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The adsorption of xyloglucan on cellulose: effects of explicit water and side chain variation
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
KTH, School of Biotechnology (BIO), Glycoscience.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0002-1763-9383
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0001-8198-9284
2011 (English)In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, no 16, 2595-2602 p.Article in journal (Refereed) Published
Abstract [en]

The interaction between para-crystalline cellulose and the cross-linking glycan xyloglucan (XG) plays a central role for the strength and extensibility of plant cell walls. The coating of XGs on cellulose surfaces is believed to be one of the most probable interaction patterns. In this work, the effects of explicit water and side chain variation on the adsorption of XGs on cellulose are investigated by means of atomistic molecular dynamics simulations. The adsorption properties are studied in detail for three XGs on cellulose I beta 1-10 surface in aqueous environment, namely GXXXGXXXG, GXXLGXXXG, and GXXFGXXXG, which differ in the length and composition of one side chain. Our work shows that when water molecules are included in the theoretical model, the total interaction energies between the adsorbed XGs and cellulose are considerably smaller than in vacuo. Furthermore, in water environment the van der Waals interactions prevail over the electrostatic interactions in the adsorption. Variation in one side chain does not have significant influence on the interaction energy and the binding affinity, but does affect the equilibrium structural properties of the adsorbed XGs to facilitate the interaction between both the backbone and the side chain residues with the cellulose surface. Together, this analysis provides new insights into the nature of the XG-cellulose interaction, which helps to further refine current molecular models of the composite plant cell wall.

Place, publisher, year, edition, pages
2011. Vol. 346, no 16, 2595-2602 p.
Keyword [en]
Xyloglucan, Cellulose I beta, Molecular dynamics, GLYCAM06
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-33440DOI: 10.1016/j.carres.2011.09.007ISI: 000297188900010Scopus ID: 2-s2.0-80055037168OAI: oai:DiVA.org:kth-33440DiVA: diva2:415507
Funder
Swedish e‐Science Research Center
Note
QC 2011121Available from: 2011-05-06 Created: 2011-05-06 Last updated: 2017-12-11Bibliographically approved
In thesis
1. Molecular Dynamics Simulations of Biomimetic Carbohydrate Materials
Open this publication in new window or tab >>Molecular Dynamics Simulations of Biomimetic Carbohydrate Materials
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The present thesis honors contemporary molecular dynamics simulation methodologies which provide powerful means to predict data, interpret observations and widen our understanding of the dynamics, structures and interactions of carbohydrate systems. With this as starting point my thesis work embarked on several cutting edge problems summarized as follows.

In my first work the thermal response in crystal cellulose Iβ was studied with special emphasis on the temperature dependence of the crystal unit cell parameters and the organization of the hydrogen bonding network. The favorable comparison with available experimental data, like the phase transition temperature, the X-ray diffraction crystal structures of cellulose Iβ at room and high temperatures, and temperature dependent IR spectra supported our conclusions on the good performance of the GLYCAM06 force field for the description of cellulose crystals, and that a cautious parameterization of the non-bonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals.

The adsorption properties of xyloglucans on the cellulose Iβ surface were investigated in my second paper. In our simulations, the interaction energies between xyloglucan and cellulose in water were found to be considerably lower than those in vacuo. The van der Waals interactions played a prevailing role over the electrostatic interactions in the adsorption. Though the variation in one side chain did not have much influence on the interaction energy and the binding affinity, it did affect the structural properties of the adsorbed xyloglucans.

The interaction of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 was studied in the third paper. The effect of the charge state of the “nucleophile helper” residue Asp87 on the PttXET16-34 active site structure was emphasized. The results indicate that the catalysis is optimal when the catalytic nucleophile is deprotonated, while the “helper” residue and general acid/base residue are both protonated.

In my forth paper, the working mechanism for a redox-responsive bistable [2]rotaxane based on an α-cyclodextrin ring was investigated. The umbrella sampling technique was employed to calculate the free energy profiles for the shuttling motion of the α-cyclodextrin ring between two recognition sites on the dumbbell of the rotaxane. The calculated free energy profiles verified the binding preferences observed experimentally. The driving force for the shuttling movement of the α-cyclodextrin ring was revealed by the analysis of the free energy components.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2011. viii, 66 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2011:12
Keyword
molecular dynamics simulation, carbohydrate, cellulose, xyloglucan, cyclodextrin
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-33439 (URN)978-91-7415-966-0 (ISBN)
Public defence
2011-05-31, FB42, AlbaNova, Roslagstullsbacken 21, Stockholm, 14:00 (English)
Opponent
Supervisors
Funder
Swedish e‐Science Research Center
Note
QC 20110513Available from: 2011-05-13 Created: 2011-05-06 Last updated: 2012-05-24Bibliographically approved

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