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Abstract
A startling array of added anions have been observed to function as replacement catalytic nucleophiles in mutant glycosidases, including formate, azide, fluoride and other halides. Likewise, the mechanism of acid-base catalysis is somewhat plastic. The carboxylic acids can be substituted by a sulfenic acid or by ascorbate, and the effective acid strength enhanced by the introduction of strong hydrogen bonds. These studies provide an interesting bridge between enzymes and models thereof.
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Affiliation(s)
- D L Zechel
- Protein Engineering Network of Centres of Excellence of Canada and Department of Chemistry, University of British Columbia, Vancouver, Canada
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102
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Affiliation(s)
- S Kobayashi
- Department of Materials Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan.
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103
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Kobayashi S, Morii H, Itoh R, Kimura S, Ohmae M. Enzymatic polymerization to artificial hyaluronan: a novel method to synthesize a glycosaminoglycan using a transition state analogue monomer. J Am Chem Soc 2001; 123:11825-6. [PMID: 11716751 DOI: 10.1021/ja017104+] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S Kobayashi
- Department of Materials Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan
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104
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105
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Sakamoto J, Watanabe T, Ariga Y, Kobayashi S. Ring-Opening Glycosylation of a Chitobiose Oxazoline Catalyzed by a Non-Chitinolytic Mutant of Chitinase. CHEM LETT 2001. [DOI: 10.1246/cl.2001.1180] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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106
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107
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Fujita M, Shoda S, Haneda K, Inazu T, Takegawa K, Yamamoto K. A novel disaccharide substrate having 1,2-oxazoline moiety for detection of transglycosylating activity of endoglycosidases. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1528:9-14. [PMID: 11514092 DOI: 10.1016/s0304-4165(01)00164-7] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A disaccharide substrate of Manbeta1-4GlcNAc-oxazoline 2 was designed and synthesized as a novel probe for detection of the transglycosylating activity of endoglycosidases. A regio- and stereoselective transglycosylation reaction of 2 to GlcNAcbeta1-O-pNP or Dns-Asn(GlcNAc)-OH catalyzed by endo-beta-N-acetylglucosaminidase from Mucor hiemalis (Endo-M) and endo-beta-N-acetylglucosaminidase from Arthrobacter protophormiae (Endo-A) has been demonstrated for the first time, resulting in the core trisaccharide derivative Manbeta1-4GlcNAcbeta1-4GlcNAcbeta1-O-pNP 8 (or -(Dns)Asn-OH). Interestingly, the transglycosylation proceeds irreversibly; the resulting trisaccharide 8 was not hydrolyzed by Endo-M and Endo-A. Based on these results, a new mechanism including an oxazolinium ion intermediate has been proposed for the endoglycosidase-catalyzed hydrolysis or transglycosylation.
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Affiliation(s)
- M Fujita
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
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108
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Kerry ME, Gregory AC, Bolwell GP. Differential behaviour of four plant polysaccharide synthases in the presence of organic solvents. PHYTOCHEMISTRY 2001; 57:1055-1060. [PMID: 11430978 DOI: 10.1016/s0031-9422(01)00126-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The behaviour of four membrane-bound glycosyl transferases involved in cell wall polysaccharide synthesis has been studied in relation to the effects of a graded series of organic solvents on their activity and type of product formed. Relative enzyme inhibition observed for some solvents was in direct relationship to the hydrophilicity of the product. This was in the order of arabinan synthase > callose synthase> xylan synthase > beta-1,4-glucan synthase. The former two were always inhibited, the xylan synthase rather less so. However, the beta-1,4-glucan synthase showed significant increases in substrate incorporation in the presence of solvents. A graded series of primary alcohols were much more effective in enhancing activity than acetone, ethyl acetate and dimethyl formamide. In the presence of the most effective solvent, methanol, there was considerable activation of beta-1,4-glucan production. This reciprocal nature of the behaviour of the beta-1,4- and beta-1,3-glucan synthases in organic solvent is supportive of recent molecular data that the two types of glucans are catalysed by separate enzyme systems. However, the results reported here do not totally negate the proposition that either enzyme is capable of synthesising the other linkage in minor amounts in vitro.
