Molecular dynamics approach to study the discrepancies in the thermal behavior of amylose and chitosan conformations

Sakajiri, Tetsuya; Kikuchi, Takeshi; Simon, István; Uchida, K.; Yamamura, Takehira; Ishii, Tadahiro; Yajima, Hirofumi

doi:10.1016/j.theochem.2006.02.016

Cited by 20 publications

(19 citation statements)

References 32 publications

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“…This transition to a linear‐like migration time increment per ΔGU is indicated by the excellent least‐squares fit from GU 9 throughout 29 ( r 2 = 0.9995). Such distinctive electromigration behavior of maltooligosaccharides was originated from their tendency to form a full helical turn upon reaching DP 6 . Due to the fluorescent labeling reaction via reductive amination, the glucose at the reducing termini was present in its open form and consequently influenced the unit numbers required to close the first helical turn.…”

Section: Resultsmentioning

confidence: 99%

Influence of molecular configuration and conformation on the electromigration of oligosaccharides in narrow bore capillaries

Mittermayr¹,

Guttman²

2012

Electrophoresis

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Capillary electrophoresis enables fast, high efficiency separations of oligosaccharides, wherein positional and/or linkage isomers, bearing the same charge-to-mass ratio, can readily be separated based on hydrodynamic radius differences. Fundamental electrophoretic mobility theory was used to investigate the correlation between changes in hydrodynamic volume equivalent radius and corresponding electrophoretic characteristics of oligosaccharides with different molecular properties. Fluorescently derivatized isomeric malto-, cello-, and isomaltooligosaccharide ladders, differing only in their linkage type of α1→4, β1→4, and α1→6, respectively, as well as a sterically larger N-acetylchitooligosaccharide ladder were used as model compounds. Mere differences in glycosidic linkage type or anomericity of isomeric oligo-glucoses had a decisive impact on their electromigration behavior, thus reflecting discrepancies in hydrodynamic radii and associated molecular conformations. The impact of hydrogen bridges, and associated availability of hydroxyl groups, on the molecular conformations, was investigated by hydrophilic interaction liquid chromatography. The experimentally observed electrophoretic and chromatographic differences between isomeric oligo-glucoses strongly suggested that special attention must be given when homooligosaccharide ladders are employed for normalization and comparability purposes, for example, in glucose unit calculation based structural elucidation.

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Section: Resultsmentioning

confidence: 99%

Influence of molecular configuration and conformation on the electromigration of oligosaccharides in narrow bore capillaries

Mittermayr¹,

Guttman²

2012

Electrophoresis

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“…As a consequence, small parts of starch structure, including representative regions that are relevant to certain processes and products, have been utilized to develop MD simulation that provides a reasonable agreement with experimental data. These simulations have provided qualitative and quantitative information on structures and mechanisms involved in the thermal behavior of starch, and the interaction of starch molecules such as amylose with other molecules, such as proteins and lipids, for their self-assembling in nanoparticles (Bhopatkar et al, 2015;Cheng et al, 2018;López, de Vries, & Marrink, 2012;Rodríguez et al, 2011;Sakajiri et al, 2006;Shimada, Kaneko, Takada, Kitamura, & Kajiwara, 2000). Recently, the mechanism for amino acids (Gly, Glu, and Lys) delaying the pasting and short-term retrogradation of rice starch was evaluated by MD simulation (Wan et al, 2017).…”

Section: Simulation Proceduresmentioning

confidence: 99%

“…Thermal effects on food enzymes such as pectin methylesterase and amylase have been studied by MD simulations (Liu & Wang, 2003;Nistor, Stanciuc, Aprodu, & Botez, 2014;Sakajiri et al, 2006). Simulations have shown that the exposure of hydrophobic core and the transition from an ordered to a disordered state are the common phenomena during the thermal denaturation of these proteins.…”

