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Shirakawa A, Manabe Y, Marchetti R, Yano K, Masui S, Silipo A, Molinaro A, Fukase K. Chemical Synthesis of Sialyl
N
‐Glycans and Analysis of Their Recognition by Neuraminidase. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Asuka Shirakawa
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Yoshiyuki Manabe
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Core for Medicine and Science Collaborative Research and Education Project Research Center for Fundamental Sciences Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Roberta Marchetti
- Department of Chemical Science University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Kumpei Yano
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Seiji Masui
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Alba Silipo
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Department of Chemical Science University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Antonio Molinaro
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Department of Chemical Science University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Koichi Fukase
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Core for Medicine and Science Collaborative Research and Education Project Research Center for Fundamental Sciences Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
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Shirakawa A, Manabe Y, Marchetti R, Yano K, Masui S, Silipo A, Molinaro A, Fukase K. Chemical Synthesis of Sialyl N-Glycans and Analysis of Their Recognition by Neuraminidase. Angew Chem Int Ed Engl 2021; 60:24686-24693. [PMID: 34520098 DOI: 10.1002/anie.202111035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Indexed: 11/07/2022]
Abstract
The chemical synthesis of a fully sialylated tetraantennary N-glycan has been achieved for the first time by using the diacetyl strategy, in which NHAc is protected as NAc2 to improve reactivity by preventing intermolecular hydrogen bonds. Another key was the glycosylation to the branched mannose in an ether solvent, which promoted the desired glycosylation by stabilizing the oxocarbenium ion intermediate. Furthermore, high α-selectivity of these glycosylation reactions was realized by utilizing remote participation. Two asymmetrically deuterium labeled sialyl N-glycans were also synthesized by the same strategy. The synthesized N-glycans were used to probe the molecular basis of H1N1 neuraminidase recognition. The asymmetrically deuterated N-glycans revealed a difference in the recognition of sialic acid on each branch. Meanwhile, the tetraantennary N-glycan was used to evaluate the effects of multivalency and steric hinderance by forming branching structures.
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Affiliation(s)
- Asuka Shirakawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Roberta Marchetti
- Department of Chemical Science, University of Naples Federico II, Via Cinthia 4, 80126, Naples, Italy
| | - Kumpei Yano
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Seiji Masui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Alba Silipo
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Department of Chemical Science, University of Naples Federico II, Via Cinthia 4, 80126, Naples, Italy
| | - Antonio Molinaro
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Department of Chemical Science, University of Naples Federico II, Via Cinthia 4, 80126, Naples, Italy
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
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Kuribara T, Usui R, Totani K. Glycan structure-based perspectives on the entry and release of glycoproteins in the calnexin/calreticulin cycle. Carbohydr Res 2021; 502:108273. [PMID: 33713911 DOI: 10.1016/j.carres.2021.108273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/16/2021] [Accepted: 02/23/2021] [Indexed: 12/16/2022]
Abstract
N-glycans are attached to newly synthesised polypeptides and are involved in the folding, secretion, and degradation of N-linked glycoproteins. In particular, the calnexin/calreticulin cycle, which is the central mechanism of the entry and release of N-linked glycoproteins depending on the folding sates, has been well studied. In addition to biological studies on the calnexin/calreticulin cycle, several studies have revealed complementary roles of in vitro chemistry-based research in the structure-based understanding of the cycle. In this mini-review, we summarise chemistry-based results and highlight their importance for further understanding of the cycle.
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Affiliation(s)
- Taiki Kuribara
- Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijoji-kitamachiMusashino-shi, Tokyo, 180-8633, Japan
| | - Ruchio Usui
- Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijoji-kitamachiMusashino-shi, Tokyo, 180-8633, Japan
| | - Kiichiro Totani
- Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijoji-kitamachiMusashino-shi, Tokyo, 180-8633, Japan.
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Shirakawa A, Manabe Y, Fukase K. Recent Advances in the Chemical Biology of N-Glycans. Molecules 2021; 26:molecules26041040. [PMID: 33669465 PMCID: PMC7920464 DOI: 10.3390/molecules26041040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 12/19/2022] Open
Abstract
Asparagine-linked N-glycans on proteins have diverse structures, and their functions vary according to their structures. In recent years, it has become possible to obtain high quantities of N-glycans via isolation and chemical/enzymatic/chemoenzymatic synthesis. This has allowed for progress in the elucidation of N-glycan functions at the molecular level. Interaction analyses with lectins by glycan arrays or nuclear magnetic resonance (NMR) using various N-glycans have revealed the molecular basis for the recognition of complex structures of N-glycans. Preparation of proteins modified with homogeneous N-glycans revealed the influence of N-glycan modifications on protein functions. Furthermore, N-glycans have potential applications in drug development. This review discusses recent advances in the chemical biology of N-glycans.
