| 1. |
- Angles d'Ortoli, Thibault, et al.
(författare)
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Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers
- 2015
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:30, s. 9559-9570
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Tidskriftsartikel (refereegranskat)abstract
- Empirical force fields for computer simulations of carbohydrates are often implicitly assumed to be valid also at temperatures different from room temperature for which they were optimited: Herein, the temperature dependence of the hydroxymethyl group rotamer populations in short oligogaccharides is invegtigated using Molecular dynamics simulations and NMR spectroscopy. Two oligosaccharides, methyl beta-cellobioside and beta-cellotetraose were simulated using three different carbohydrate force fields (CHARMM C35, GLYCAM06, and GROMOS 56A(carbo)) in combination with different water models (SPC, SPC/E, and TIP3P) using replica exchange molecular dynamics simulations. For comparison, hydroxymethyl group rotamer populations were investigated for methyl beta-cellobioside and cellopentaose based- on measured NMR (3)J(H5,H6) coupling constants, in the latter case by using a chemical shift selective NMR-filter. Molecular dynamics simulations in combination with NMR spectroscopy show that the temperature dependence of the hydroxymethyl rotamer population in these short cellooligomers, in the range 263-344 K, generally becomes exaggerated in simulations when compared to experimental data, but also that it is dependent on simulation conditions, and most notably properties of the water model.
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| 2. |
- Beckham, Gregg T., et al.
(författare)
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The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase Is a Flexible, Disordered Protein
- 2010
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 99:11, s. 3773-3781
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Tidskriftsartikel (refereegranskat)abstract
- Fungi and bacteria secrete glycoprotein cocktails to deconstruct cellulose Cellulose degrading enzymes (cellulases) are often modular with catalytic domains for cellulose hydrolysis and carbohydrate binding modules connected by linkers rich in serine and threonine with O-glycosylation Few studies have probed the role that the linker and O-glycans play in catalysis Since different expression and growth conditions produce different glycosylation patterns that affect enzyme activity the structure function relationships that glycosylation imparts to linkers are relevant for understanding cellulase mechanisms Here the linker of the Trichoderma reesei Family 7 cellobiohydrolase (Cel7A) is examined by simulation Our results suggest that the Cel7A linker is an intrinsically disordered protein with and without glycosylation Contrary to the predominant view the O-glycosylation does not change the stiffness of the linker as measured by the relative fluctuations in the end to end distance rather it provides a 16 A extension thus expanding the operating range of Cel7A We explain observations from previous biochemical experiments in the light of results obtained here and compare the Cel7A linker with linkers from other cellulases with sequence based tools to predict disorder This preliminary screen indicates that linkers from Family 7 enzymes from other genera and other cellulases within T reesei may not be as disordered warranting further study
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| 3. |
- Bergenstråhle, Malin, et al.
(författare)
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Cellulose crystal structure and force fields
- 2010
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Ingår i: International Conference on Nanotechnology for the Forest Products Industry 2010. - 9781618390011 ; , s. 674-689
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Konferensbidrag (refereegranskat)abstract
- Classical molecular mechanics force fields for carbohydrates are widely used for molecular dynamics simulations of crystalline cellulose, in particular, cellulose Iβ. To investigate the impact of choice of force field on crystalline cellulose structure and properties we have performed a comparative study of four different carbohydrate force fields. Molecular dynamics simulations applying the different force fields were performed on a solvated cellulose Iβ crystal. The crystal consisted of 36 cellulose chains, each of them 40 glucose units long, arranged in a crystal manner with a square cross section. These simulations show that the differences in force fields are of great importance for the resulting relaxed cellulose structure. The orientation of the hydroxymethyl groups is a key parameter and an indicator of different hydrogen bonding patterns that may be found in crystalline cellulose.
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| 4. |
- Bergenstråhle, Malin, 1977-
(författare)
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Crystalline cellulose in bulk and at interfaces as studied by atomistic computer simulations
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cellulose is a linear polysaccharide, serving as reinforcement in plant cell walls.Understanding its structure and properties is of importance in the developmentof nanostructured cellulose materials. The aim of this thesis is to address thisquestion by applying the computer simulation technique Molecular Dynamics(MD) onto an atomistic model of a native crystal form of cellulose.A molecular model of crystalline cellulose Iβ was developed and simulatedwith the GROMACS simulation software package.Temperature dependence of the crystal bulk model was investigated. A gradualtransition was observed between 350 K and 500 K in concordance with experimentalresults. The high temperature structure differed from the originalstructure in terms of crystal cell parameters, hydrogen bonding network andelastic modulus.Spin-lattice relaxation times, T1, from solid-state Nuclear Magnetic Resonancespectroscopy were compared with values calculated from the dynamics ofthe C4-H4 vector in MD simulations. Calculated T1 compared well with experimentallyobtained, suggesting well reproduced dynamics. Moreover, a differencein T1 of about a factor 2 was found for C4 atoms at surfaces parallel to differentcrystallographic planes. This supports a proposed explanation regarding anobserved doublet for C4 atoms in the NMR spectrum.Interaction energies between crystalline cellulose and water and 6− hydroxyhexanal(CL) were determined from simulations. Water was found to interactstronger with cellulose than CL. Moreover, the effect of grafting CL onto surfacecellulose chains was examined. For both water and CL interfaces, grafting ledto increased interaction. Electrostatic interactions were dominating in all cases,however grafting increased the importance of van der Waals interactions.The experimental approach to investigate polymer desorption by pulling itfrom a surface by the use of Atomic Force Microscopy (AFM) was enlightenedwith a modelling study. A single cellulose octamer was pulled from a cellulosecrystal into water and cyclohexane. Resulting pull-off energies proved a clearsolvent effect, 300 − 400 [kJ/mole] in cyclohexane and 100 − 200 [kJ/mole] inwater.In general, MD was shown to be useful when applied in combination withfeasible experimental techniques such as NMR and AFM to increase the fundamentalunderstanding of cellulose structure and properties.
