Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides
- Publication type:
- Journal article
- Metadata:
-
- Autoren
- Rodrigo A Moreira
- Stefan AL Weber
- Adolfo B Poma
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000756591900001&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.3390/molecules27030976
- eISSN
- 1420-3049
- Externe Identifier
- Clarivate Analytics Document Solution ID: ZB1DR
- PubMed Identifier: 35164241
- Ausgabe der Veröffentlichung
- 3
- Zeitschrift
- MOLECULES
- Schlüsselwörter
- cellulose I allomorphs
- cellulose II
- Martini 3
- large conformational changes
- twist
- molecular dynamics
- coarse-grained model
- aggregation
- Artikelnummer
- ARTN 976
- Datum der Veröffentlichung
- 2022
- Status
- Published
- Titel
- Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides
- Sub types
- Article
- Ausgabe der Zeitschrift
- 27
Data source: Web of Science (Lite)
- Other metadata sources:
-
- Abstract
- <jats:p>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.</jats:p>
- Autoren
- Rodrigo A Moreira
- Stefan AL Weber
- Adolfo B Poma
- DOI
- 10.3390/molecules27030976
- eISSN
- 1420-3049
- Ausgabe der Veröffentlichung
- 3
- Zeitschrift
- Molecules
- Sprache
- en
- Online publication date
- 2022
- Paginierung
- 976 - 976
- Status
- Published online
- Herausgeber
- MDPI AG
- Herausgeber URL
- http://dx.doi.org/10.3390/molecules27030976
- Datum der Datenerfassung
- 2022
- Titel
- Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides
- Ausgabe der Zeitschrift
- 27
Data source: Crossref
- Abstract
- 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.
- Addresses
- Biosystems and Soft Matter Divison, Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland.
- Autoren
- Rodrigo A Moreira
- Stefan AL Weber
- Stefan AL Weber
- Adolfo B Poma
- DOI
- 10.3390/molecules27030976
- eISSN
- 1420-3049
- Externe Identifier
- PubMed Identifier: 35164241
- PubMed Central ID: PMC8838816
- Funding acknowledgements
- National Science Center: 2017/26/D/NZ1/00466
- Foundation for Polish Science: MAB PLUS/2019/11
- Open access
- true
- ISSN
- 1420-3049
- Ausgabe der Veröffentlichung
- 3
- Zeitschrift
- Molecules (Basel, Switzerland)
- Sprache
- eng
- Medium
- Electronic
- Online publication date
- 2022
- Open access status
- Open Access
- Paginierung
- 976
- Datum der Veröffentlichung
- 2022
- Status
- Published
- Publisher licence
- CC BY
- Datum der Datenerfassung
- 2022
- Titel
- Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides.
- Sub types
- research-article
- Journal Article
- Ausgabe der Zeitschrift
- 27
Files
https://www.mdpi.com/1420-3049/27/3/976/pdf?version=1644387300 https://europepmc.org/articles/PMC8838816?pdf=render
Data source: Europe PubMed Central
- Abstract
- 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.
- Date of acceptance
- 2022
- Autoren
- Rodrigo A Moreira
- Stefan AL Weber
- Adolfo B Poma
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/35164241
- DOI
- 10.3390/molecules27030976
- eISSN
- 1420-3049
- Externe Identifier
- PubMed Central ID: PMC8838816
- Funding acknowledgements
- National Science Center: 2017/26/D/NZ1/00466
- Foundation for Polish Science: MAB PLUS/2019/11
- Ausgabe der Veröffentlichung
- 3
- Zeitschrift
- Molecules
- Schlüsselwörter
- Martini 3
- aggregation
- cellulose I allomorphs
- cellulose II
- coarse-grained model
- large conformational changes
- molecular dynamics
- twist
- Sprache
- eng
- Country
- Switzerland
- PII
- molecules27030976
- Datum der Veröffentlichung
- 2022
- Status
- Published online
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2022
- Titel
- Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 27
Data source: PubMed
- Beziehungen:
-