| Partner: Stefan A.L. Weber |
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Ostatnie publikacje
| 1. | Thi Minh Thu T.♦, Moreira R.A., Weber S.A.L.♦, Poma A.B., Molecular Insight into the Self-Assembly Process of Cellulose Iβ Microfibril, International Journal of Molecular Sciences, ISSN: 1422-0067, DOI: 10.3390/ijms23158505, Vol.23, No.15, pp.8505-1-18, 2022 Streszczenie: The self-assembly process of β-D-glucose oligomers on the surface of cellulose Iβ microfibril involves crystallization, and this process is analyzed herein, in terms of the length and flexibility of the oligomer chain, by means of molecular dynamics (MD) simulations. The characterization of this process involves the structural relaxation of the oligomer, the recognition of the cellulose I microfibril, and the formation of several hydrogen bonds (HBs). This process is monitored on the basis of the changes in non-bonded energies and the interaction with hydrophilic and hydrophobic crystal faces. The oligomer length is considered a parameter for capturing insight into the energy landscape and its stability in the bound form with the cellulose I microfibril. We notice that the oligomer–microfibril complexes are more stable by increasing the number of hydrogen bond interactions, which is consistent with a gain in electrostatic energy. Our studies highlight the interaction with hydrophilic crystal planes on the microfibril and the acceptor role of the flexible oligomers in HB formation. In addition, we study by MD simulation the interaction between a protofibril and the cellulose I microfibril in solution. In this case, the main interaction consists of the formation of hydrogen bonds between hydrophilic faces, and those HBs involve donor groups in the protofibril. Słowa kluczowe: cellulose I, self-assembly, stability, molecular dynamics, Charmm36, β-D-glucose Afiliacje autorów:
|  | 140p. | ||||||||||||
| 2. | Moreira R.A., Weber S.A.L.♦, Poma A.B.♦, Martini 3 model of cellulose microfibrils: on the route to capture large conformational changes of polysaccharides, Molecules, ISSN: 1420-3049, DOI: 10.3390/molecules27030976, Vol.27, No.3, pp.976-1-11, 2022 Streszczenie: 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. Słowa kluczowe: cellulose I allomorphs, cellulose II, Martini 3, large conformational changes, twist, molecular dynamics, coarse-grained model, aggregation Afiliacje autorów:
| | 140p. |