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Affiliation(s)
- Asuka Shirakawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
| | - Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Correspondence: (Y.M.); (K.F.); Tel.: +81-6-6850-5391 (Y.M.); +81-6-6850-5388 (K.F.)
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Correspondence: (Y.M.); (K.F.); Tel.: +81-6-6850-5391 (Y.M.); +81-6-6850-5388 (K.F.)
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Abstract
Folding of proteins is essential so that they can exert their functions. For proteins that transit the secretory pathway, folding occurs in the endoplasmic reticulum (ER) and various chaperone systems assist in acquiring their correct folding/subunit formation. N-glycosylation is one of the most conserved posttranslational modification for proteins, and in eukaryotes it occurs in the ER. Consequently, eukaryotic cells have developed various systems that utilize N-glycans to dictate and assist protein folding, or if they consistently fail to fold properly, to destroy proteins for quality control and the maintenance of homeostasis of proteins in the ER.
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Ninagawa S, George G, Mori K. Mechanisms of productive folding and endoplasmic reticulum-associated degradation of glycoproteins and non-glycoproteins. Biochim Biophys Acta Gen Subj 2020; 1865:129812. [PMID: 33316349 DOI: 10.1016/j.bbagen.2020.129812] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND The quality of proteins destined for the secretory pathway is ensured by two distinct mechanisms in the endoplasmic reticulum (ER): productive folding of newly synthesized proteins, which is assisted by ER-localized molecular chaperones and in most cases also by disulfide bond formation and transfer of an oligosaccharide unit; and ER-associated degradation (ERAD), in which proteins unfolded or misfolded in the ER are recognized and processed for delivery to the ER membrane complex, retrotranslocated through the complex with simultaneous ubiquitination, extracted by AAA-ATPase to the cytosol, and finally degraded by the proteasome. SCOPE OF REVIEW We describe the mechanisms of productive folding and ERAD, with particular attention to glycoproteins versus non-glycoproteins, and to yeast versus mammalian systems. MAJOR CONCLUSION Molecular mechanisms of the productive folding of glycoproteins and non-glycoproteins mediated by molecular chaperones and protein disulfide isomerases are well conserved from yeast to mammals. Additionally, mammals have gained an oligosaccharide structure-dependent folding cycle for glycoproteins. The molecular mechanisms of ERAD are also well conserved from yeast to mammals, but redundant expression of yeast orthologues in mammals has been encountered, particularly for components involved in recognition and processing of glycoproteins and components of the ER membrane complex involved in retrotranslocation and simultaneous ubiquitination of glycoproteins and non-glycoproteins. This may reflect an evolutionary consequence of increasing quantity or quality needs toward mammals. GENERAL SIGNIFICANCE The introduction of innovative genome editing technology into analysis of the mechanisms of mammalian ERAD, as exemplified here, will provide new insights into the pathogenesis of various diseases.
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Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Ginto George
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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Koda Y, Terashima T, Ouchi M. Unnatural Oligoaminosaccharides with N-1,2-Glycosidic Bonds Prepared by Cationic Ring-Opening Polymerization of 2-Oxazoline-Based Heterobicyclic Sugar Monomers. ACS Macro Lett 2019; 8:1456-1460. [PMID: 35651175 DOI: 10.1021/acsmacrolett.9b00674] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Glycooligomers and glycopolymers (glycocompounds) play important roles in maintaining homeostasis in biological systems. Glycobiology is a burgeoning area in the elucidation of biological systems for which the molecular design of glycocompounds requires further diversification, including both natural and unnatural glycocompounds. Herein, we proposed a synthesis strategy based on the chain polymerization of deliberately designed sugar monomers. Unnatural oligoaminosaccharides comprising N-1,2-glycosidic bonds were synthesized without enzymes through the cationic ring-opening polymerization of 2-oxazoline-based heterobicyclic sugar monomers. To achieve this, a heterobicyclic monomer [Glc(MeOx)], comprising protected glucosamine (GlcN) and 2-methyl-2-oxazoline (MeOx) rings, was designed. This monomer was polymerized using a binary initiating system of tert-butyl iodide (t-BuI) and GaCl3 to afford oligo[Glc(MeOx)]. The resulting structure corresponded to the condensation product of GlcN with N-1,2-glycosidic bonds. After deprotection of oligo[Glc(MeOx)], the resulting oligoaminosaccharide had a secondary structure different to that of protected oligo[Glc(MeOx)]. Owing to the N-1,2-glycosidic bonds, the oligoaminosaccharide was not degraded by chitinase, which hydrolyzes the condensation product of GlcN with O-1,4-glycosidic bonds.