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Affiliation(s)
- M E Kerry
- Division of Biochemistry, School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
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109
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van Aalten DM, Komander D, Synstad B, Gåseidnes S, Peter MG, Eijsink VG. Structural insights into the catalytic mechanism of a family 18 exo-chitinase. Proc Natl Acad Sci U S A 2001; 98:8979-84. [PMID: 11481469 PMCID: PMC55359 DOI: 10.1073/pnas.151103798] [Citation(s) in RCA: 334] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chitinase B (ChiB) from Serratia marcescens is a family 18 exo-chitinase whose catalytic domain has a TIM-barrel fold with a tunnel-shaped active site. We have solved structures of three ChiB complexes that reveal details of substrate binding, substrate-assisted catalysis, and product displacement. The structure of an inactive ChiB mutant (E144Q) complexed with a pentameric substrate (binding in subsites -2 to +3) shows closure of the "roof" of the active site tunnel. It also shows that the sugar in the -1 position is distorted to a boat conformation, thus providing structural evidence in support of a previously proposed catalytic mechanism. The structures of the active enzyme complexed to allosamidin (an analogue of a proposed reaction intermediate) and of the active enzyme soaked with pentameric substrate show events after cleavage of the glycosidic bond. The latter structure shows reopening of the roof of the active site tunnel and enzyme-assisted product displacement in the +1 and +2 sites, allowing a water molecule to approach the reaction center. Catalysis is accompanied by correlated structural changes in the core of the TIM barrel that involve conserved polar residues whose functions were hitherto unknown. These changes simultaneously contribute to stabilization of the reaction intermediate and alternation of the pKa of the catalytic acid during the catalytic cycle.
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Affiliation(s)
- D M van Aalten
- Wellcome Trust Biocentre, Department of Biochemistry, University of Dundee, Dundee DD1 5EH, Scotland.
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110
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Fukase K, Yasukochi T, Kusumoto S. Chemoenzymatic Synthesis of a Trisaccharide–Serine Conjugate, Gal(β1-3)Gal(β1-4)Xyl(β1-O)–L-Ser, Use of Galactosyl Fluoride as a Donor for Transglycosylation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2001. [DOI: 10.1246/bcsj.74.1123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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111
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Kumar A, Garg K, Gross RA. Copolymerizations of ω-Pentadecalactone and Trimethylene Carbonate by Chemical and Lipase Catalysis. Macromolecules 2001. [DOI: 10.1021/ma0100246] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ajay Kumar
- NSF-IUCRC Center for Biocatalysis and Bioprocessing of Macromolecules, Polytechnic University, Department of Chemistry and Chemical Engineering, Six Metrotech Center, Brooklyn, New York 11201
| | - Karan Garg
- NSF-IUCRC Center for Biocatalysis and Bioprocessing of Macromolecules, Polytechnic University, Department of Chemistry and Chemical Engineering, Six Metrotech Center, Brooklyn, New York 11201
| | - Richard A. Gross
- NSF-IUCRC Center for Biocatalysis and Bioprocessing of Macromolecules, Polytechnic University, Department of Chemistry and Chemical Engineering, Six Metrotech Center, Brooklyn, New York 11201
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112
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Kobayashi S, Uyama H, Ohmae M. Enzymatic Polymerization for Precision Polymer Synthesis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2001. [DOI: 10.1246/bcsj.74.613] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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113
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114
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Abstract
New catalytic synthetic methods in organic chemistry that satisfy increasingly stringent environmental constraints are in great demand by the pharmaceutical and chemical industries. In addition, novel catalytic procedures are necessary to produce the emerging classes of organic compounds that are becoming the targets of molecular and biomedical research. Enzyme-catalysed chemical transformations are now widely recognized as practical alternatives to traditional (non-biological) organic synthesis, and as convenient solutions to certain intractable synthetic problems.
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Affiliation(s)
- K M Koeller
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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115
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Letizia Focarete M, Scandola M, Kumar A, Gross RA. Physical characterization of poly(?-pentadecalactone) synthesized by lipase-catalyzed ring-opening polymerization. ACTA ACUST UNITED AC 2001. [DOI: 10.1002/polb.1145] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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116
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Koeller KM, Wong CH. Synthesis of complex carbohydrates and glycoconjugates: enzyme-based and programmable one-pot strategies. Chem Rev 2000; 100:4465-94. [PMID: 11749355 DOI: 10.1021/cr990297n] [Citation(s) in RCA: 347] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K M Koeller
- Department of Chemistry, The Scripps Research Institute and Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California 92037
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117
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Kumar A, Kalra B, Dekhterman A, Gross RA. Efficient Ring-Opening Polymerization and Copolymerization of ε-Caprolactone and ω-Pentadecalactone Catalyzed byCandidaantarticaLipase B. Macromolecules 2000. [DOI: 10.1021/ma000344+] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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118
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Oguchi T, Tawaki SI, Uyama H, Kobayashi S. Enzymatic Synthesis of Soluble Polyphenol. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2000. [DOI: 10.1246/bcsj.73.1389] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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119
