Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study

Yu, Haibo; Amann, Manfred; Hansson, Tomas; Köhler, Jutta; Wich, Günter; Gunsteren, Wilfred F. van

doi:10.1016/j.carres.2004.05.003

Cited by 43 publications

(37 citation statements)

References 48 publications

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“…On average, RMSD values of the hightemperature simulations of Top7 CB1 and Top7 CB1a diverge from the There is also a systematic increase in the radius of gyration (R g ) for all systems relative to initial X-ray structure ( Table 2) with Top7 in solution adopting a less compact conformation than in the crystalline environment. The increase of the R g of proteins in liquid phase compared to the corresponding crystalline phase has been widely reported in simulations of biomolecules [5,6,21,24,87,89]. Lines represent the smoothed average of three spectra from which a buffer background has been subtracted.…”

Section: Resultsmentioning

confidence: 98%

Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions

Soares¹,

Boschek²,

Apiyo³

et al. 2010

Journal of Molecular Graphics and Modelling

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Section: Resultsmentioning

confidence: 98%

Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions

Soares¹,

Boschek²,

Apiyo³

et al. 2010

Journal of Molecular Graphics and Modelling

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“…For trehalose: from X-ray crystallography (I: trehalose dihydrate; 91,92 II: anhydrous trehalose 93 ) and three independent NMR experiments (I, 94 II, 95 Note, finally, that two studies relying on of the present 45A4 carbohydrate force field have been reported. 87,88 In the first article, an early version of the force field was used to investigate the influence of methylation at specific hydroxyl groups on the stability of amylose and cellulose fragments. 87 In the second article, the parameters for trehalose were used to investigate the effect of this disaccharide on the stability of dipalmitoyl-phosphatidyl-choline lipid bilayer at elevated temperature.…”

Section: Resultsmentioning

confidence: 99%

“…87,88 In the first article, an early version of the force field was used to investigate the influence of methylation at specific hydroxyl groups on the stability of amylose and cellulose fragments. 87 In the second article, the parameters for trehalose were used to investigate the effect of this disaccharide on the stability of dipalmitoyl-phosphatidyl-choline lipid bilayer at elevated temperature. 88 …”

Section: Resultsmentioning

confidence: 99%

A new GROMOS force field for hexopyranose‐based carbohydrates

2005

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A new parameter set (referred to as 45A4) is developed for the explicit-solvent simulation of hexopyranose-based carbohydrates. This set is compatible with the most recent version of the GROMOS force field for proteins, nucleic acids, and lipids, and the SPC water model. The parametrization procedure relies on: (1) reassigning the atomic partial charges based on a fit to the quantum-mechanical electrostatic potential around a trisaccharide; (2) refining the torsional potential parameters associated with the rotations of the hydroxymethyl, hydroxyl, and anomeric alkoxy groups by fitting to corresponding quantum-mechanical profiles for hexopyranosides; (3) adapting the torsional potential parameters determining the ring conformation so as to stabilize the (experimentally predominant) (4)C(1) chair conformation. The other (van der Waals and nontorsional covalent) parameters and the rules for third and excluded neighbors are taken directly from the most recent version of the GROMOS force field (except for one additional exclusion). The new set is general enough to define parameters for any (unbranched) hexopyranose-based mono-, di-, oligo- or polysaccharide. In the present article, this force field is validated for a limited set of monosaccharides (alpha- and beta-D-glucose, alpha- and beta-D-galactose) and disaccharides (trehalose, maltose, and cellobiose) in solution, by comparing the results of simulations to available experimental data. More extensive validation will be the scope of a forthcoming article. (c) 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1400-1412, 2005.

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“…11,[20][21][22] However, previous MD studies of amylose have mainly dealt with small amylose fragments in water or studies of V-amylose in low polarity solvents. [23][24][25] The object of the present study was to deepen the understanding of the structure and formation of V-amylose inclusion complexes in view of its anticipated use as a delivery system of long chain fatty acids and other nutraceuticals. To that aim, we consider a short amylose fragment, and simulate its structure and dynamics in the presence of either dipalmitoyl-phosphatidylcholine (diC 16 -PC) or glycerol monooleate (GMO) in aqueous solution.…”

Section: Introductionmentioning

confidence: 99%

Amylose folding under the influence of lipids

López

Vries

Marrink

2012

Carbohydrate Research

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a b s t r a c tThe molecular dynamics simulation technique was used to study the folding and complexation process of a short amylose fragment in the presence of lipids. In aqueous solution, the amylose chain remains as an extended left-handed helix. After the addition of lipids in the system, however, we observe spontaneous folding of the amylose chain into a helical structure, with helical pitch and hydrogen bond network compatible with the V-amylose structure observed in X-ray experiments. Our results suggest that under the influence of external non polar ligands, the conformation of amylose undergoes a transition from an extended to a V-amylose structure in line with experimental evidence.

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Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study

Cited by 43 publications

References 48 publications

Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions

Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions

A new GROMOS force field for hexopyranose‐based carbohydrates

Amylose folding under the influence of lipids

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