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Khodayari A, Hirn U, Spirk S, Ogawa Y, Seveno D, Thielemans W. Advancing plant cell wall modelling: Atomistic insights into cellulose, disordered cellulose, and hemicelluloses - A review. Carbohydr Polym 2024; 343:122415. [PMID: 39174111 DOI: 10.1016/j.carbpol.2024.122415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/27/2024] [Accepted: 06/16/2024] [Indexed: 08/24/2024]
Abstract
The complexity of plant cell walls on different hierarchical levels still impedes the detailed understanding of biosynthetic pathways, interferes with processing in industry and finally limits applicability of cellulose materials. While there exist many challenges to readily accessing these hierarchies at (sub-) angström resolution, the development of advanced computational methods has the potential to unravel important questions in this field. Here, we summarize the contributions of molecular dynamics simulations in advancing the understanding of the physico-chemical properties of natural fibres. We aim to present a comprehensive view of the advancements and insights gained from molecular dynamics simulations in the field of carbohydrate polymers research. The review holds immense value as a vital reference for researchers seeking to undertake atomistic simulations of plant cell wall constituents. Its significance extends beyond the realm of molecular modeling and chemistry, as it offers a pathway to develop a more profound comprehension of plant cell wall chemistry, interactions, and behavior. By delving into these fundamental aspects, the review provides invaluable insights into future perspectives for exploration. Researchers within the molecular modeling and carbohydrates community can greatly benefit from this resource, enabling them to make significant strides in unraveling the intricacies of plant cell wall dynamics.
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Affiliation(s)
- Ali Khodayari
- Department of Materials Engineering, KU Leuven, Kasteelpark Arenberg 44, Leuven 3001, Belgium.
| | - Ulrich Hirn
- Institute of Bioproducts and Paper Technology, TU Graz, Inffeldgasse 23, Graz 8010, Austria
| | - Stefan Spirk
- Institute of Bioproducts and Paper Technology, TU Graz, Inffeldgasse 23, Graz 8010, Austria
| | - Yu Ogawa
- Centre de recherches sur les macromolécules végétales, CERMAV-CNRS, CS40700, 38041 Grenoble cedex 9, France
| | - David Seveno
- Department of Materials Engineering, KU Leuven, Kasteelpark Arenberg 44, Leuven 3001, Belgium
| | - Wim Thielemans
- Sustainable Materials Lab, Department of Chemical Engineering, KU Leuven, Campus Kulak Kortrijk, Etienne Sabbelaan 53, 8500 Kortrijk, Belgium
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Bourassi L, El Mrani M, Merzouki M, Abidi R, Bouammali H, Bouammali B, Elfarh L, Touzani R, Challioui A, Siaj M. Study of Cellulose Dissolution in ZnO/NaOH/Water Solvent Solution and Its Temperature-Dependent Effect Using Molecular Dynamics Simulation. Polymers (Basel) 2024; 16:1211. [PMID: 38732680 PMCID: PMC11085821 DOI: 10.3390/polym16091211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Cellulose is a biopolymer with numerous advantages that make it an ecological, economical, and high-performing choice for various applications. To fully exploit the potential of cellulose, it is often necessary to dissolve it, which poses a current challenge. The aqueous zinc oxide/sodium hydroxide (ZnO/NaOH/Water) system is a preferred solvent for its rapid dissolution, non-toxicity, low cost, and environmentally friendly nature. In this context, the behavior of cellulose chains in the aqueous solution of ZnO/NaOH and the impact of temperature on the solubility of this polymer were examined through a molecular dynamics simulation. The analysis of the root means square deviation (RMSD), interaction energy, hydrogen bond curves, and radial distribution function revealed that cellulose is insoluble in the ZnO/NaOH solvent at room temperature (T = 298 K). Decreasing the temperature in the range of 273 K to 268 K led to a geometric deformation of cellulose chains, accompanied by a decrease in the number of interchain hydrogen bonds over the simulation time, thus confirming the solubility of cellulose in this system between T = 273 K and T = 268 K.
