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Lang W, Tagami T, Kumagai Y, Tanaka S, Kang HJ, Okuyama M, Saburi W, Mori H, Hira T, Lee C, Isono T, Satoh T, Hara H, Kurokawa T, Sakairi N, Yuguchi Y, Kimura A. Tunable structure of chimeric isomaltomegalosaccharides with double α-(1 → 4)-glucosyl chains enhances the solubility of water-insoluble bioactive compounds. Carbohydr Polym 2023; 319:121185. [PMID: 37567719 DOI: 10.1016/j.carbpol.2023.121185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/24/2023] [Accepted: 07/07/2023] [Indexed: 08/13/2023]
Abstract
Isomaltomegalosaccharides with α-(1 → 4) and α-(1 → 6)-segments solubilize water-insoluble ligands since the former complexes with the ligand and the latter solubilizes the complex. Previously, we enzymatically synthesized isomaltomegalosaccharide with a single α-(1 → 4)-segment at the reducing end (S-IMS) by dextran dextrinase (DDase), but the chain length [average degree of polymerization (DP) ≤ 9] was insufficient for strong encapsulation. We hypothesized that the conjugation of longer α-(1 → 4)-segment afforded the promising function although DDase is incapable to do so. In this study, the cyclodextrin glucanotransferase-catalyzed coupling reaction of α-cyclodextrin to S-IMS synthesized a new α-(1 → 4)-segment at the nonreducing end (N-4S) of S-IMS to form D-IMS [IMS harboring double α-(1 → 4)-segments]. The length of N-4S was modulated by the ratio between α-cyclodextrin and S-IMS, generating N-4Ss with DPs of 7-50. Based on phase-solubility analysis, D-IMS-28.3/13/3 bearing amylose-like helical N-4S with DP of 28.3 displayed a water-soluble complex with aromatic drugs and curcumin. Small-angle X-ray scattering revealed the chain adapted to rigid in solution in which the radius of gyration was estimated to 2.4 nm. Furthermore, D-IMS with short N-4S solubilized flavonoids of less-soluble multifunctional substances. In our research, enzyme-generated functional biomaterials from DDase were developed to maximize the hydrophobic binding efficacy towards water-insoluble bioactive compounds.
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Affiliation(s)
- Weeranuch Lang
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan.
| | - Takayoshi Tagami
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yuya Kumagai
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Japan
| | - Seiya Tanaka
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hye-Jin Kang
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Tohru Hira
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Chaehun Lee
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Takuya Isono
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Toshifumi Satoh
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Hiroshi Hara
- Department of Food Science and Human Nutrition, Fuji Women's University, Ishikari 061-3204, Japan
| | - Takayuki Kurokawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nobuo Sakairi
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yoshiaki Yuguchi
- Faculty of Engineering, Osaka Electro-Communication University, Osaka 572-8530, Japan
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
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Imamura W, Yamasaki T, Kato H, Ishikawa T. Insights into the molecular interaction of cyclodextran with a guest molecule: A computational study. Carbohydr Polym 2022; 301:120315. [DOI: 10.1016/j.carbpol.2022.120315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
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Liu JY, Hou XX, Li ZY, Shan SH, Chang MC, Feng CP, Wei Y. Isolation and structural characterization of a novel polysaccharide from Hericium erinaceus fruiting bodies and its arrest of cell cycle at S-phage in colon cancer cells. Int J Biol Macromol 2020; 157:288-295. [DOI: 10.1016/j.ijbiomac.2020.04.162] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/09/2020] [Accepted: 04/20/2020] [Indexed: 12/30/2022]
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4
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Isomalto-oligosaccharides: Recent insights in production technology and their use for food and medical applications. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.04.098] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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Ryoki A, Yokobatake H, Hasegawa H, Takenaka A, Ida D, Kitamura S, Terao K. Topology-Dependent Chain Stiffness and Local Helical Structure of Cyclic Amylose Tris(3,5-dimethylphenylcarbamate) in Solution. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b00706] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Akiyuki Ryoki
- Department
of Macromolecular Science, Graduate School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Hiromi Yokobatake
- Department
of Macromolecular Science, Graduate School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Hirokazu Hasegawa
- Department
of Macromolecular Science, Graduate School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Materials
Characterization Laboratories, Toray Research Center, Inc., 3-3-7, Sonoyama, Otsu, Shiga 520-8567, Japan
| | - Aya Takenaka
- Materials
Characterization Laboratories, Toray Research Center, Inc., 3-3-7, Sonoyama, Otsu, Shiga 520-8567, Japan
| | - Daichi Ida
- Department
of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
| | - Shinichi Kitamura
- Graduate
School of Life and Environmental Sciences, Osaka Prefecture University, Gakuen-cho,
Nakaku, Sakai 599-8531, Japan
| | - Ken Terao
- Department
of Macromolecular Science, Graduate School of Science, Osaka University, 1-1
Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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Scattering function of semi-rigid cyclic polymers analyzed in terms of worm-like rings: cyclic amylose tris(phenylcarbamate) and cyclic amylose tris(n-butylcarbamate). Polym J 2017. [DOI: 10.1038/pj.2017.27] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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8
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Zhang Z, Wang L, Xuan X. The CN⋯C–X σ-hole interaction acts as a conformational lock. NEW J CHEM 2017. [DOI: 10.1039/c6nj02622b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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9
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Yuguchi Y, Hasegawa A, Padoł AM, Draget KI, Stokke BT. Local structure of Ca(2+) induced hydrogels of alginate-oligoguluronate blends determined by small-angle-X-ray scattering. Carbohydr Polym 2016; 152:532-540. [PMID: 27516301 DOI: 10.1016/j.carbpol.2016.07.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/28/2016] [Accepted: 07/05/2016] [Indexed: 10/21/2022]
Abstract
Short oligoguluronates, oligoG's, are reported to affect the ionotropic gelation of alginates both with respect to altered gelation kinetics and elastic properties of the resulting gels. The local structure of Ca(2+) induced changes in oligoguluronates and blends of oligoguluronates and alginates was determined by small angle X-ray scattering (SAXS). Calcium was introduced in the aqueous polysaccharide solutions by in situ release of Ca(2+) from Ca-EGTA. The scattering profiles of the Ca(2+)-induced structures in the alginate-oligoG blends were accounted for by a two-component broken rod-like model, also with an additional term representing structural inhomogeneity by a Debye-Bueche term. Adding oligoG to the alginate yields an increase in the largest cross-sectional radius in the region of fractional Ca(2+) saturation of α-l-GulA units from 0.5 to 1. The time-lapse characterization during the Ca-induced changes in the alginate-oligoG blends shows that oligoG delays the emergence of the more extensive laterally aggregated junction zones.