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Affiliation(s)
- Yuta Koda
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615−8510, Japan
| | - Takaya Terashima
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615−8510, Japan
| | - Makoto Ouchi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615−8510, Japan
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Yanaka S, Yagi H, Yogo R, Yagi-Utsumi M, Kato K. Stable isotope labeling approaches for NMR characterization of glycoproteins using eukaryotic expression systems. JOURNAL OF BIOMOLECULAR NMR 2018; 71:193-202. [PMID: 29492730 DOI: 10.1007/s10858-018-0169-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/17/2018] [Indexed: 05/25/2023]
Abstract
Glycoproteins are characterized by the heterogeneous and dynamic nature of their glycan moieties, which hamper crystallographic analysis. NMR spectroscopy provides potential advantages in dealing with such complicated systems, given that the target molecules can be isotopically labeled. Methods of metabolic isotope labeling in recombinant glycoproteins have been developed recently using a variety of eukaryotic production vehicles, including mammalian, yeast, insect, and plant cells, each of which has a distinct N-glycan diversification pathway. Yeast genetic engineering has enabled the overexpression of homogeneous high-mannose-type oligosaccharides with 13C labeling for NMR characterization of their conformational dynamics. The utility of stable isotope-assisted NMR spectroscopy has also been demonstrated using the Fc fragment of immunoglobulin G (IgG) as a model glycoprotein, providing useful information regarding intramolecular carbohydrate-protein interactions. Transverse relaxation optimization of intact IgG with a molecular mass of 150 kDa has been achieved by tailored deuteration of selected amino acid residues using a mammalian expression system. This offers a useful probe for the characterization of molecular interaction networks in multimolecular crowded systems typified by serum. Perspectives regarding the development of techniques for tailoring glycoform designs and isotope labeling of recombinant glycoproteins are also discussed.
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Affiliation(s)
- Saeko Yanaka
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Rina Yogo
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Maho Yagi-Utsumi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
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Satoh T, Kato K. Structural Aspects of ER Glycoprotein Quality-Control System Mediated by Glucose Tagging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1104:149-169. [PMID: 30484248 DOI: 10.1007/978-981-13-2158-0_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
N-linked oligosaccharides attached to proteins act as tags for glycoprotein quality control, ensuring their appropriate folding and trafficking in cells. Interactions with a variety of intracellular lectins determine glycoprotein fates. Monoglucosylated glycoforms are the hallmarks of incompletely folded glycoproteins in the protein quality-control system, in which glucosidase II and UDP-glucose/glycoprotein glucosyltransferase are, respectively, responsible for glucose trimming and attachment. In this review, we summarize a recently emerging view of the structural basis of the functional mechanisms of these key enzymes as well as substrate N-linked oligosaccharides exhibiting flexible structures, as revealed by applying a series of biophysical techniques including small-angle X-ray scattering, X-ray crystallography, high-speed atomic force microscopy , electron microscopy , and computational simulation in conjunction with NMR spectroscopy.
