Simulation and analysis of single-ribosome translation

Phys Biol. 2009 Jul 1;6(2):025006. doi: 10.1088/1478-3975/6/2/025006.

Abstract

In the cell, proteins are synthesized by ribosomes in a multi-step process called translation. The ribosome translocates along the messenger RNA to read the codons that encode the amino acid sequence of a protein. Elongation factors, including EF-G and EF-Tu, are used to catalyze the process. Recently, we have shown that translation can be followed at the single-molecule level using optical tweezers; this technique allows us to study the kinetics of translation by measuring the lifetime the ribosome spends at each codon. Here, we analyze the data from single-molecule experiments and fit the data with simple kinetic models. We also simulate the translation kinetics based on a multi-step mechanism from ensemble kinetic measurements. The mean lifetimes from the simulation were consistent with our experimental single-molecule measurements. We found that the calculated lifetime distributions were fit in general by equations with up to five rate-determining steps. Two rate-determining steps were only obtained at low concentrations of elongation factors. These analyses can be used to design new single-molecule experiments to better understand the kinetics and mechanism of translation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Codon
  • Computer Simulation
  • Kinetics
  • Models, Biological
  • Models, Molecular
  • Optical Tweezers
  • Peptide Elongation Factor G / metabolism
  • Peptide Elongation Factor Tu / metabolism
  • Protein Biosynthesis*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Ribosomes / genetics
  • Ribosomes / metabolism*
  • Thermus thermophilus / metabolism

Substances

  • Codon
  • Peptide Elongation Factor G
  • RNA, Messenger
  • Peptide Elongation Factor Tu