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. Here, 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.
Zhao, Mingfei, et al. "MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids." Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry, vol. 124, no. 36, Aug. 2020. https://doi.org/10.1021/acs.jpcb.0c04567
Zhao, Mingfei, Sampath, Janani, Alamdari, Sarah, Shen, Gillian, Chen, Chun-Long, Mundy, Christopher J., Pfaendtner, Jim, & Ferguson, Andrew L. (2020). MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids. Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry, 124(36). https://doi.org/10.1021/acs.jpcb.0c04567
Zhao, Mingfei, Sampath, Janani, Alamdari, Sarah, et al., "MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids," Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry 124, no. 36 (2020), https://doi.org/10.1021/acs.jpcb.0c04567
@article{osti_1673420,
author = {Zhao, Mingfei and Sampath, Janani and Alamdari, Sarah and Shen, Gillian and Chen, Chun-Long and Mundy, Christopher J. and Pfaendtner, Jim and Ferguson, Andrew L.},
title = {MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids},
annote = {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. Here, 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.},
doi = {10.1021/acs.jpcb.0c04567},
url = {https://www.osti.gov/biblio/1673420},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
issn = {ISSN 1520-6106},
number = {36},
volume = {124},
place = {United States},
publisher = {American Chemical Society},
year = {2020},
month = {08}}