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Affiliation(s)
- Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan. .,Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
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Calles-Garcia D, Yang M, Soya N, Melero R, Ménade M, Ito Y, Vargas J, Lukacs GL, Kollman JM, Kozlov G, Gehring K. Single-particle electron microscopy structure of UDP-glucose:glycoprotein glucosyltransferase suggests a selectivity mechanism for misfolded proteins. J Biol Chem 2017; 292:11499-11507. [PMID: 28490633 DOI: 10.1074/jbc.m117.789495] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/07/2017] [Indexed: 11/06/2022] Open
Abstract
The enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) mediates quality control of glycoproteins in the endoplasmic reticulum by attaching glucose to N-linked glycan of misfolded proteins. As a sensor, UGGT ensures that misfolded proteins are recognized by the lectin chaperones and do not leave the secretory pathway. The structure of UGGT and the mechanism of its selectivity for misfolded proteins have been unknown for 25 years. Here, we used negative-stain electron microscopy and small-angle X-ray scattering to determine the structure of UGGT from Drosophila melanogaster at 18-Å resolution. Three-dimensional reconstructions revealed a cage-like structure with a large central cavity. Particle classification revealed flexibility that precluded determination of a high-resolution structure. Introduction of biotinylation sites into a fungal UGGT expressed in Escherichia coli allowed identification of the catalytic and first thioredoxin-like domains. We also used hydrogen-deuterium exchange mass spectrometry to map the binding site of an accessory protein, Sep15, to the first thioredoxin-like domain. The UGGT structural features identified suggest that the central cavity contains the catalytic site and is lined with hydrophobic surfaces. This enhances the binding of misfolded substrates with exposed hydrophobic residues and excludes folded proteins with hydrophilic surfaces. In conclusion, we have determined the UGGT structure, which enabled us to develop a plausible functional model of the mechanism for UGGT's selectivity for misfolded glycoproteins.
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Affiliation(s)
- Daniel Calles-Garcia
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Meng Yang
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Naoto Soya
- Department of Physiology, McGill University, Montreal, Quebec H3G1Y6, Canada
| | - Roberto Melero
- Biocomputing Unit, Centro Nacional de Biotectnologíay, 28049 Madrid, Spain
| | - Marie Ménade
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
| | - Javier Vargas
- Biocomputing Unit, Centro Nacional de Biotectnologíay, 28049 Madrid, Spain.,Bioengineering Lab, Escuela Politécnica Superior, Universidad San Pablo CEU, 28668 Madrid, Spain, and
| | - Gergely L Lukacs
- Department of Physiology, McGill University, Montreal, Quebec H3G1Y6, Canada
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350
| | - Guennadi Kozlov
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada
| | - Kalle Gehring
- From the Department of Biochemistry, McGill University, Montreal, Quebec H3G0B1, Canada,
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Suzuki T, Kajino M, Yanaka S, Zhu T, Yagi H, Satoh T, Yamaguchi T, Kato K. Conformational Analysis of a High-Mannose-Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR-Validated Molecular Dynamics Simulation. Chembiochem 2017; 18:396-401. [PMID: 27995699 DOI: 10.1002/cbic.201600595] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Indexed: 12/11/2022]
Abstract
Exploration of the conformational spaces of flexible oligosaccharides is essential to gain deeper insights into their functional mechanisms. Here we characterised dynamic conformation of a high-mannose-type dodecasaccharide with a terminal glucose residue, a critical determinant recognised by molecular chaperones. The dodecasaccharide was prepared by our developed chemoenzymatic technique, which uses 13 C labelling and lanthanide tagging to detect conformation-dependent paramagnetic effects by NMR spectroscopy. The NMR-validated molecular dynamics simulation produced the dynamic conformational ensemble of the dodecasaccharide. This determined its spatial distribution as well as the glycosidic linkage conformation of the terminal glucose determinant. Moreover, comparison of our results with previously reported crystallographic data indicates that the chaperone binding to its target oligosaccharides involves an induced-fit mechanism.
