NMR and modelling studies of disaccharide conformation

Cheetham, Norman W.H.; Dasgupta, Paramita; Ball, Graham E.

doi:10.1016/s0008-6215(03)00069-7

Cited by 74 publications

(75 citation statements)

References 38 publications

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“…The speed of production of the maps was enhanced by approximately tenfold over that using the full DFT, by the use of a reduced basis set on the carbon atoms in conjunction with the B3LYP functional (B3LYP/4-31G), while maintaining the B3LYP/6-31?G* functional for all other atoms, thus preserving the hydrogen bonding abilities of the higher level DFT calculations. The production of these maps enhances our abilities in making more specific comparisons to experimental results Sivchik and Zhbankov 1977;Andrianov et al 1980; Hamer et al 1978;Horii et al 1982Horii et al , 1983Korolik et al 1985;Tvaroska and Taravel 1992;Duus et al 1994;Sugiyama et al 2000;Suzuki et al 2009;Cheetham et al 2003;Larsson et al 2004;Olsson et al 2008;Cocinero et al 2009;Asensio and Jimenez-Barbero 1995; Chu and Jeffrey 1968) as will be described later. Examination of previous DFT optimization studies on cellobiose (Strati et al 2002a, b;Bosma et al 2006a, b) showed that different rotamers of the hydroxymethyl groups influenced the conformational low energy regions at the glycosidic bonds.…”

Section: Introductionmentioning

confidence: 93%

“…In our previous cellobiose studies (Strati et al 2002a, b;Bosma et al 2006a, b), there was some question as to the lowest energy rotamer conformations and solvent dependence. Resolving the 'r' and 'c' question is of interest to us, but the observation that the / H -anti form was found to be the lowest energy conformation (Strati et al 2002a) is contrary to experimental solution studies that indicated that the syn conformer is preferred (Hardy and Sarko 1993a, b;Wacowich-Sgarbi et al 2001;Sivchik and Zhbankov 1977;Andrianov et al 1980;Hamer et al 1978;Horii et al 1982Horii et al , 1983Korolik et al 1985;Tvaroska and Taravel 1992;Duus et al 1994;Sugiyama et al 2000;Cheetham et al 2003;Larsson et al 2004;Olsson et al 2008;Cocinero et al 2009), and this must be resolved. Upon addition of explicit water molecules the syn conformation water complex does become of lower relative energy than the / H -anti-form (Bosma et al 2006a, b) water complex, while application of COSMO during optimization did not show a complete shift to the syn form.…”

Section: Introductionmentioning

confidence: 96%

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Rapidly calculated DFT relaxed iso-potential ϕ/ψ maps: β-cellobiose

Schnupf

Momany

2011

Cellulose

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New cellobiose / H /w H maps are generated using a mixed basis set DFTr method, found to achieve a high level of confidence while reducing computer resources dramatically. Relaxed iso-potential maps are created for different conformational states of cellobiose, showing how glycosidic bond dihedral angles vary as different sets of hydroxymethyl rotamers and hydroxyl directions are examined. These maps are generated, fixing the dihedral / H and w H values at ten degree intervals and energy optimizing the remaining geometry using the B3LYP/6-31?G* functional for all atoms except carbon atoms, where the functional B3LYP was used with the mixed basis set, 4-31G. Mapping results are compared between in vacuo structures using the mixed basis set, in vacuo using the full basis set, and those in which the implicit solvent method, COSMO, is included with the mixed basis set. Results show significant changes in position of energy minima with variation in hydroxyl rotamers and with application of solvent. Unique to this study is the mapping of the hydration energy at each / H /w H point on the map using the energy derived at each point by applying COSMO. Using hydration gradients as a guide one observes directional solvent driven changes in the minimum energy positions. Interesting internal coordinate variances are described.

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Section: Introductionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 96%

Rapidly calculated DFT relaxed iso-potential ϕ/ψ maps: β-cellobiose

Schnupf

Momany

2011

Cellulose

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“…These intramolecular hydrogen bonds should directly affect the backbone torsion angles of glycosidic linkages. Actually, analyses of the torsion angles of these disaccharides using NMR and X-ray methods [6,29,32] revealed differences in the types of glycosidic linkages, such as φ and ϕ values of 96.8 and 105.2, respectively, for maltose, and −69.1 and −109.1 for laminaribiose in the crystal structures, where φ and ϕ are the dihedral angles of O 5 -C 1 -O 1 -C n ' and C 1 -O 1 -C n '-C n−1 ' (n = 3 or 4), respectively (see Fig. 1).…”

Section: Unique Torsion Angles Of Constituent Disaccharides Affect Vumentioning

confidence: 99%

Vacuum-ultraviolet circular dichroism study of oligosaccharides using a synchrotron-radiation spectrophotometer

Matsuo

2017

BSI

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Abstract. Vacuum-ultraviolet circular dichroism (VUVCD) spectra of malto-, laminari-, isomalto-, and cello-oligosaccharide series and their corresponding polysaccharides (laminarin and dextran) were measured from 200 to 168 nm in aqueous solution at 25°C using a synchrotron-radiation VUVCD spectrophotometer. Disaccharides exhibited markedly different CD spectra depending on the types of glycosidic linkages, and the CD spectra of each oligosaccharide series (with the exception of the isomalto-oligosaccharide series) varied with the chain length below 190 nm while retaining the spectral shape of the constituent disaccharide. These results indicate that the basic structures of oligosaccharides were greatly affected by the configurations of their constituent disaccharides, which had unique torsion angles restricted by the intramolecular hydrogen bonds between glucose units. Based on comparisons between the experimental and theoretical data, we suggest that the chain-length dependence of CD above 180 nm reflects the backbone structure of oligosaccharides (e.g., helical structures), while those below 180 nm are influenced by other factors associated with higher-energy chromophores such as the hydroxyl groups. The reported comprehensive VUVCD spectra provide basic information for understanding the complicated structures of oligosaccharides in aqueous solution that can be used in their theoretical assignments.

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“…The presence of left-handed helical stretches is consistent with experimental data. 42 Population around x was defined as tg = 180°, gg = 60°and gt = À60°.…”

Section: Gromos Force Field Adjustmentmentioning

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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NMR and modelling studies of disaccharide conformation

Cited by 74 publications

References 38 publications

Rapidly calculated DFT relaxed iso-potential ϕ/ψ maps: β-cellobiose

Rapidly calculated DFT relaxed iso-potential ϕ/ψ maps: β-cellobiose

Vacuum-ultraviolet circular dichroism study of oligosaccharides using a synchrotron-radiation spectrophotometer

Amylose folding under the influence of lipids

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