Sucrose in aqueous solution revisited, Part 1: Molecular dynamics simulations and direct and indirect dipolar coupling analysis

Xia, Junchao; Case, David A.

doi:10.1002/bip.22017

Cited by 29 publications

(37 citation statements)

References 66 publications

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“…The glycoscidic angles are similar to those observed in the sucrose crystal structure (108, −55) [37], and structures near this state are predicted to be highly populated in solution [21, 27]. Distances between 2 and 3 Å are also consistent with this glycosidic linkage orientation, but with an ω angle of approximately 180°, or with a second highly populated conformer predicted in previous MD studies with ϕ, ψ, and ω angles near 70, −75, and 180° [28]. Except for very occasional sampling of a much longer distance, transitions between the major states are frequent (occurring on a timescale of a ns).…”

Section: Resultsmentioning

confidence: 53%

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Direct NOE simulation from long MD trajectories

Chalmers

Glushka

Foley

et al. 2016

Journal of Magnetic Resonance

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A software package, MD2NOE, is presented which calculates nuclear Overhauser effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected.

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Section: Resultsmentioning

confidence: 53%

“…Sucrose (β-D-fructofuranosyl-(2-1)-α-D-glucopyranoside) is a disaccharide that exhibits a range of internal motions, both slow and fast compared to its overall tumbling time; sucrose has become a standard for testing the validity of MD simulations, as well as analyzing NMR spin relaxation measurements [25–28]. …”

Section: Introductionmentioning

confidence: 99%

Direct NOE simulation from long MD trajectories

Chalmers

Glushka

Foley

et al. 2016

Journal of Magnetic Resonance

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“…Recent developed GLY-CAM06 [162], CHARMM36 [163], GROMOS 53A6 GLYC [164], and OPLS-AA-SEI (scaling electrostatic interaction) [165] force fields are well defined for the conformational prediction of carbohydrates. Nowadays, modern carbohydrate force fields allowed to predicted the most important set of parameters of the structure of carbohydrates.…”

Section: Force Fieldsmentioning

confidence: 99%

Recent Advances in NMR Studies of Carbohydrates

Buda¹,

Nawój²,

Młynarski³

2016

Annual Reports on NMR Spectroscopy

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“…190 One of the distinct features of the oligosaccharides is their flexibility, which is important to their function. 182,191,192 Mass spectrometry is widely used to study the oligosaccharides conformers, 184,[193][194][195][196] including Ion Mobility Spectrometry. [197][198][199][200] The question of the extent to which the flexible ion retains the solution phase conformation is still under debates.…”

Section: In-esi Source H/d Exchange Of Saccharidesmentioning

confidence: 99%

Hydrogen/deuterium exchange in mass spectrometry

Kostyukevich

Acter

Zherebker

et al. 2018

Mass Spectrometry Reviews

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The isotopic exchange approach is in use since the first observation of such reactions in 1933 by Lewis. This approach allows the investigation of the pathways of chemical and biochemical reactions, determination of structure, composition, and conformation of molecules. Mass spectrometry has now become one of the most important analytical tools for the monitoring of the isotopic exchange reactions. Investigation of conformational dynamics of proteins, quantitative measurements, obtaining chemical, and structural information about individual compounds of the complex natural mixtures are mainly based on the use of isotope exchange in combination with high resolution mass spectrometry. The most important reaction is the Hydrogen/Deuterium exchange, which is mainly performed in the solution. Recently we have developed the approach allowing performing of the Hydrogen/Deuterium reaction on-line directly in the ionization source under atmospheric pressure. Such approach simplifies the sample preparation and can accelerate the exchange reaction so that certain hydrogens that are considered as non-labile will also participate in the exchange. The use of in-ionization source H/D exchange in modern mass spectrometry for structural elucidation of molecules serves as the basic theme in this review. We will focus on the mechanisms of the isotopic exchange reactions and on the application of in-ESI, in-APCI, and in-APPI source Hydrogen/Deuterium exchange for the investigation of petroleum, natural organic matter, oligosaccharides, and proteins including protein-protein complexes. The simple scenario for adaptation of H/D exchange reactions into mass spectrometric method is also highlighted along with a couple of examples collected from previous studies.

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Sucrose in aqueous solution revisited, Part 1: Molecular dynamics simulations and direct and indirect dipolar coupling analysis

Cited by 29 publications

References 66 publications

Direct NOE simulation from long MD trajectories

Direct NOE simulation from long MD trajectories

Recent Advances in NMR Studies of Carbohydrates

Hydrogen/deuterium exchange in mass spectrometry

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