • Kinetics
  • Peptide Biosynthesis
  • Peptide Elongation Factor Tu / metabolism
  • Protein Biosynthesis*
  • RNA, Transfer, Amino Acyl / metabolism
  • Reproducibility of Results
  • Stereoisomerism

Substances

  • Amino Acids
  • RNA, Transfer, Amino Acyl
  • Guanosine Triphosphate
  • Peptide Elongation Factor Tu