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Title: A spin-1 representation for dual-funnel energy landscapes

Abstract

The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. In this study, we explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model—left, right, and unstructured—can account for most key intermediates during chiral interconversion. Additionally, competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 kBT to 0.3 kBT along the left-to-right interconversion pathway.

Authors:
 [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 Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1471315
Report Number(s):
LA-UR-18-28756
Journal ID: ISSN 0021-9606
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 149; Journal Issue: 3; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Elenewski, Justin E., Velizhanin, Kirill A., and Zwolak, Michael. A spin-1 representation for dual-funnel energy landscapes. United States: N. p., 2018. Web. doi:10.1063/1.5036677.
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Elenewski, Justin E., Velizhanin, Kirill A., & Zwolak, Michael. A spin-1 representation for dual-funnel energy landscapes. United States. https://doi.org/10.1063/1.5036677
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Elenewski, Justin E., Velizhanin, Kirill A., and Zwolak, Michael. Fri . "A spin-1 representation for dual-funnel energy landscapes". United States. https://doi.org/10.1063/1.5036677. https://www.osti.gov/servlets/purl/1471315.
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@article{osti_1471315,
title = {A spin-1 representation for dual-funnel energy landscapes},
author = {Elenewski, Justin E. and Velizhanin, Kirill A. and Zwolak, Michael},
abstractNote = {The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. In this study, we explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model—left, right, and unstructured—can account for most key intermediates during chiral interconversion. Additionally, competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 kBT to 0.3 kBT along the left-to-right interconversion pathway.},
doi = {10.1063/1.5036677},
journal = {Journal of Chemical Physics},
number = 3,
volume = 149,
place = {United States},
year = {2018},
month = {7}
}
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  • DOI: 10.5167/uzh-10236

Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics
text, January 2003

  • Iannuzzi, Marcella; Laio, Alessandro; Parrinello, Michele
  • American Physical Society
  • DOI: 10.5167/uzh-138232

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

Transforming the Energy Landscape of a Coiled-Coil Peptide via Point Mutations
text, January 2017

  • Roeder, Konstantin; Wales, David
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.35711

Probing helical transitions in a DNA duplex
text, January 2017

  • Chakraborty, Debayan; Wales, David
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.8074

Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA.
text, January 2018

  • Chakraborty, Debayan; Wales, David
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.23792

Probing helical transitions in a DNA duplex†
text, January 2018

  • Wales, David; Chakraborty, Debayan
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.23556

Simulating structural transitions by direct transition current sampling: the example of LJ38
text, January 2011

The double-funnel energy landscape of the 38-atom Lennard-Jones cluster
text, January 1998

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    Works referencing / citing this record:

    Topology, landscapes, and biomolecular energy transport
    journal, October 2019

    • Elenewski, Justin E.; Velizhanin, Kirill A.; Zwolak, Michael
    • Nature Communications, Vol. 10, Issue 1
    • DOI: 10.1038/s41467-019-12700-w

    Topology, Landscapes, and Biomolecular Energy Transport
    text, January 2019

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