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MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

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Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Phys. Chem. B 2020, 124, 36, 7745-7764
    B: Biophysics; Physical Chemistry of Biological Systems and Biomolecules

    MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids
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    • Mingfei Zhao
      Mingfei Zhao
      Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
      More by Mingfei Zhao
    • Janani Sampath
      Janani Sampath
      Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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    • Sarah Alamdari
      Sarah Alamdari
      Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
      More by Sarah Alamdari
    • Gillian Shen
      Gillian Shen
      Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
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    • Chun-Long Chen
      Chun-Long Chen
      Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
      Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
      More by Chun-Long Chen
      Orcidhttp://orcid.org/0000-0002-5584-824X
    • Christopher J. Mundy
      Christopher J. Mundy
      Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
      Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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      Orcidhttp://orcid.org/0000-0003-1378-5241
    • Jim Pfaendtner
      Jim Pfaendtner
      Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
      Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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      Orcidhttp://orcid.org/0000-0001-6727-2957
    • Andrew L. Ferguson*
      Andrew L. Ferguson
      Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
      *Email: [email protected]
      More by Andrew L. Ferguson
      Orcidhttp://orcid.org/0000-0002-8829-9726
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    The Journal of Physical Chemistry B

    Cite this: J. Phys. Chem. B 2020, 124, 36, 7745–7764
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    https://doi.org/10.1021/acs.jpcb.0c04567
    Published August 10, 2020
    Copyright © 2020 American Chemical Society
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    Abstract

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    Peptoids (poly-N-substituted glycines) are a class of synthetic polymers that are regioisomers of peptides (poly-C-substituted glycines), in which the point of side-chain connectivity is shifted from the backbone C to the N atom. Peptoids have found diverse applications as peptidomimetic drugs, protein mimetic polymers, surfactants, and catalysts. Computational modeling is valuable in the understanding and design of peptoid-based nanomaterials. In this work, we report the bottom-up parameterization of coarse-grained peptoid force fields based on the MARTINI peptide force field against all-atom peptoid simulation data. Our parameterization pipeline iteratively refits coarse-grained bonded interactions using iterative Boltzmann inversion and nonbonded interactions by matching the potential of mean force for chain extension. We assure good sampling of the amide bond cis/trans isomerizations in the all-atom simulation data using parallel bias metadynamics. We develop coarse-grained models for two representative peptoids—polysarcosine (poly(N-methyl glycine)) and poly(N-((4-bromophenyl)ethyl)glycine)—and show their structural and thermodynamic properties to be in excellent accord with all-atom calculations but up to 25-fold more efficient and compatible with MARTINI force fields. This work establishes a new rigorously parameterized coarse-grained peptoid force field for the understanding and design of peptoid nanomaterials at length and time scales inaccessible to all-atom calculations.

    Copyright © 2020 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jpcb.0c04567.

    • Dependence of all-atom distribution functions on chain length (PDF)

    • Input and force field files necessary to perform all-atom parallel bias metadynamics simulations and coarse-grained simulations of polysarcosine and poly-Nbrpe (ZIP)

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    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

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    This article is cited by 37 publications.

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    The Journal of Physical Chemistry B

    Cite this: J. Phys. Chem. B 2020, 124, 36, 7745–7764
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jpcb.0c04567
    Published August 10, 2020
    Copyright © 2020 American Chemical Society
    Request reuse permissions

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