A spin-1 representation for dual-funnel energy landscapes

Elenewski, Justin E.; Velizhanin, Kirill A.; Zwolak, Michael

doi:10.1063/1.5036677

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

Journal Article · 20 July 2018 · Journal of Chemical Physics

DOI: https://doi.org/10.1063/1.5036677 · OSTI ID:1471315

Elenewski, Justin E. ^[1];

^[2];

^[3]

National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States); Univ. of Maryland, College Park, MD (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States)

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 k_BT to 0.3 k_BT along the left-to-right interconversion pathway.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); Laboratory Directed Research and Development (LDRD)

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1471315

Report Number(s):: LA-UR--18-28756

Journal Information:: Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 3 Vol. 149; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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Left-Handed Helical Preference in an Achiral Peptide Chain is Induced by an L-Amino Acid in an N-Terminal Type II β-Turn De Poli, Matteo; De Zotti, Marta; Raftery, James Peptides Across the Pacific: The Proceedings of the Twenty-Third American and the Sixth International Peptide Symposium https://doi.org/10.17952/23aps.2013.118	conference	January 2013
Simulating structural transitions by direct transition current sampling: the example of LJ38 Picciani, Massimiliano; Athenes, Manuel; Kurchan, Jorge arXiv https://doi.org/10.48550/arxiv.1103.0492	text	January 2011
Flows in Complex Networks: Theory, Algorithms, and Application to Lennard-Jones Cluster Rearrangement Cameron, Maria; Vanden-Eijnden, Eric arXiv https://doi.org/10.48550/arxiv.1402.1736	text	January 2014
The double-funnel energy landscape of the 38-atom Lennard-Jones cluster Doye, Jonathan; Miller, Mark; Wales, David arXiv https://doi.org/10.48550/arxiv.cond-mat/9808265	text	January 1998
Phase changes in 38 atom Lennard-Jones clusters. II: A parallel tempering study of equilibrium and dynamic properties in the molecular dynamics and microcanonical Calvo, F.; Neirotti, J. P.; Freeman, David L. arXiv https://doi.org/10.48550/arxiv.physics/0003072	text	January 2000
Structural flexibility of a helical peptide regulates vibrational energy transport properties Backus, E. H. G.; Nguyen, P. H.; Botan, V. American Chemical Society https://doi.org/10.5167/uzh-10236	text	January 2008
Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics Iannuzzi, Marcella; Laio, Alessandro; Parrinello, Michele American Physical Society https://doi.org/10.5167/uzh-138232	text	January 2003
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Topology, Landscapes, and Biomolecular Energy Transport Elenewski, Justin E.; Velizhanin, Kirill A.; Zwolak, Michael arXiv https://doi.org/10.48550/arxiv.1904.11154	text	January 2019
Topology, landscapes, and biomolecular energy transport Elenewski, Justin E.; Velizhanin, Kirill A.; Zwolak, Michael Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12700-w	journal	October 2019
Topology, Landscapes, and Biomolecular Energy Transport Elenewski, Justin E.; Velizhanin, Kirill A.; Zwolak, Michael arXiv https://doi.org/10.48550/arxiv.1904.11154	text	January 2019

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