Molecular Dynamics Simulations Illuminate the Role of Counterion Condensation in the Electrophoretic Transport of Homogalacturonans

Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria

The honeybee gut microbiome is crucial for degrading diverse pollen glycans. Yet it is unclear how this process shapes the interactions among bacteria. Here, we demonstrate a conditional mutualistic interaction between strains of two honeybee gut bacteria Bifidobacterium asteroides and Gilliamella apicola. When co-occurring in vitro and in vivo, Bifidobacterium provides complementary demethylation service to promote Gilliamella growth on methylated homogalacturonan, an enriched polysaccharide of pectin. In exchange, Gilliamella shares digestive products with Bifidobacterium, through which a positive interaction is established. This positive interaction vanishes when Bifidobacterium is not required on a non-methylated diet. Results from biochemical and gene expression analyses combined with model simulation further suggest that the ratio change of the two major homogalacturonan breakdown products, galacturonic acid (GalA) and di-GalA, determines the bacterial interaction. This study unravels how glycan metabolism may shape the interactions between honeybee gut bacteria.

Molecular dynamics simulations and X-ray scattering show the κ-carrageenan disorder-to-order transition to be the formation of double-helices

Recent molecular dynamics simulations, verified experimentally by solution-state x-ray scattering experiments, have found that κ-carrageenan chains contain helical secondary structure, akin to that found in the solid-state, even in aqueous solution. Furthermore, upon the addition of ions to single chains the simulations found no evidence that any conformational transitions take place. These findings challenge the long-held assumption that the so-called disorder-to-order transition in carrageenan systems involves a uni-molecular 'coil-to-helix transition'. Herein, the results of further molecular dynamics simulations undertaken using pairs of κ-carrageenan chains in 0.1 M NaI solutions are reported, and are validated experimentally using state-of-the-art solution-state WAXS experiments. From initially separated chains double-helices are shown to form, leading the authors to propose 'two single helices-to-stabilized double-helix' as a description of the molecular events taking place during the disorder-to-order transition.

Influence of cations, pH and dispersed phases on pectin emulsification properties

The cooperativity of six cations (Ca²⁺, Mg²⁺, Zn²⁺, Al³⁺, Cr³⁺ and Fe³⁺), three pectins (sugar beet, high and low methyl esterified), three dispersed phases (medium chain triglycerides (MCT), orange oil and hexadecane), time (30 days) and pH (2.0 and 6.0) has been investigated in the formation and stability against coarsening of oil-in-water emulsions. Cations generally influenced emulsion stability in the following order (most stable) Ca²⁺ ​> ​Mg²⁺ ​> ​Al³⁺ ​> ​Cr³⁺ ​> ​Zn²⁺ ​> ​Fe³⁺ (least stable). This order largely coincided with that of the strength of pectin-cation interactions showing that the higher the affinity of cation for pectin the less stable the emulsion. More stable emulsions were formed with sugar beet pectin, which was also unresponsive to the presence of cations, followed by high- and then low-methyl esterified samples. At pH 2.0 all pectins showed their best emulsification performance whereas shifting pH to 6.0 severely impaired emulsification capacity and longer term stability against droplet growth. Smaller droplets were created with hexadecane under all conditions studied followed by MCT and orange oil in agreement with their aqueous solubilities. The present results advance our understanding of the stabilisation of emulsions using pectin and allow us to tailor their functionality for applications in food, pharmaceutical and biomedical industries.

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Cations influence stability in the order: Ca²⁺ ​> ​Mg²⁺ ​> ​Al³⁺ ​> ​Cr³⁺ ​> ​Zn²⁺ ​> ​Fe³⁺.

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Pectins showed best emulsification performance at pH 2.0

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Pectins showed poor emulsification performance at pH 6.0

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Pectin stability order: sugar beet ​> ​high methoxy ​> ​low methoxy pectin.

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Oil stability order at pH 2.0: hexadecane ​< ​medium chain triglycerides ​< ​orange oil.

Resolving solution conformations of the model semi-flexible polyelectrolyte homogalacturonan using molecular dynamics simulations and small-angle x-ray scattering

The conformation of polyelectrolytes in the solution state has long been of interest in polymer science. Herein we utilize all atom molecular dynamics simulations (MD) and small-angle x-ray scattering experiments (SAXS) to elucidate the molecular structure of the model polyelectrolyte homogalacturonan. Several degrees of polymerization were studied and in addition partial methylesterification of the otherwise charge-carrying carboxyl groups was used in order to generate samples with varying intra-chain charge distributions. It is shown that at length scales above around 1nm the conformation of isolated chains has surprisingly little dependence on the charge distribution or the concentration of attendant monovalent salts, reflective of the intrinsic stiffness of the saccharide rings and the dynamical constraints of the glycosidic linkage. Indeed the conformation of isolated chains over all accessible length scales is well described by the atomic coordinates available from fibre diffraction studies. Furthermore, in more concentrated systems it is shown that, after careful analysis of the SAXS data, the form of the inter-particle effects heralded by the emergence of a so-called polyelectrolyte peak, can be extracted, and that this phenomena can be reproduced by multiple chain MD simulations.

On the electrophoretic mobilities of partially charged oligosaccharides as a function of charge patterning and degree of polymerization

Fully or partially charged oligosaccharide molecules play a key role in many areas of biology, where their fine structures are crucial in determining their functionality. However, the separation of specific charged oligosaccharides from similar moieties that typically coexist in extracted samples, even for those that are unbranched, and in cases where each saccharide moiety can only carry a single charge or not, is far from trivial. Typically such molecules are characterized by a degree of polymerization n and a number m (and distribution) of charged residues, and must be separated from a plethora of similar species possessing different combinations of n and m. Furthermore, the separation of the possible n!/m!(n-m)! isomers of each species of fixed n and m is a formidable challenge to analytical chemists. Herein, we report the results of molecular dynamics simulations that have been performed in order to calculate the free solution electrophoretic mobilities of galacturonides and charged oligosaccharides derived from digests of the important plant cell-wall polysaccharide pectin. The simulations are compared with an experiment and are found to correctly predict the loss of resolution of fully charged species above a critical degree of polymerization n and the ionic strength dependence of the electrophoretic mobilities of different partially charged oligosaccharides. It is expected that having a predictive tool for the calculation of the electrophoretic mobilities of differently charged oligosaccharide species in hand will allow experimental conditions that optimize the resolution of particular species to be ascertained and understood.