MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids
| Autor: | Gillian Shen, Andrew L. Ferguson, Mingfei Zhao, Sarah Alamdari, Janani Sampath, Jim Pfaendtner, Christopher J. Mundy, Chun-Long Chen |
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| Rok vydání: | 2020 |
| Předmět: |
Materials science
Peptidomimetic Glycine 010402 general chemistry 01 natural sciences Force field (chemistry) Peptoids chemistry.chemical_compound 0103 physical sciences Materials Chemistry Peptide bond Physical and Theoretical Chemistry Potential of mean force chemistry.chemical_classification 010304 chemical physics Metadynamics Peptoid Polymer Amides 0104 chemical sciences Surfaces Coatings and Films Protein mimetic chemistry Chemical physics Thermodynamics Peptidomimetics |
| Zdroj: | The Journal of Physical Chemistry B. 124:7745-7764 |
| ISSN: | 1520-5207 1520-6106 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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