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Molecular Dynamics Simulations of Biomimetic Carbohydrate Materials
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. (Theoretical Chemistry and Biology)
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 [en]
molecular dynamics simulation, carbohydrate, cellulose, xyloglucan, cyclodextrin
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-33439ISBN: 978-91-7415-966-0OAI: oai:DiVA.org:kth-33439DiVA: diva2:416145
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
List of papers
1. A molecular dynamics study of the thermal response of crystalline cellulose I beta
Open this publication in new window or tab >>A molecular dynamics study of the thermal response of crystalline cellulose I beta
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.

Keyword
Cellulose I beta, Molecular dynamics, GLYCAM06, Thermal response
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-31887 (URN)10.1007/s10570-010-9491-x (DOI)000288253000002 ()2-s2.0-79952533565 (ScopusID)
Funder
Swedish e‐Science Research Center
Note
QC 20110329Available from: 2011-03-29 Created: 2011-03-28 Last updated: 2012-05-24Bibliographically approved
2. The adsorption of xyloglucan on cellulose: effects of explicit water and side chain variation
Open this publication in new window or tab >>The adsorption of xyloglucan on cellulose: effects of explicit water and side chain variation
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.

Keyword
Xyloglucan, Cellulose I beta, Molecular dynamics, GLYCAM06
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-33440 (URN)10.1016/j.carres.2011.09.007 (DOI)000297188900010 ()2-s2.0-80055037168 (ScopusID)
Funder
Swedish e‐Science Research Center
Note
QC 2011121Available from: 2011-05-06 Created: 2011-05-06 Last updated: 2012-05-24Bibliographically approved
3. Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucan endo-transglycosylase
Open this publication in new window or tab >>Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucan endo-transglycosylase
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(English)In: Molecular Simulation, ISSN 0892-7022Article in journal (Refereed) In press
Abstract [en]

Molecular dynamics (MD) simulations of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 have been performed and analyzed with respect to structure, dynamics, flexibility and ligand interactions. Notably, the charge state of the so-called “helper residue” Asp87, which lies between the catalytic nucleophile (Glu85) and general acid/base (Glu89) residues on the same beta strand, had a significant effect on PttXET16-34 active site structure. When Asp87 was deprotonated, electrostatic repulsion forced the nucleophile Glu85 away from C-1 of the sugar ring in subsite -1 and the electrophile Glu89 was also weakened due to the formation of a hydrogen bond to Asp87, whereas the protonation of Asp87 resulted in the formation of a hydrogen bond with the catalytic nucleophile and correct positioning of the catalytic machinery. The results suggest that catalysis in glycoside hydrolase family 16, and by extension clan GH-B enzymes, is optimal when the catalytic nucleophile is deprotonated for nucleophilic attack on the substrate, while the “helper residue” and general acid/base residue are both in their conjugate-acid forms to align the nucleophile and deliver a proton to the departing sugar, respectively.

Place, publisher, year, edition, pages
Taylor and Francis
Keyword
Xyloglucan, Xyloglucan binding protein, Complex, Molecular Dynamics simulation, Glycam force field
Identifiers
urn:nbn:se:kth:diva-33574 (URN)
Note
QS 2011Available from: 2011-05-10 Created: 2011-05-10 Last updated: 2011-05-13Bibliographically approved
4. Working Mechanism for a Redox Switchable Molecular Machine Based on Cyclodextrin: A Free Energy Profile Approach
Open this publication in new window or tab >>Working Mechanism for a Redox Switchable Molecular Machine Based on Cyclodextrin: A Free Energy Profile Approach
Show others...
2010 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 19, 6561-6566 p.Article in journal (Refereed) Published
Abstract [en]

This paper reports the working mechanism for a redox-responsive bistable [2]rotaxane incorporating an alpha-cyclodextrin (alpha-CD) ring (J. Am. Chem. Soc. 2008, 130, 11294-11296), based on free energy profiles obtained from all-atom molecular dynamics simulations. Employing an umbrella sampling technique, the free energy profiles (potential of mean force, PMF) were calculated for the shuttling motion of the alpha-CD ring between a tetrathiafulvalene (TTF) recognition site and a triazole (TZ) unit on the dumbbell of the rotaxane for three oxidation states (0, +1, +2) of the TTF unit. These calculated free energy profiles verified the experimentally observed binding preference for each state. Analysis of the free energy components reveals that, for these alpha-CD-based rotaxanes with charged TTF units, the real driving force for the shuttling in the oxidized states is actually the interactions between water and the rotaxane components, which overwhelms the attractive interactions between the alpha-CD ring and the charged dumbbell. In this work, we put forward a feasible approach to correctly describe the complexation behavior of CD with charged species, that is, free energy profiles obtained from all-atom molecular dynamics simulation.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-27876 (URN)10.1021/jp102834k (DOI)000277499700038 ()2-s2.0-77952514332 (ScopusID)
Note
QC 20110110Available from: 2011-01-10 Created: 2011-01-03 Last updated: 2011-05-13Bibliographically approved

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