Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations

Many-body dissipative particle dynamics simulations of micellization of sodium alkyl sulfates

We present a study of micelle formation in alkyl sulfate surfactants using the simulation method of many-body dissipative particle dynamics (MDPD). We parametrise our model by tuning the intermolecular interactions in order to reproduce experimental values for the chemical potential and density at room temperature. Using this approach, we find that our model shows good agreement with experimental values for the critical micelle concentration (CMC). Furthermore, we show that our model can accurately predict CMC trends, which result from varying properties such as surfactant tail length and the salt concentration. We apply our model to investigate the effect of aggregation number on various micellar properties, such as the shape of individual micelles and the fraction of bound counterions. We show that micelles become aspherical at large aggregation numbers, in line with experimental predictions, and that longer tail surfactants are generally more spherical at all aggregation numbers compared to those which are shorter. We find excellent agreement between our simulations and experimental values for the degree of counterion binding, a factor that is crucial to accurately studying micellar shape, but one that is typically overlooked in the existing literature.

A Structure Independent Molecular Fragment Interfuse Model for Mesoscale Dissipative Particle Dynamics Simulation of Peptides

There is a need to develop robust computational models for mesoscale simulation of the structure of peptides over large length scales toward the discovery of novel peptides for medical applications to address the issues of peptide aggregation, enzymatic degradation, and short half-life. The primary objective was to predict the structure and conformation of peptides whose native structures are not known. This work presents a new model for computation of interaction parameters between the beads in coarse-grained dissipative particle dynamics (DPD) simulation that is properly calibrated for amino acids, supports compressibility requirement of water molecules, and accounts for subtle differences in the structure of amino acids and the charge in the side chain of charged amino acids. This new model is referred to as Structure Independent Molecular Fragment Interfuse Model, abbreviated as SIMFIM, because it accounts for specific interactions between different beads, which represent molecular fragments of the amino acids, in calculating nonbonded interaction parameters in the absence of knowing the actual peptide structure. The electrostatic interactions are incorporated in this model by using a normal distribution of charges around the center of the beads to prevent the collapse of oppositely charged soft beads. The uniquely parameterized DPD force field in the SIMFIM model is optimized for a given peptide with respect to the degree of coarse-grained graining for simulating the peptide over long times and length scales. The SIMFIM model was tested in this work using four peptides, namely, TrpZip2, Rubrivinodin, Lihuanodin, and IC3-CB1/Gai peptides, whose structures were sourced from the Protein Data Bank. The SIMFIM model predicted radius of gyration (Rg) values for the peptides closer to the actual structures as compared to the conventional model, and there was less deviation between the predicted and actual structures of the peptides.

Brownian motion of soft particles near a fluctuating lipid bilayer

The dynamics of a soft particle suspended in a viscous fluid can be changed by the presence of an elastic boundary. Understanding the mechanisms and dynamics of soft-soft surface interactions can provide valuable insights into many important research fields, including biomedical engineering, soft robotics development, and materials science. This work investigates the anomalous transport properties of a soft nanoparticle near a visco-elastic interface, where the particle consists of a polymer assembly in the form of a micelle and the interface is represented by a lipid bilayer membrane. Mesoscopic simulations using a dissipative particle dynamics model are performed to examine the impact of micelle's proximity to the membrane on its Brownian motion. Two different sizes are considered, which correspond to ≈10-20nm in physical units. The wavelengths typically seen by the largest micelle fall within the range of wavenumbers where the Helfrich model captures fairly well the bilayer mechanical properties. Several independent simulations allowed us to compute the micelle trajectories during an observation time smaller than the diffusive time scale (whose order of magnitude is similar to the membrane relaxation time of the largest wavelengths), this time scale being hardly accessible by experiments. From the probability density function of the micelle normal position with respect to the membrane, it is observed that the position remains close to the starting position during ≈0.05τd (where τd corresponds to the diffusion time), which allowed us to compare the negative excess of mean-square displacement (MSD) to existing theories. In that time range, the MSD exhibits different behaviors along parallel and perpendicular directions. When the micelle is sufficiently close to the bilayer (its initial distance from the bilayer equals approximately twice its gyration radius), the micelle motion becomes quickly subdiffusive in the normal direction. Moreover, the temporal evolution of the micelle MSD excess in the perpendicular direction follows that of a nanoparticle near an elastic membrane. However, in the parallel direction, the MSD excess is rather similar to that of a nanoparticle near a liquid interface.

Dioctyl sodium sulfosuccinate surfactant self-assembly dependency of solvent hydrophilicity: a modelling study

The self-assembly of dioctyl sodium sulfosuccinate (AOT) model surfactant in solvent environments of differing polarity is examined by means of dissipative particle dynamics (DPD) bead model parametrized against Hildebrand solubility parameters from atomistic molecular dynamics (MD) simulations. The model predicts that in hydrophobic solvents (e.g. dodecane) the surfactant forms small (Nagg ∼ 8) reverse micellar aggregates, while in a solvent corresponding to water lamellar assembly takes place, in good agreement with literature structural parameters. Interestingly, solvents of intermediate polarity lead to formation of large, internally structured aggregates. In these, the surfactant headgroups cluster within the aggregate, surrounded by a continuous phase formed by the hydrocarbon tails. We show that the partitioning of the headgroups between the aggregate surface layer and the inner clustered phase depends primarily on solvent polarity, and can be controlled by the solvent, but also system composition. Finally, we compare the DPD assembly response to simplified effective interaction potentials derived at dilute concentration limit for the interactions. The comparison reveals that the simplified effective potential descriptions provide good level of insight on the assembly morphologies, despite drastic, isotropic interactions simplification involved.

