Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations

P M Pieczywek,A Zdunek,W Płaziński

doi:10.1038/s41598-020-71820-2

Abstract

In this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations. The model of the homogalacturonan was designed to test the ability of the formation of large-scale structures via hydrogen bonding in water. The extraction of coarse-grained parameters from atomistic molecular dynamics was achieved by means of the proposed molecule aggregation algorithm based on an iterative nearest neighbour search. A novel approach to a time-scale calibration scheme based on matching the average velocities of coarse-grained particles enabled the DPD forcefield to reproduce essential structural features of homogalacturonan molecular chains. The successful application of the proposed parametrization method allowed for the reproduction of the shapes of radial distribution functions, particle velocities and diffusivity of the atomistic molecular dynamics model using DPD force field. The structure of polygalacturonic acid molecules was mapped into the DPD force field by means of the distance and angular bond characteristics, which closely matched the MD results. The resulting DPD trajectories showed that randomly dispersed homogalacturonan chains had a tendency to aggregate into highly organized 3D structures. The final structure resembled a three-dimensional network created by tightly associated homogalacturonan chains organized into thick fibres.

Highlights

In this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations
In this study we present an alternative parametrization strategy of standard DPD force field based on data extracted from a united-atom molecular dynamics model and solving an inverse problem targeting certain
In order to achieve this goal, the dissipative particle dynamics systems were related to reference models created using atomistic molecular dynamics simulations

Summary

Introduction

In this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations. Compared to methods based on atomistic force fields such as molecular dynamics (MD), DPD permits the simulation of large systems over relatively long-time scales[4]. This is achieved by the utilization of simplified soft potentials and coarse-grained representations of modelled structures. In this study we present an alternative parametrization strategy of standard DPD force field based on data extracted from a united-atom molecular dynamics model and solving an inverse problem targeting certain. Molecular studies of pectic polysaccharides have been limited to the interaction of two or three molecular chains with up to 20 r esidues[19,20,21,22,23] or conformations of single chains consisting of 50 r esidues[24]

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Conclusion