Conformation and physical properties of cycloisomaltooligosaccharides in aqueous solution

Suzuki, Shiho; Yukiyama, Takashi; Ishikawa, Arata; Yuguchi, Yoshiaki; Funane, Kazumi; Kitamura, Shinichi

doi:10.1016/j.carbpol.2013.07.089

Cited by 17 publications

(4 citation statements)

References 19 publications

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“…The experimental SAXS profile was compared to theoretical flexible Gaussian ring and rigid ring models. MD simulation was performed to find a ring model that better fit the SAXS data ( 106 ). The combination of MD and SAXS to determine a ring model fit demonstrates how simulation and experimental data may be incorporated in an effective manner.…”

Section: Saxs-md Applicationsmentioning

confidence: 99%

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

2015

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In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

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Section: Saxs-md Applicationsmentioning

confidence: 99%

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

2015

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“…Isomaltohexaose (IG-6), isomaltoheptaose (IG-7), and isomaltooctaose (IG-8) were produced from Fujioligo G67 (maltohexaose-and maltoheptaose-rich maltooligosaccharides, Nihon Shokuhin Kako Co Ltd., Tokyo, Japan) by Acetobacter capsulatum ATCC 11894 dextrin dextranase (23) and purified by gel permeation chromatography using a Toyopearl HW-40S column (5 ϫ 62 cm, Tosoh Corp., Tokyo, Japan) (22).…”

Section: Methodsmentioning

confidence: 99%

“…Sugar Ligands-CI-8 was produced from dextran 40 (GE Healthcare) by BcCITase (10) and purified to homogeneity by reversed-phase chromatography using an ODS column (Daisopak SP-120-5-ODS-BP, 20 ϫ 250 mm, Daiso, Osaka, Japan) as described previously (22). Isomaltohexaose (IG-6), isomaltoheptaose (IG-7), and isomaltooctaose (IG-8) were produced from Fujioligo G67 (maltohexaose-and maltoheptaose-rich maltooligosaccharides, Nihon Shokuhin Kako Co Ltd., Tokyo, Japan) by Acetobacter capsulatum ATCC 11894 dextrin dextranase (23) and purified by gel permeation chromatography using a Toyopearl HW-40S column (5 ϫ 62 cm, Tosoh Corp., Tokyo, Japan) (22).…”

Section: Methodsmentioning

confidence: 99%

Structural Elucidation of the Cyclization Mechanism of α-1,6-Glucan by Bacillus circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase

Suzuki

Fujimoto

Kim

et al. 2014

Journal of Biological Chemistry

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Background: Cycloisomaltooligosaccharide glucanotransferase catalyzes an intramolecular transglucosylation reaction and produces cycloisomaltooligosaccharides from dextran. Results: The crystal structure of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase was determined. Conclusion:The enzyme structures complexed with isomaltooligosaccharides and cycloisomaltooctaose revealed the molecular mechanism of action. Significance: CBM35 functions in the product size determination and substrate recruitment.

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“…ADMPC also behaves as a semiflexible or rigid polymer in 4-methyl-2-pentanone (MIBK) for which λ –1 is nearly equal to 75 nm and equivalent to that for ATBC in THF because of the hydrogen bonding between ADMPC and MIBK molecules, as mentioned above, although the stiffness of ATBC in THF is mainly due to the intramolecular hydrogen bonding. Solution properties of cyclic polymers having high chain stiffness have not been reported except for some comb-shaped ring polymers , and cyclic DNA , though conformational properties for flexible cyclic polymers are widely investigated including cyclic polysaccharides, − poly(dimethylsiloxane), and polystyrene; − note that cyclic DNA is not a good example of the rigid cyclic chains because of the supercoiling behavior. Furthermore, if we consider that the difference in the origin of the high stiffness between ADMPC and ATBC, it is necessary from a fundamental point of view to make a detailed comparison of the dilute solution behavior between ADMPC and its cyclic analogue (cADMPC).…”

Section: Introductionmentioning

confidence: 99%

Topology-Dependent Chain Stiffness and Local Helical Structure of Cyclic Amylose Tris(3,5-dimethylphenylcarbamate) in Solution

et al. 2017

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Conformational properties of rigid and semiflexible cyclic chains are still unclear owing to few experimental researches on dilute solution properties. Five cyclic amylose tris(3,5dimethylphenylcarbamate) (cADMPC) samples ranging in the weight-average degree of polymerization from 23 to 150 were prepared from enzymatically synthesized cyclic amylose. Light scattering and small-angle X-ray scattering measurements were made on the samples to determine the weight-average molar mass Mw, the particle scattering function P(q), and the zaverage mean-square radius of gyration S 2 z in methyl acetate (MEA), 4-methyl-2-pentanone (MIBK), and tetrahydrofuran (THF) at 25 C. The obtained P(q) and S 2 z data were analyzed on the basis of the cyclic wormlike chain model to determine the wormlike chain parameters, that is, the helix pitch (or helix rise) per residue h and the Kuhn segment length  −1 (the stiffness parameter or twice of the persistence length) as a function of Mw. Although the chain stiffness parameter  −1 for the corresponding linear polymer was reported to be 22 nm and 73 nm in MEA and MIBK, respectively, those for cADMPC in the three solvents were determined to be about 20 nm, this value being still significantly larger than that for cyclic amylose in aqueous sodium hydroxide. On the other hand, the former parameter h is somewhat larger than those for the linear ADMPC. The extended main chain of cADMPC by the topological constraint does not retain the chain stiffness as high as the corresponding linear chain. This phenomenon only becomes significant when the corresponding linear polymer behaves as a stiff chain with a small value of the Kuhn segment number NK. The threshold value of NK to achieve the significant difference in NK between the linear and cyclic chains is about less than 1.0 -1.5 at which the probability to link the both ends (ring closure probability) of the linear wormlike chain significantly decreases with decreasing NK.

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Conformation and physical properties of cycloisomaltooligosaccharides in aqueous solution

Cited by 17 publications

References 19 publications

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

Structural Elucidation of the Cyclization Mechanism of α-1,6-Glucan by Bacillus circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase

Topology-Dependent Chain Stiffness and Local Helical Structure of Cyclic Amylose Tris(3,5-dimethylphenylcarbamate) in Solution

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