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Affiliation(s)
- Yoshiaki Yuguchi
- Department of Environmental Science, Faculty of Engineering, Osaka Electro-Communication University, 18-8, Hatsu-cho, Neyagawa, Osaka 572-8530, Japan
| | - Ami Hasegawa
- Department of Environmental Science, Faculty of Engineering, Osaka Electro-Communication University, 18-8, Hatsu-cho, Neyagawa, Osaka 572-8530, Japan
| | - Anna Maria Padoł
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway
| | - Kurt Ingar Draget
- Department of Biotechnology, The Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway
| | - Bjørn Torger Stokke
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway.
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Boldon L, Laliberte F, Liu L. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application. NANO REVIEWS 2015; 6:25661. [PMID: 25721341 PMCID: PMC4342503 DOI: 10.3402/nano.v6.25661] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 11/24/2014] [Accepted: 01/18/2015] [Indexed: 12/16/2022]
Abstract
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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Affiliation(s)
- Lauren Boldon
- Department of Mechanical Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA;
| | - Fallon Laliberte
- Department of Mechanical Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Li Liu
- Department of Mechanical Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA;
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Brovarets’ OO, Yurenko YP, Hovorun DM. The significant role of the intermolecular CH⋯O/N hydrogen bonds in governing the biologically important pairs of the DNA and RNA modified bases: a comprehensive theoretical investigation. J Biomol Struct Dyn 2014; 33:1624-52. [DOI: 10.1080/07391102.2014.968623] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Vibhute AM, Sureshan KM. Strength from Weakness: Conformational Divergence between Solid and Solution States of Substituted Cyclitols Facilitated by CH···O Hydrogen Bonding. J Org Chem 2014; 79:4892-908. [DOI: 10.1021/jo5004778] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amol M. Vibhute
- School
of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Thiruvananthapuram, Kerala 695016, India
| | - Kana M. Sureshan
- School
of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Thiruvananthapuram, Kerala 695016, India
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13
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Suzuki N, Fujimoto Z, Kim YM, Momma M, Kishine N, Suzuki R, Suzuki S, Kitamura S, Kobayashi M, Kimura A, Funane K. Structural elucidation of the cyclization mechanism of α-1,6-glucan by Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase. J Biol Chem 2014; 289:12040-12051. [PMID: 24616103 DOI: 10.1074/jbc.m114.547992] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase belongs to the glycoside hydrolase family 66 and catalyzes an intramolecular transglucosylation reaction that produces cycloisomaltooligosaccharides from dextran. The crystal structure of the core fragment from Ser-39 to Met-738 of B. circulans T-3040 cycloisomaltooligosaccharide glucanotransferase, devoid of its N-terminal signal peptide and C-terminal nonconserved regions, was determined. The structural model contained one catalytic (β/α)8-barrel domain and three β-domains. Domain N with an immunoglobulin-like β-sandwich fold was attached to the N terminus; domain C with a Greek key β-sandwich fold was located at the C terminus, and a carbohydrate-binding module family 35 (CBM35) β-jellyroll domain B was inserted between the 7th β-strand and the 7th α-helix of the catalytic domain A. The structures of the inactive catalytic nucleophile mutant enzyme complexed with isomaltohexaose, isomaltoheptaose, isomaltooctaose, and cycloisomaltooctaose revealed that the ligands bound in the catalytic cleft and the sugar-binding site of CBM35. Of these, isomaltooctaose bound in the catalytic site extended to the second sugar-binding site of CBM35, which acted as subsite -8, representing the enzyme·substrate complex when the enzyme produces cycloisomaltooctaose. The isomaltoheptaose and cycloisomaltooctaose bound in the catalytic cleft with a circular structure around Met-310, representing the enzyme·product complex. These structures collectively indicated that CBM35 functions in determining the size of the product, causing the predominant production of cycloisomaltooctaose by the enzyme. The canonical sugar-binding site of CBM35 bound the mid-part of isomaltooligosaccharides, indicating that the original function involved substrate binding required for efficient catalysis.
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Affiliation(s)
- Nobuhiro Suzuki
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602
| | - Zui Fujimoto
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602.
| | - Young-Min Kim
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602; Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589
| | - Mitsuru Momma
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602
| | - Naomi Kishine
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602
| | - Ryuichiro Suzuki
- Applied Microbiology Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642
| | - Shiho Suzuki
- College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Sakai 599-8531
| | - Shinichi Kitamura
- College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Sakai 599-8531
| | - Mikihiko Kobayashi
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602; Applied Microbiology Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642; Department of Food and Health Science, Jissen Women's University, Hino 191-8510, Japan
| | - Atsuo Kimura
- Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589
| | - Kazumi Funane
- Applied Microbiology Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642.
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