Understanding the origin of structural colors in Margaritaria nobilis fruit: A molecular dynamics simulation study

Informazioni relative al progetto

NatColor-MD

ID dell’accordo di sovvenzione: 101155052

DOI

10.3030/101155052

Progetto chiuso

Data della firma CE 10 Aprile 2024

Data di avvio 1 Maggio 2024

Data di completamento 30 Aprile 2026

Finanziato da

• Marie Skłodowska-Curie Actions (MSCA)

Costo totale

Nessun dato

Contributo UE

€ 173 847,36

Coordinato da

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Germany

Periodic Reporting for period 1 - NatColor-MD (Understanding the origin of structural colors in Margaritaria nobilis fruit: A molecular dynamics simulation study)

Periodo di rendicontazione: 2024-05-01 al 2026-04-30

Sintesi del contesto e degli obiettivi generali del progetto

Investigating molecular interactions between cellulose surfaces and hemicelluloses is crucial for understanding plant cell wall architecture. Here, we employed molecular dynamics (MD) simulations to study how strongly xylan, the most common type of hemicelluloses, interact with cellulose surfaces. We systematically investigated effects from xylan substitution pattern, degree of polymerization, cellulose surface structure and the explicit water models. We studied four xylan models: a bare xylan without substitutions, an acetylated xylan where every other xylose unit is acetylated, and two acetylated xylan models with a Methyl-D-glucuronic unit (either in the middle of the chain or at the end). We then calculated the free energy of adsorption to see how strongly each of these xylans adhere to the hydrophobic (100) and the hydrophilic (110) cellulose surfaces. Our results show that the acetylated xylan adheres more strongly to the cellulose surfaces, compared to the unsubstituted xylan. This is more pronounced on the (100) cellulose surface and is consistent for all the common water models including SPC, SPC/E, TIP3P and TIP4P_2005. The presence of Methyl-D-glucuronic unit also enhanced the adhesion to the (100) surface, but it reduces the adhesion to the (110) surface. We also observed a linear relationship between the xylan degree of polymerization and the predicted adsorption energies, which can be used for predicting the adhesion of xylan polymers to the cellulose surfaces. Such molecular level understanding of xylan-cellulose adhesion is provide insights into plant cell wall biosynthesis, and is importnat for better understanding of the plant cell wall architecture.

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Multiple MD simulations were set up and performed to study the extent of interactions between cellulose and hemicelluloses, specifically xylan. different models were constructed for xylan oligomers and their interactions with cellulose surfaces was investigated in details using umbrella sampling method. Free energy of adsorption was then calculated to quantify the adhesion between xylan and cellulose surfaces. The conformation of different xylan oligomers on cellulose surfaces was also investigated to give insights into the stabilizing effect from different cellulose surfaces, including the hydrophobic and hydrophilic surfaces.

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Results from our study show that the acetylation of xylan improves adsorption to the cellulose surfaces by 7-10%. This effect is more pronounced for the hydrophobic surface of cellulose compared to the hydrophilic surface. We also show that the presence of Methyl-D-glucuronic unit on the acetylated xylan, increases the free energy of adsorption of xylan to the hydrophobic cellulose surface. It however reduces adsorption to the hydrophilic cellulose surface. The effect from the Methyl-D-glucuronic unit is less pronounced for longer xylan chains, where the acetyl groups play a major role in facilitating the stabilization of xylan on the hydrophilic surface. When normalized by the molecular weight of xylan, the free energy of adsorption for unsubstituted and acetylated xylan does not show a significant difference. We showed that this is consistent for different water models, including SPC, SPC/E, TIP3P and TIP4P_2005, and is agreement with published experimental data.

Because of computational limitations, calculation of free energy of adsorption for longer xylan chains (more than 10 repeating unit) is very tedious. However, we observed a linear relationship between the xylan chain length and the free energy of adsorption to cellulose surfaces. One can use the adsorption energies calculated for xylan oligomers to predict the adsorption of xylan polymers to cellulose surfaces.