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Title: Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

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.

Authors:
 [1];  [2];  [3];  [4]
+ Show Author Affiliations
  1. Northeastern Univ., Boston, MA (United States). Dept. of Physics; Rice Univ., Houston, TX (United States). Center for Theoretical Biological Physics; Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Biology and Biophysics
  2. Cornell Univ., Ithaca, NY (United States). Weill Medical College. Dept. of Physiology and Biophysics
  3. Univ. of California, Berkeley, CA (United States). Depts. of Molecular and Cell Biology and Chemistry; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division
  4. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Biology and Biophysics
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Science (SC); USDOE Laboratory Directed Research and Development (LDRD) Program; National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1627229
Grant/Contract Number:  
AC52-06NA25396; AC02-05CH11231; R01-GM072686; 1R01GM65050; PHY-0822283; TG-MCB110021
Resource Type:
Accepted Manuscript
Journal Name:
PLoS Computational Biology (Online)
Additional Journal Information:
Journal Name: PLoS Computational Biology (Online); Journal Volume: 9; Journal Issue: 3; Journal ID: ISSN 1553-7358
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 97 MATHEMATICS AND COMPUTING; Biochemistry & Molecular Biology; Mathematical & Computational Biology

Citation Formats

Whitford, Paul C., Blanchard, Scott C., Cate, Jamie H. D., and Sanbonmatsu, Karissa Y. Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome. United States: N. p., 2013. Web. doi:10.1371/journal.pcbi.1003003.
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Whitford, Paul C., Blanchard, Scott C., Cate, Jamie H. D., & Sanbonmatsu, Karissa Y. Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome. United States. https://doi.org/10.1371/journal.pcbi.1003003
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Whitford, Paul C., Blanchard, Scott C., Cate, Jamie H. D., and Sanbonmatsu, Karissa Y. Thu . "Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome". United States. https://doi.org/10.1371/journal.pcbi.1003003. https://www.osti.gov/servlets/purl/1627229.
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@article{osti_1627229,
title = {Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome},
author = {Whitford, Paul C. and Blanchard, Scott C. and Cate, Jamie H. D. and Sanbonmatsu, Karissa Y.},
abstractNote = {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.},
doi = {10.1371/journal.pcbi.1003003},
journal = {PLoS Computational Biology (Online)},
number = 3,
volume = 9,
place = {United States},
year = {Thu Mar 21 00:00:00 EDT 2013},
month = {Thu Mar 21 00:00:00 EDT 2013}
}
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Key Intermolecular Interactions in the E. coli 70S Ribosome Revealed by Coarse-Grained Analysis
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journal, December 2009

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Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy
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A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
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Messenger RNA interactions in the decoding center control the rate of translocation
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Ultrafast dynamics of protein collapse from single-molecule photon statistics
journal, February 2007

  • Nettels, D.; Gopich, I. V.; Hoffmann, A.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 8
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Side-chain recognition and gating in the ribosome exit tunnel
journal, October 2008

  • Petrone, P. M.; Snow, C. D.; Lucent, D.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 43
  • DOI: 10.1073/pnas.0801795105

Structure of ratcheted ribosomes with tRNAs in hybrid states
journal, October 2008

  • Julian, P.; Konevega, A. L.; Scheres, S. H. W.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 44
  • DOI: 10.1073/pnas.0809587105

Crystal structure of a translation termination complex formed with release factor RF2
journal, December 2008

  • Korostelev, A.; Asahara, H.; Lancaster, L.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 50
  • DOI: 10.1073/pnas.0810953105

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
journal, July 2003

  • Tama, F.; Valle, M.; Frank, J.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 16
  • DOI: 10.1073/pnas.1632476100

Biomolecular dynamics: order–disorder transitions and energy landscapes
journal, June 2012

  • Whitford, Paul C.; Sanbonmatsu, Karissa Y.; Onuchic, José N.
  • Reports on Progress in Physics, Vol. 75, Issue 7
  • DOI: 10.1088/0034-4885/75/7/076601

Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome
journal, October 2010

MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures
journal, June 2010

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA
journal, June 2007

  • Rázga, Filip; Koča, Jaroslav; Mokdad, Ali
  • Nucleic Acids Research, Vol. 35, Issue 12
  • DOI: 10.1093/nar/gkm245

Dynamics of translation on the ribosome: molecular mechanics of translocation
journal, June 1999

Structures of the Ribosome in Intermediate States of Ratcheting
journal, August 2009

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  • Science, Vol. 325, Issue 5943, p. 1014-1017
  • DOI: 10.1126/science.1175275

The energy landscapes and motions of proteins
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THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective
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Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways
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A-Site Residues Move Independently from P-Site Residues in all-Atom Molecular Dynamics Simulations of the 70S Bacterial Ribosome
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Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations
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Comparison of tRNA Motions in the Free and Ribosomal Bound Structures
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Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics
journal, March 2009

  • Hills, Ronald; Brooks, Charles
  • International Journal of Molecular Sciences, Vol. 10, Issue 3
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Protein dynamics from single-molecule fluorescence intensity correlation functions
text, January 2009

  • V., Gopich, I.; D., Nettels,; B., Schuler,
  • American Institute of Physics
  • DOI: 10.5167/uzh-21149
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