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| 5. |
- Bergenstråhle, Malin, 1977-, et al.
(författare)
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Dynamics of Cellulose-Water Interfaces : NMR Spin-Lattice Relaxation Times Calculated from Atomistic Computer Simulations
- 2008
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Ingår i: Journal of Physical Chemistry B. - Washington : ACS Publications. - 1520-6106 .- 1520-5207. ; 112:9, s. 2590-2595
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Tidskriftsartikel (refereegranskat)abstract
- Solid-state nuclear magnetic resonance (CP/MAS 13C NMR) spectroscopy has often been used to study cellulose structure, but some features of the cellulose NMR spectrum are not yet fully understood. One such feature is a doublet around 84 ppm, a signal that has been proposed to originate from C4 atoms at cellulose fibril surfaces. The two peaks yield different T1, differing by approximately a factor of 2 at 75 MHz. In this study, we calculate T1 from C4-H4 vector dynamics obtained from molecular dynamics computer simulations of cellulose Iβ-water interfacial systems. Calculated and experimentally obtained T1 values for C4 atoms in surface chains fell within the same order of magnitude, 3-20 s. This means that the applied force field reproduces relevant surface dynamics for the cellulose-water interface sufficiently well. Furthermore, a difference in T1 of about a factor of 2 in the range of Larmor frequencies 25-150 MHz was found for C4 atoms in chains located on top of two different crystallographic planes, namely, (110) and (10). A previously proposed explanation that the C4 peak doublet could derive from surfaces parallel to different crystallographic planes is herewith strengthened by computationally obtained evidence. Another suggested basis for this difference is that the doublet originates from C4 atoms located in surface anhydro-glucose units with hydroxymethyl groups pointing either inward or outward. This was also tested within this study but was found to yield no difference in calculated T1.
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| 6. |
- Bergenstråhle, Malin, 1977-, et al.
(författare)
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Force Pulling of Single Cellulose Chains at the Crystalline Cellulose-Liquid Interface : A Molecular Dynamics Study
- 2009
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 25:8, s. 4635-4642
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Tidskriftsartikel (refereegranskat)abstract
- Pulling single cellulose molecules from a crystalline cellulose surface has been modeled by molecular dynamics (MD) simulations of the experimental procedure used in atomic force microscopy (AFM). Specifically, the aim of the study was to investigate cellulose interactions at desorption. Simulations were performed in both water and the organic solvent cyclohexane. Moreover, the effects of initial octamer conformation and orientation with respect to the surface chains were studied. A strong effect from the solvent was observed. In cyclohexane, normal forces of 200-500 pN and energies of 43.5 +/- 6.0 kJ/mol glucose unit were required to pull off the octamer. The normal forces in water were substantially lower, around 58 pN, and the energies were 18.2 +/- 3.6 kJ/mol glucose unit. In addition, the lateral components of the pull-off force were shown to provide information on initial conformation and orientation. Hydrogen bonds between the octamer and surface were analyzed and found to be an important factor in the pull-off behavior. Altogether, it was shown that MD provides detailed information on the desorption processes that may be useful for the interpretation of AFM experiments.
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| 7. |
- Bergenstråhle, Malin, 1977-, et al.
(författare)
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Molecular modeling of interfaces between cellulose crystals and surrounding molecules : Effects of caprolactone surface grafting
- 2008
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Ingår i: European Polymer Journal. - Amsterdam : Elsevier. - 0014-3057 .- 1873-1945. ; 44:11, s. 3662-3669
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Tidskriftsartikel (refereegranskat)abstract
- A technical problem in cellulosic nanocomposite materials is the weak interaction between hydrophilic cellulose and hydrophobic polymer matrices. One approach to solve this difficulty is to chemically graft monomers of the matrix polymer onto the cellulose surface. An important question is to understand the effect such surface modification has on the interfacial properties. Semi-empirical approaches to estimate work of adhesion based on surface energies do not provide information on specific molecular interactions. Details about these interactions were obtained using molecular dynamics (MD) simulation. Cellulose interfaces with water and caprolactone medium were modeled with different amounts of grafted caprolactone. The modification lead to an increased work of adhesion between the surface and its surrounding medium. Furthermore, the MD simulations showed that the interaction between cellulose, both modified and non-modified, and surrounding medium is dominated by Coulomb interactions, predominantly as hydrogen bonds.
