Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides
High resolution data from all-atom molecular simulations is used to parameterize a Martini 3 coarse-grained (CG) model of cellulose I allomorphs and cellulose type-II fibrils. In this case, elementary molecules are represented by four effective beads centred in the positions of O2, O3, C6, and O6 at...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-02-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/27/3/976 |
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| author | Rodrigo A. Moreira Stefan A. L. Weber Adolfo B. Poma |
| author_facet | Rodrigo A. Moreira Stefan A. L. Weber Adolfo B. Poma |
| author_sort | Rodrigo A. Moreira |
| collection | DOAJ |
| description | High resolution data from all-atom molecular simulations is used to parameterize a Martini 3 coarse-grained (CG) model of cellulose I allomorphs and cellulose type-II fibrils. In this case, elementary molecules are represented by four effective beads centred in the positions of O2, O3, C6, and O6 atoms in the D-glucose cellulose subunit. Non-bonded interactions between CG beads are tuned according to a low statistical criterion of structural deviation using the Martini 3 type of interactions and are capable of being indistinguishable for all studied cases. To maintain the crystalline structure of each single cellulose chain in the microfibrils, elastic potentials are employed to retain the ribbon-like structure in each chain. We find that our model is capable of describing different fibril-twist angles associated with each type of cellulose fibril in close agreement with atomistic simulation. Furthermore, our CG model poses a very small deviation from the native-like structure, making it appropriate to capture large conformational changes such as those that occur during the self-assembly process. We expect to provide a computational model suitable for several new applications such as cellulose self-assembly in different aqueous solutions and the thermal treatment of fibrils of great importance in bioindustrial applications. |
| first_indexed | 2024-03-09T23:27:29Z |
| format | Article |
| id | doaj.art-9af1d6fba5a84c28a22e893af8df2d9f |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-09T23:27:29Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-9af1d6fba5a84c28a22e893af8df2d9f2023-11-23T17:15:34ZengMDPI AGMolecules1420-30492022-02-0127397610.3390/molecules27030976Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of PolysaccharidesRodrigo A. Moreira0Stefan A. L. Weber1Adolfo B. Poma2Biosystems and Soft Matter Divison, Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, PolandMax Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, GermanyInternational Center for Research on Innovative Biobased Materials (ICRI-BioM)—International Research Agenda, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, PolandHigh resolution data from all-atom molecular simulations is used to parameterize a Martini 3 coarse-grained (CG) model of cellulose I allomorphs and cellulose type-II fibrils. In this case, elementary molecules are represented by four effective beads centred in the positions of O2, O3, C6, and O6 atoms in the D-glucose cellulose subunit. Non-bonded interactions between CG beads are tuned according to a low statistical criterion of structural deviation using the Martini 3 type of interactions and are capable of being indistinguishable for all studied cases. To maintain the crystalline structure of each single cellulose chain in the microfibrils, elastic potentials are employed to retain the ribbon-like structure in each chain. We find that our model is capable of describing different fibril-twist angles associated with each type of cellulose fibril in close agreement with atomistic simulation. Furthermore, our CG model poses a very small deviation from the native-like structure, making it appropriate to capture large conformational changes such as those that occur during the self-assembly process. We expect to provide a computational model suitable for several new applications such as cellulose self-assembly in different aqueous solutions and the thermal treatment of fibrils of great importance in bioindustrial applications.https://www.mdpi.com/1420-3049/27/3/976cellulose I allomorphscellulose IIMartini 3large conformational changestwistmolecular dynamics |
| spellingShingle | Rodrigo A. Moreira Stefan A. L. Weber Adolfo B. Poma Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides Molecules cellulose I allomorphs cellulose II Martini 3 large conformational changes twist molecular dynamics |
| title | Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides |
| title_full | Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides |
| title_fullStr | Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides |
| title_full_unstemmed | Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides |
| title_short | Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides |
| title_sort | martini 3 model of cellulose microfibrils on the route to capture large conformational changes of polysaccharides |
| topic | cellulose I allomorphs cellulose II Martini 3 large conformational changes twist molecular dynamics |
| url | https://www.mdpi.com/1420-3049/27/3/976 |
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