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A molecular dynamics study of the thermal response of crystalline cellulose I beta
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
KTH, School of Biotechnology (BIO), Glycoscience.
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.ORCID iD: 0000-0002-1763-9383
2011 (English)In: Cellulose (London), ISSN 0969-0239, E-ISSN 1572-882X, Vol. 18, no 2, 207-221 p.Article in journal (Refereed) Published
Abstract [en]

Molecular dynamics simulations were performed to better understand the atomic details of thermal induced transitions in cellulose I beta. The latest version of the GLYCAM force field series (GLYCAM06) was used for the simulations. The unit cell parameters, density, torsion angles and hydrogen-bonding network of the crystalline polymer were carefully analyzed. The simulated data were validated against the experimental results obtained by X-ray diffraction for the crystal structure of cellulose I beta at room and high temperatures, as well as against the temperature-dependent IR measurements describing the variation of hydrogen bonding patterns. Distinct low and high temperature structures were identified, with a phase transition temperature of 475-500 K. In the high-temperature structure, all the origin chains rotated around the helix axis by about 30A degrees and the conformation of all hydroxymethyl groups changed from tg to either gt on origin chains or gg on center chains. The hydrogen-bonding network was reorganized along with the phase transition. Compared to the previously employed GROMOS 45a4 force field, GLYCAM06 yields data in much better agreement with experimental observations, which reflects that a cautious parameterization of the nonbonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals.

Place, publisher, year, edition, pages
2011. Vol. 18, no 2, 207-221 p.
Keyword [en]
Cellulose I beta, Molecular dynamics, GLYCAM06, Thermal response
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-31887DOI: 10.1007/s10570-010-9491-xISI: 000288253000002Scopus ID: 2-s2.0-79952533565OAI: oai:DiVA.org:kth-31887DiVA: diva2:406948
Funder
Swedish e‐Science Research Center
Note
QC 20110329Available from: 2011-03-29 Created: 2011-03-28 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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Ågren, Hans

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