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Kadokawa J, Hino D, Karasu M, Tagaya H, Chiba K. Synthesis of new aminopolysaccharides by polymerization of 6-amino-6-deoxy-D-glucose and 2,6-diamino-2,6-dideoxy-D-glucose. Eur Polym J 2000. [DOI: 10.1016/s0014-3057(99)00096-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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120
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Shoda SI, Kiyosada T, Mori H, Kobayashi S. Chitinase-catalyzed Synthesis of Oligosaccharides by Using a Sugar Oxazoline as Glycosyl Donor. HETEROCYCLES 2000. [DOI: 10.3987/com-99-s40] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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121
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122
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123
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Küllmer K, Kikuchi H, Uyama H, Kobayashi S. Lipase-catalyzed ring-opening polymerization of α-methyl-δ-valerolactone and α-methyl-ε-caprolactone. Macromol Rapid Commun 1998. [DOI: 10.1002/(sici)1521-3927(19980201)19:2<127::aid-marc127>3.0.co;2-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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124
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Kobayashi S, Uyama H, Namekawa S, Hayakawa H. Enzymatic Ring-Opening Polymerization and Copolymerization of 8-Octanolide by Lipase Catalyst. Macromolecules 1998. [DOI: 10.1021/ma980396n] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shiro Kobayashi
- Department of Materials Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan, and Department of Materials Chemistry, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Hiroshi Uyama
- Department of Materials Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan, and Department of Materials Chemistry, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Shuhei Namekawa
- Department of Materials Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan, and Department of Materials Chemistry, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Hiroshi Hayakawa
- Department of Materials Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan, and Department of Materials Chemistry, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
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125
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Fujita M, Shoda SI, Kobayashi S. Xylanase-Catalyzed Synthesis of a Novel Polysaccharide Having a Glucose-Xylose Repeating Unit, a Cellulose-Xylan Hybrid Polymer. J Am Chem Soc 1998. [DOI: 10.1021/ja980893j] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Masaya Fujita
- Department of Materials Chemistry Graduate School of Engineering Tohoku University, Sendai 980-8579, Japan
| | - Shin-ichiro Shoda
- Department of Materials Chemistry Graduate School of Engineering Tohoku University, Sendai 980-8579, Japan
| | - Shiro Kobayashi
- Department of Materials Chemistry Graduate School of Engineering Kyoto University, Kyoto 606-8501, Japan
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126
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Kadokawa JI, Hino D, Karasu M, Tagaya H, Chiba K. Polymerization of 6-Amino-6-deoxy-D-glucose Involving Amadori Rearrangement: A New Method for Synthesis of Aminopolysaccharide. CHEM LETT 1998. [DOI: 10.1246/cl.1998.383] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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127
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Namekawa S, Uyama H, Kobayashi S. Lipase-Catalyzed Ring-Opening Polymerization of Lactones in Water. Polym J 1998. [DOI: 10.1295/polymj.30.269] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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128
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Küllmer K, Kikuchi H, Uyama H, Kobayashi S. Lipase-catalyzed ring-opening polymerization of α-methyl-δ-valerolactone and α-methyl-ɛ-caprolactone. Macromol Rapid Commun 1998. [DOI: 10.1002/marc.1998.030190210] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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129
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In vitro biosynthesis of polyesters with isolated enzymes in aqueous systems and organic solvents. Polym Degrad Stab 1998. [DOI: 10.1016/s0141-3910(97)00178-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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130
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Kadokawa JI, Kasai S, Watanabe Y, Karasu M, Tagaya H, Chiba K. Synthesis of Natural- and Non-natural-type Aminopolysaccharides: 2-Acetamido-2-deoxy-β-d-glucopyranan Derivatives by Acid-Catalyzed Polymerization of 2-Methyl(3,6- and 3,4-di-O-benzyl-1,2-dideoxy-α-d-glucopyrano)-[2,1-d]- 2-oxazolines Involving Stereoregular Glycosylation. Macromolecules 1997. [DOI: 10.1021/ma971117j] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun-ichi Kadokawa
- Department of Materials Science and Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Yamagata 992, Japan
| | - Shigeto Kasai
- Department of Materials Science and Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Yamagata 992, Japan
| | - Yoshikatsu Watanabe
- Department of Materials Science and Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Yamagata 992, Japan
| | - Masa Karasu
- Department of Materials Science and Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Yamagata 992, Japan
| | - Hideyuki Tagaya
- Department of Materials Science and Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Yamagata 992, Japan
| | - Koji Chiba
- Department of Materials Science and Engineering, Faculty of Engineering, Yamagata University, Yonezawa, Yamagata 992, Japan
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131
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McGarvey GJ, Wong CH. Chemical, Enzymatic and Structural Studies in Molecular Glycobiology. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/jlac.199719970604] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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132
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Kobayashi S, Kiyosada T, Shoda SI. A novel method for synthesis of chitobiose via enzymatic glycosylation using a sugar oxazoline as glycosyl donor. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)00319-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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