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Affiliation(s)
- Lamiae Bourassi
- Laboratory of Applied Chemistry and Environment (LCAE), Organic Macromolecular Chemistry & Phytochemistry (ECOMP), Faculty of Sciences, Mohammed First University, Oujda 62000, Morocco; (L.B.); (M.E.M.); (M.M.); (R.A.); (H.B.); (B.B.); (A.C.)
| | - Meriem El Mrani
- Laboratory of Applied Chemistry and Environment (LCAE), Organic Macromolecular Chemistry & Phytochemistry (ECOMP), Faculty of Sciences, Mohammed First University, Oujda 62000, Morocco; (L.B.); (M.E.M.); (M.M.); (R.A.); (H.B.); (B.B.); (A.C.)
| | - Mohammed Merzouki
- Laboratory of Applied Chemistry and Environment (LCAE), Organic Macromolecular Chemistry & Phytochemistry (ECOMP), Faculty of Sciences, Mohammed First University, Oujda 62000, Morocco; (L.B.); (M.E.M.); (M.M.); (R.A.); (H.B.); (B.B.); (A.C.)
| | - Rania Abidi
- Laboratory of Applied Chemistry and Environment (LCAE), Organic Macromolecular Chemistry & Phytochemistry (ECOMP), Faculty of Sciences, Mohammed First University, Oujda 62000, Morocco; (L.B.); (M.E.M.); (M.M.); (R.A.); (H.B.); (B.B.); (A.C.)
| | - Haytham Bouammali
- Laboratory of Applied Chemistry and Environment (LCAE), Organic Macromolecular Chemistry & Phytochemistry (ECOMP), Faculty of Sciences, Mohammed First University, Oujda 62000, Morocco; (L.B.); (M.E.M.); (M.M.); (R.A.); (H.B.); (B.B.); (A.C.)
| | - Boufelja Bouammali
- Laboratory of Applied Chemistry and Environment (LCAE), Organic Macromolecular Chemistry & Phytochemistry (ECOMP), Faculty of Sciences, Mohammed First University, Oujda 62000, Morocco; (L.B.); (M.E.M.); (M.M.); (R.A.); (H.B.); (B.B.); (A.C.)
| | - Larbi Elfarh
- Laboratory of Theoretical Physics, Particles, Modeling and Energies (LPTPME), Faculty of Sciences, Mohammed First University, Oujda 62000, Morocco
| | - Rachid Touzani
- Laboratory of Applied Chemistry and Environment (LCAE), Organic Macromolecular Chemistry & Phytochemistry (ECOMP), Faculty of Sciences, Mohammed First University, Oujda 62000, Morocco; (L.B.); (M.E.M.); (M.M.); (R.A.); (H.B.); (B.B.); (A.C.)
| | - Allal Challioui
- Laboratory of Applied Chemistry and Environment (LCAE), Organic Macromolecular Chemistry & Phytochemistry (ECOMP), Faculty of Sciences, Mohammed First University, Oujda 62000, Morocco; (L.B.); (M.E.M.); (M.M.); (R.A.); (H.B.); (B.B.); (A.C.)
