Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. Academic Article uri icon

Overview

MeSH

  • Algorithms
  • Computational Biology
  • Diffusion
  • Kinetics
  • Molecular Dynamics Simulation
  • Nucleic Acid Conformation
  • Thermodynamics

MeSH Major

  • RNA, Transfer
  • Ribosomes

abstract

  • Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.

publication date

  • 2013

has subject area

  • Algorithms
  • Computational Biology
  • Diffusion
  • Kinetics
  • Molecular Dynamics Simulation
  • Nucleic Acid Conformation
  • RNA, Transfer
  • Ribosomes
  • Thermodynamics

Research

keywords

  • Journal Article

Identity

Language

  • eng

PubMed Central ID

  • PMC3605090

Digital Object Identifier (DOI)

  • 10.1371/journal.pcbi.1003003

PubMed ID

  • 23555233

Additional Document Info

start page

  • e1003003

volume

  • 9

number

  • 3