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| 8. |
- Bergenstråhle, Malin, 1977-, et al.
(författare)
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Simulation studies of the insolubility of cellulose
- 2010
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Ingår i: Carbohydrate Research. - : Elsevier BV. - 0008-6215 .- 1873-426X. ; 345:14, s. 2060-2066
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics simulations have been used to calculate the potentials of mean force for separating short cellooligomers in aqueous solution as a means of estimating the contributions of hydrophobic stacking and hydrogen bonding to the insolubility of crystalline cellulose. A series of four potential of mean force (pmf) calculations for glucose, cellobiose, cellotriose, and cellotetraose in aqueous solution were performed for situations in which the molecules were initially placed with their hydrophobic faces stacked against one another, and another for the cases where the molecules were initially placed adjacent to one another in a co-planar, hydrogen-bonded arrangement, as they would be in cellulose ID. From these calculations, it was found that hydrophobic association does indeed favor a crystal-like structure over solution, as might be expected. Somewhat more surprisingly, hydrogen bonding also favored the crystal packing, possibly in part because of the high entropic cost for hydrating glucose hydroxyl groups, which significantly restricts the configurational freedom of the hydrogen-bonded waters. The crystal was also favored by the observation that there was no increase in chain configurational entropy upon dissolution, because the free chain adopts only one conformation, as previously observed, but against intuitive expectations, apparently due to the persistence of the intramolecular O3-O5 hydrogen bond.
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| 9. |
- Bergenstråhle, Malin, 1977-, et al.
(författare)
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Thermal Response in Crystalline Iβ Cellulose : A Molecular Dynamics Study
- 2007
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Ingår i: Journal of Physical Chemistry B. - Washington : ACS Publications. - 1520-6106 .- 1520-5207. ; 111:30, s. 9138-9145
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Tidskriftsartikel (refereegranskat)abstract
- The influence of temperature on structure and properties of the cellulose Iβ crystal was studied by molecular dynamics simulations with the GROMOS 45a4 force-field. At 300 K, the modeled crystal agreed reasonably with several sets of experimental data, including crystal density, corresponding packing and crystal unit cell dimensions, chain conformation parameters, hydrogen bonds, Young's modulus, and thermal expansion coefficient at room temperature. At high-temperature (500 K), the cellulose chains remained in sheets, despite differences in the fine details compared to the room-temperature structure. The density decreased while the a and b cell parameters expanded by 7.4% and 6%, respectively, and the c parameter (chain axis) slightly contracted by 0.5%. Cell angles α and β divided into two populations. The hydroxymethyl groups mainly adopted the gt orientation, and the hydrogen-bonding pattern thereby changed. One intrachain hydrogen bond, O2'H2'···O6, disappeared and consequently the Young's modulus decreased by 25%. A transition pathway between the low- and high-temperature structures has been proposed, with an initial step being an increased intersheet separation, which allowed every second cellulose chain to rotate around its helix axis by about 30°. Second, all hydroxymethyl groups changed their orientations, from tg to gg (rotated chains) and from tg to gt (non-rotated chains). When temperature was further increased, the rotated chains returned to their original orientation and their hydroxymethyl groups again changed their conformation, from gg to gt. A transition temperature of about 450 K was suggested; however, the transition seems to be more gradual than sudden. The simulated data on temperature-induced changes in crystal unit cell dimensions and the hydrogen-bonding pattern also compared well with experimental results.
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| 10. |
- Bergenstråhle-Wohlert, Malin, et al.
(författare)
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Concentration enrichment of urea at cellulose surfaces : results from molecular dynamics simulations and NMR spectroscopy
- 2012
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Ingår i: Cellulose. - : Springer Science and Business Media LLC. - 0969-0239 .- 1572-882X. ; 19:1, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- A combined solid-state NMR and Molecular Dynamics simulation study of cellulose in urea aqueous solution and in pure water was conducted. It was found that the local concentration of urea is significantly enhanced at the cellulose/solution interface. There, urea molecules interact directly with the cellulose through both hydrogen bonds and favorable dispersion interactions, which seem to be the driving force behind the aggregation. The CP/MAS (13)C spectra was affected by the presence of urea at high concentrations, most notably the signal at 83.4 ppm, which has previously been assigned to C4 atoms in cellulose chains located at surfaces parallel to the (110) crystallographic plane of the cellulose I beta crystal. Also dynamic properties of the cellulose surfaces, probed by spin-lattice relaxation time (13)CT (1) measurements of C4 atoms, are affected by the addition of urea. Molecular Dynamics simulations reproduce the trends of the T (1) measurements and lends new support to the assignment of signals from individual surfaces. That urea in solution is interacting directly with cellulose may have implications on our understanding of the mechanisms behind cellulose dissolution in alkali/urea aqueous solutions.
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