| | - Mohamed Siaj
- Chemistry Department, Université Québec A Montréal, Montréal, QC H3C 3P8, Canada;
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Chen JQ, Miao W, Liu Y, Zhou J, Han J, Zhang L, Bian XQ, Zhong T, Wu JL, Li N. Structural characterization, molecular dynamic simulation, and conformational visualization of a water-soluble glucan with high molecular weight from Gastrodia elata Blume. Int J Biol Macromol 2024; 263:130207. [PMID: 38365156 DOI: 10.1016/j.ijbiomac.2024.130207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024]
Abstract
Polysaccharides have been widely used in the development of natural drugs and health food. However, polysaccharide characterization lags due to inherently complicated features and the limitations of existing detection approaches. We aimed to provide new insight into the fine structure and conformational visualization of polysaccharides from Gastrodia elata Blume, a medicinal and edible plant. A water-soluble polysaccharide (GEP2-6) with the high molecular weight of 2.7 × 106 Da was first obtained, and its purity reached 99.2 %. Chemical and spectroscopic analyses jointly revealed that GEP2-6 was a glucan linked by α-(1 → 4) and α-(1 → 6) glycosidic bonds. After enzymolysis, the local structure of GEP2-6 included α-1,4-Glcp, α-1,6-Glcp, α-1,4,6-Glcp, and α-1-Glcp at a molar ratio of 31.27∶1.32∶1.08∶0.93. The glycosidic linkage pattern of repeating units was further simulated by a glycan database and spatial examination software. The good dissolution performance was interpreted by dynamics simulation and practical molecular characteristics. Spherical flexible chains and the porous stable conformation were corroborated using atomic force microscopy. In addition, GEP2-6 could effectively scavenge DPPH and hydroxyl radicals as a promising natural antioxidant. These efforts will contribute to the expansion of clinical applications of this G. elata polysaccharide and the structural elucidation for macromolecular polysaccharides combined with traditional and modern analysis techniques.
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Affiliation(s)
- Jia-Qian Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Wen Miao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Ying Liu
- School of Basic Medicinal Sciences and Nursing, Chengdu University, Chengdu 610106, PR China
| | - Jie Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Jie Han
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Li Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Xi-Qing Bian
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Tian Zhong
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao.
| | - Na Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao.
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Liu J, Chen C, Tu W, Liu W, Zhang Y. Analysis of the microscopic interactions between processed Polygonatum cyrtonema polysaccharides and water. J Mol Graph Model 2023; 118:108350. [PMID: 36194990 DOI: 10.1016/j.jmgm.2022.108350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 10/14/2022]
Abstract
The dissolution and microscopic interactions of processed Polygonatum cyrtonema polysaccharides in water are extremely important because they strongly influence the process to extract these polysaccharides from water. In this paper, molecular dynamics simulation methods were used to analyse the influence of extraction temperature, concentration and molecular weight on the radial distribution function (RDF), mean square displacement (MSD), diffusion coefficient (D), radius of gyration (Rg), and microstructure of processed Polygonatum cyrtonema polysaccharides in water as well as the intrinsic viscosity (η), hydrogen bond characteristics and microscopic interactions in the solutions. The research results showed that the extraction temperature, concentration and molecular weight of the polysaccharides had important effects on the RDF, MSD, D, Rg, η, hydrogen bond characteristics and the microstructure of the polysaccharide molecules, but there were some major differences. The order of the influence of the factors affecting the dissolution of polysaccharides in water was temperature > concentration > molecular weight. Extraction temperature, material fluid ratio and molecular weight had greater influence on the fluidity and dissolution state of the polysaccharides in water. As the solute concentration and molecular weight increased, hydrogen bonds between polysaccharides and water inhibited their dissolution and diffusion. Properly increasing the temperature, reducing the concentration and selecting low molecular weight polysaccharides enhanced the dissolution and diffusion of the polysaccharides in the solution system. Molecular weight was the main factor affecting the η of the polysaccharide solutions. These results can provide theoretical guidance for the extraction or tea brewing process of Polygonatum cyrtonema polysaccharides in future work.
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Affiliation(s)
- Jun Liu
- School of Resources and Environment, Nanchang University, Nanchang, 330031, Jiangxi, China.
| | - Changzhou Chen
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, Guangxi, China
| | - Wenfeng Tu
- School of Resources and Environment, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Wei Liu
- Jiangxi Shanbaotang Food Technology Co., Ltd., Nanchang, 330044, Jiangxi, China
| | - Yanru Zhang
- School of Material Science and Engineering, Hebei University of Engineering, Handan, 056038, Hebei, China
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