Section: Influences Of Processing Conditions (Pressure and Temperaturmentioning

confidence: 99%

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Chen

Huang

Miao

et al. 2018

Comp Rev Food Sci Food Safe

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Molecular dynamics (MD) simulation is a useful technique to study the interaction between molecules and how they are affected by various processes and processing conditions. This review summarizes the application of MD simulations in food processing and safety, with an emphasis on the effects that emerging nonthermal technologies (for example, high hydrostatic pressure, pulsed electric field) have on the molecular and structural characteristics of foods and biomaterials. The advances and potential projection of MD simulations in the science and engineering aspects of food materials are discussed and focused on research work conducted to study the effects of emerging technologies on food components. It is expected by showing key case studies that it will stir novel developments as a valuable tool to study the effects of emerging food technologies on biomaterials. This review is useful to food researchers and the food industry, as well as researchers and practitioners working on flavor and nutraceutical encapsulations, dietary carbohydrate product developments, modified starches, protein engineering, and other novel food applications.

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“…In our study, helicity was associated to the dihedral angle that better represented a biunivocal correspondence of this “turning angle” with a few, relevant, helical structures. This was achieved by constructing decamers with perfect 2 1 , 3 2 , and 4 1 helical geometries, using the glycosidic (φ, ψ) angles proposed by X‐ray crystallographic and MD studies . It was determined, by inspection, that the dihedral angle η i (defined by atoms C2‐O5‐O5'‐C2') permitted a one‐to‐one determination of these helical structures.…”

Section: Resultsmentioning

confidence: 99%

“…They also find a separated and much shallower potential well (D), which develops for positive values of the both glycosidic angles (using the glycosidic angle convention described below in Section ). More recently, the molecular dynamics (MD) simulations of Sakajiri et al for β‐chitobiose at very low temperature (250K) develop only in region A, while at very high temperature (450K), the simulation also visits another potential well, about 4 kcal/mol higher than A. In contrast the related work by Skovstrup et al on di, tri, and tetramers of different GlcNAc and GlcNH 2 building blocks show that their MD simulations only visit points corresponding to the main basin of Braccini et al The same preference is found by the exhaustive work of Peric et al on the conformational properties of glucuronan octamers and nonamers, whose simulations started from glycosidic angles corresponding to perfect 2 1 and 3 2 helical conformations.…”

Section: Introductionmentioning

confidence: 96%

Dissecting the conformational determinants of chitosan and chitlac oligomers

et al. 2018

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Chitosan and its highly hydrophilic 1-deoxy-lactit-1-yl derivative (Chitlac) are polysaccharides with increasing biomedical applications. Aimed to unravel their conformational properties we have performed a series of molecular dynamics simulations of Chitosan/Chitlac decamers, exploring different degrees of substitution (DS) of lactitol side chains. At low DS, two conformational regions with different populations are visited, while for DS ≥ 20% the oligomers remain mostly linear and only one main region of the glycosidic angles is sampled. These conformers are (locally) characterized by extended helical "propensities". Helical conformations 3 and 2 by far the most abundant, only develop in the main region. The accessible conformational space is clearly enlarged at high ionic strength, evidencing also a new region accessible to the glycosidic angles, with short and frequent interchange between regions. Simulations of neutral decamers share these features, pointing to a central role of electrostatic repulsion between charged moieties. These interactions seem to determine the conformational behavior of the chitosan backbone, with no evident influence of H-bond interactions. Finally, it is also shown that increasing temperature only slightly enlarges the available conformational space, but certainly without signs of a temperature-induced conformational transition.

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Molecular dynamics approach to study the discrepancies in the thermal behavior of amylose and chitosan conformations

Cited by 20 publications

References 32 publications

Influence of molecular configuration and conformation on the electromigration of oligosaccharides in narrow bore capillaries

Influence of molecular configuration and conformation on the electromigration of oligosaccharides in narrow bore capillaries

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Dissecting the conformational determinants of chitosan and chitlac oligomers

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