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

J Phys Chem B. 2020 Sep 10;124(36):7745-7764. doi: 10.1021/acs.jpcb.0c04567. Epub 2020 Aug 31.

Abstract

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amides
  • Glycine
  • Peptidomimetics*
  • Peptoids*
  • Thermodynamics

Substances

  • Amides
  • Peptidomimetics
  • Peptoids
  • Glycine