Extending the Martini 3 Coarse-Grained Force Field to Carbohydrates

Carbohydrates play an essential role in a large number of chemical and biochemical processes. High structural diversity and conformational heterogeneity make it problematic to link their measurable properties to molecular features. Molecular dynamics simulations carried out at the level of classical force fields are routinely applied to study the complex processes occurring in carbohydrate-containing systems, while the usefulness of such simulations relies on the accuracy of the underlying theoretical model. In this article, we present the coarse-grained force field dedicated to glucopyranose-based carbohydrates and compatible with the recent version of the Martini force field (v. 3.0). The parameterization was based on optimizing bonded and nonbonded parameters with a reference to the all-atom simulation results and the experimental data. Application of the newly developed coarse-grained carbohydrate model to oligosaccharides curdlan and cellulose displays spontaneous formation of aggregates of experimentally identified features. In contact with other biomolecules, the model is capable of recovering the protective effect of glucose monosaccharides on a lipid bilayer and correctly identifying the binding pockets in carbohydrate-binding proteins. The features of the newly proposed model make it an excellent candidate for further extensions, aimed at modeling more complex, functionalized, and biologically relevant carbohydrates.

Building an extensible cell wall

This article recounts, from my perspective of four decades in this field, evolving paradigms of primary cell wall structure and the mechanism of surface enlargement of growing cell walls. Updates of the structures, physical interactions, and roles of cellulose, xyloglucan, and pectins are presented. This leads to an example of how a conceptual depiction of wall structure can be translated into an explicit quantitative model based on molecular dynamics methods. Comparison of the model's mechanical behavior with experimental results provides insights into the molecular basis of complex mechanical behaviors of primary cell wall and uncovers the dominant role of cellulose-cellulose interactions in forming a strong yet extensible network.

Molecular and biochemical basis of softening in tomato

We review the latest information related to the control of fruit softening in tomato and where relevant compare the events with texture changes in other fleshy fruits. Development of an acceptable texture is essential for consumer acceptance, but also determines the postharvest life of fruits. The complex modern supply chain demands effective control of shelf life in tomato without compromising colour and flavour.The control of softening and ripening in tomato (Solanum lycopersicum) are discussed with respect to hormonal cues, epigenetic regulation and transcriptional modulation of cell wall structure-related genes. In the last section we focus on the biochemical changes closely linked with softening in tomato including key aspects of cell wall disassembly. Some important elements of the softening process have been identified, but our understanding of the mechanistic basis of the process in tomato and other fruits remains incomplete, especially the precise relationship between changes in cell wall structure and alterations in fruit texture.

DEM-Based Approach for the Modeling of Gelation and Its Application to Alginate

The gelation of biopolymers is of great interest in the material science community and has gained increasing relevance in the past few decades, especially in the context of aerogels─lightweight open nanoporous materials. Understanding the underlying gel structure and influence of process parameters is of great importance to predict material properties such as mechanical strength. In order to improve understanding of the gelation mechanism in aqueous solution, this work presents a novel approach based on the discrete element method for the mesoscale for modeling gelation of hydrogels, similarly to an extremely coarse-grained molecular dynamics (MD) approach. For this, polymer chains are abstracted as dimer units connected by flexible bonds and interactions between units and with the environment, that is, diffusion in implicit water, are described. The model is based on Langevin dynamics and includes an implicit probabilistic ion model to capture the effects of ion availability during ion-mediated gelation. The model components are fully derived and parameterized using literature data and theoretical considerations based on a simplified representation of atomistic processes. The presented model enables investigations of the higher-scale network formation during gelation on the micrometer and millisecond scale, which are beyond classical modeling approaches such as MD. As a model system, calcium-mediated alginate gelation is investigated including the influence of ion concentration, polymer composition, polymer concentration, and molecular weight. The model is verified against numerous literature data as well as own experimental results for the corresponding Ca-alginate hydrogels using nitrogen porosimetry, NMR cryoporometry, and small-angle neutron scattering. The model reproduces both bundle size and pore size distribution in a reasonable agreement with the experiments. Overall, the modeling approach paves the way to physically motivated design of alginate gels.

Pectate lyase action in vivo and fruit softening. A commentary on: 'Fruit softening: evidence for pectate lyase action in vivo in date (Phoenix dactylifera) and rosaceous fruit cell walls'

This article comments on: Thurayya Z. S. Al Hinai, Robert A. M. Vreeburg, C. Logan Mackay, Lorna Murray, Ian H. Sadler and Stephen C. Fry. Fruit softening: evidence for pectate lyase action in vivo in date (Phoenix dactylifera) and rosaceous fruit cell walls, Annals of Botany, Volume 128, Issue 5, 8 October 2021, Pages 511–526, https://doi.org/10.1093/aob/mcab072

Aggregation and weak gel formation by pectic polysaccharide homogalacturonan

This study presents a novel model of homogalacturonan (HG) based on the dissipative particle dynamics (DPD). The model was applied to investigate the mechanism of self-aggregation of low-methoxylated homogalacturonan in aqueous solutions in the absence of cations. The coarse-grained model provided new insights into the structural features of HG aggregates and networks in aqueous solutions. Depending on the properties and concentration of polysaccharides, two major patterns of self-assembly were observed for HG - ellipsoidal aggregates and a continuous three-dimensional network. Simulations showed that a decrease in the degree of dissociation of HG results in a higher rate of self-aggregation, as well as facilitating the formation of larger assemblies or thicker nanofilaments depending on the type of final self-assembly. Simulations of polysaccharides of different chain lengths suggested the existence of a structural threshold for the formation of a spatial network for HG consisting of less than 35 GalA units.