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Title: Topology, landscapes, and biomolecular energy transport

Abstract

While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior that diverges from the macroscale. Here, we show that transient thermal transport reflects macromolecular energy landscape architecture through the topological characteristics of molecular contacts and the nonlinear processes that mediate dynamics. While the former determines transport pathways via pairwise interactions, the latter reflects frustration within the landscape for local conformational rearrangements. Unlike transport through small-molecule systems, such as alkanes, nonlinearity dominates over coherent processes at even quite short time- and length-scales. Our exhaustive all-atom simulations and novel local-in-time and space analysis, applicable to both theory and experiment, permit dissection of energy migration in biomolecules. The approach demonstrates that vibrational energy transport can probe otherwise inaccessible aspects of macromolecular dynamics and interactions that underly biological function.

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]
+ Show Author Affiliations
  1. National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States); Univ. of Maryland, College Park, MD (United States)
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States)
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1572330
Report Number(s):
LA-UR-19-23856
Journal ID: ISSN 2041-1723
Grant/Contract Number:  
89233218CNA000001
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Elenewski, Justin E., Velizhanin, Kirill A., and Zwolak, Michael Philip. Topology, landscapes, and biomolecular energy transport. United States: N. p., 2019. Web. doi:10.1038/s41467-019-12700-w.
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Elenewski, Justin E., Velizhanin, Kirill A., & Zwolak, Michael Philip. Topology, landscapes, and biomolecular energy transport. United States. https://doi.org/10.1038/s41467-019-12700-w
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Elenewski, Justin E., Velizhanin, Kirill A., and Zwolak, Michael Philip. Fri . "Topology, landscapes, and biomolecular energy transport". United States. https://doi.org/10.1038/s41467-019-12700-w. https://www.osti.gov/servlets/purl/1572330.
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@article{osti_1572330,
title = {Topology, landscapes, and biomolecular energy transport},
author = {Elenewski, Justin E. and Velizhanin, Kirill A. and Zwolak, Michael Philip},
abstractNote = {While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior that diverges from the macroscale. Here, we show that transient thermal transport reflects macromolecular energy landscape architecture through the topological characteristics of molecular contacts and the nonlinear processes that mediate dynamics. While the former determines transport pathways via pairwise interactions, the latter reflects frustration within the landscape for local conformational rearrangements. Unlike transport through small-molecule systems, such as alkanes, nonlinearity dominates over coherent processes at even quite short time- and length-scales. Our exhaustive all-atom simulations and novel local-in-time and space analysis, applicable to both theory and experiment, permit dissection of energy migration in biomolecules. The approach demonstrates that vibrational energy transport can probe otherwise inaccessible aspects of macromolecular dynamics and interactions that underly biological function.},
doi = {10.1038/s41467-019-12700-w},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {Fri Oct 11 00:00:00 EDT 2019},
month = {Fri Oct 11 00:00:00 EDT 2019}
}
Copy to clipboard
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https://doi.org/10.1038/s41467-019-12700-w
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Vibrational Energy Transfer and Heat Conduction in a Protein
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Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study
journal, July 2009

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Uncoupling proteins: current status and therapeutic prospects
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Heat flow in proteins: Computation of thermal transport coefficients
journal, February 2005

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Frequency-resolved communication maps for proteins and other nanoscale materials
journal, May 2009

  • Leitner, David M.
  • The Journal of Chemical Physics, Vol. 130, Issue 19
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Vibrational energy transport in the presence of intrasite vibrational energy redistribution
journal, July 2009

  • Schade, Marco; Hamm, Peter
  • The Journal of Chemical Physics, Vol. 131, Issue 4
  • DOI: 10.1063/1.3185152

Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study
journal, July 2010

  • Kobus, Maja; Nguyen, Phuong H.; Stock, Gerhard
  • The Journal of Chemical Physics, Vol. 133, Issue 3
  • DOI: 10.1063/1.3462961

Coherent vibrational energy transfer along a peptide helix
journal, March 2011

  • Kobus, Maja; Nguyen, Phuong H.; Stock, Gerhard
  • The Journal of Chemical Physics, Vol. 134, Issue 12
  • DOI: 10.1063/1.3574395

Mixed quantum classical simulations of excitons in peptide helices
journal, May 2011

  • Goj, Anne; Bittner, Eric R.
  • The Journal of Chemical Physics, Vol. 134, Issue 20
  • DOI: 10.1063/1.3592155

Communication maps computed for homodimeric hemoglobin: Computational study of water-mediated energy transport in proteins
journal, August 2011

  • Gnanasekaran, Ramachandran; Agbo, Johnson K.; Leitner, David M.
  • The Journal of Chemical Physics, Vol. 135, Issue 6
  • DOI: 10.1063/1.3623423

Vibrational energy flow in the villin headpiece subdomain: Master equation simulations
journal, February 2015

  • Leitner, David M.; Buchenberg, Sebastian; Brettel, Paul
  • The Journal of Chemical Physics, Vol. 142, Issue 7
  • DOI: 10.1063/1.4907881

Room-temperature ballistic energy transport in molecules with repeating units
journal, June 2015

  • Rubtsova, Natalia I.; Nyby, Clara M.; Zhang, Hong
  • The Journal of Chemical Physics, Vol. 142, Issue 21
  • DOI: 10.1063/1.4916326

The nonequilibrium mechanism for ultrasensitivity in a biological switch: Sensing by Maxwell's demons
journal, August 2008

Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin
journal, September 2016

  • Brinkmann, Levin U. L.; Hub, Jochen S.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 38
  • DOI: 10.1073/pnas.1603539113

Time-resolved observation of protein allosteric communication
journal, July 2017

  • Buchenberg, Sebastian; Sittel, Florian; Stock, Gerhard
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 33
  • DOI: 10.1073/pnas.1707694114

Protein states and proteinquakes.
journal, August 1985

  • Ansari, A.; Berendzen, J.; Bowne, S. F.
  • Proceedings of the National Academy of Sciences, Vol. 82, Issue 15
  • DOI: 10.1073/pnas.82.15.5000

Diffusive Model of Protein Folding Dynamics with Kramers Turnover in Rate
journal, June 2006

Ultrafast Flash Thermal Conductance of Molecular Chains
journal, August 2007

Photolysis of the Carbon Monoxide Complex of Myoglobin: Nanosecond Time-Resolved Crystallography
journal, December 1996

Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation
journal, September 2015

Tunable Thermal Switching via DNA-Based Nano Devices
text, January 2012

Crossover behavior of the thermal conductance and Kramers' transition rate theory
text, January 2013

A Spin-1 Representation for Dual-Funnel Energy Landscapes
text, January 2018

Structural flexibility of a helical peptide regulates vibrational energy transport properties
text, January 2008

  • Backus, E. H. G.; Nguyen, P. H.; Botan, V.
  • American Chemical Society
  • DOI: 10.5167/uzh-10236

Vibrational Energy Transport in Peptide Helices after Excitation of Cāˆ’D Modes in Leu-d10
text, January 2009

  • M., Schade,; A., Moretto,; M., Crisma,
  • American Chemical Society
  • DOI: 10.5167/uzh-24992

Dynamical Transition in a Small Helical Peptide and Its Implication for Vibrational Energy Transport
text, January 2009

  • Backus, E. H. G.; Bloem, R.; Pfister, R.
  • American Chemical Society
  • DOI: 10.5167/uzh-24997
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