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Affiliation(s)
- Tatsuya Suzuki
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Institute for Molecular Science, Okazaki Institute for Integrative Biosciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
| | - Megumi Kajino
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Saeko Yanaka
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Institute for Molecular Science, Okazaki Institute for Integrative Biosciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
| | - Tong Zhu
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Institute for Molecular Science, Okazaki Institute for Integrative Biosciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
| | - Hirokazu Yagi
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Tadashi Satoh
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Takumi Yamaguchi
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Institute for Molecular Science, Okazaki Institute for Integrative Biosciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.,School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, 923-1292, Japan
| | - Koichi Kato
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.,Institute for Molecular Science, Okazaki Institute for Integrative Biosciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
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12
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Cuyàs E, Fernández-Arroyo S, Corominas-Faja B, Rodríguez-Gallego E, Bosch-Barrera J, Martin-Castillo B, De Llorens R, Joven J, Menendez JA. Oncometabolic mutation IDH1 R132H confers a metformin-hypersensitive phenotype. Oncotarget 2016; 6:12279-96. [PMID: 25980580 PMCID: PMC4494938 DOI: 10.18632/oncotarget.3733] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/11/2015] [Indexed: 02/07/2023] Open
Abstract
Metabolic flexibility might be particularly constrained in tumors bearing mutations in isocitrate dehydrogenase 1 (IDH1) leading to the production of the oncometabolite 2-hydroxygluratate (2HG). To test the hypothesis that IDH1 mutations could generate metabolic vulnerabilities for therapeutic intervention, we utilized an MCF10A cell line engineered with an arginine-to-histidine conversion at position 132 (R132H) in the catalytic site of IDH1, which equips the enzyme with a neomorphic α-ketoglutarate to 2HG reducing activity in an otherwise isogenic background. IDH1 R132H/+ and isogenic IDH1 +/+ parental cells were screened for their ability to generate energy-rich NADH when cultured in a standardized high-throughput Phenotype MicroArrayplatform comprising >300 nutrients. A radical remodeling of the metabotype occurred in cells carrying the R132H mutation since they presented a markedly altered ability to utilize numerous carbon catabolic fuels. A mitochondria toxicity-screening modality confirmed a severe inability of IDH1-mutated cells to use various carbon substrates that are fed into the electron transport chain at different points. The mitochondrial biguanide poisons, metformin and phenformin, further impaired the intrinsic weakness of IDH1-mutant cells to use certain carbon-energy sources. Additionally, metabolic reprogramming of IDH1-mutant cells increased their sensitivity to metformin in assays of cell proliferation, clonogenic potential, and mammosphere formation. Targeted metabolomics studies revealed that the ability of metformin to interfere with the anaplerotic entry of glutamine into the tricarboxylic acid cycle could explain the hypersensitivity of IDH1-mutant cells to biguanides. Moreover, synergistic interactions occurred when metformin treatment was combined with the selective R132H-IDH1 inhibitor AGI-5198. Together, these results suggest that therapy involving the simultaneous targeting of metabolic vulnerabilities with metformin, and 2HG overproduction with mutant-selective inhibitors (AGI-5198-related AG-120 [Agios]), might represent a worthwhile avenue of exploration in the treatment of IDH1-mutated tumors.
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Affiliation(s)
- Elisabet Cuyàs
- Metabolism and Cancer Group, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Girona, Catalonia, Spain.,Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain
| | - Salvador Fernández-Arroyo
- Unitat de Recerca Biomèdica (URB-CRB), Institut d'Investigació Sanitaria Pere i Virgili (IISPV), Universitat Rovira i Virgili, Reus, Catalonia. Spain
| | - Bruna Corominas-Faja
- Metabolism and Cancer Group, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Girona, Catalonia, Spain.,Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain
| | - Esther Rodríguez-Gallego
- Unitat de Recerca Biomèdica (URB-CRB), Institut d'Investigació Sanitaria Pere i Virgili (IISPV), Universitat Rovira i Virgili, Reus, Catalonia. Spain
| | - Joaquim Bosch-Barrera
- Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain.,Medical Oncology, Catalan Institute of Oncology (ICO), Girona, Catalonia, Spain
| | - Begoña Martin-Castillo
- Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain.,Clinical Research Unit, Catalan Institute of Oncology (ICO), Girona, Catalonia, Spain
| | - Rafael De Llorens
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona, Girona, Catalonia, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica (URB-CRB), Institut d'Investigació Sanitaria Pere i Virgili (IISPV), Universitat Rovira i Virgili, Reus, Catalonia. Spain
| | - Javier A Menendez
- Metabolism and Cancer Group, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Girona, Catalonia, Spain.,Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain
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13
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Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control. Sci Rep 2016; 6:20575. [PMID: 26847925 PMCID: PMC4742823 DOI: 10.1038/srep20575] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/06/2016] [Indexed: 01/10/2023] Open
Abstract
The endoplasmic reticulum (ER) has a sophisticated protein quality control system for the efficient folding of newly synthesized proteins. In this system, a variety of N-linked oligosaccharides displayed on proteins serve as signals recognized by series of intracellular lectins. Glucosidase II catalyzes two-step hydrolysis at α1,3-linked glucose–glucose and glucose–mannose residues of high-mannose-type glycans to generate a quality control protein tag that is transiently expressed on glycoproteins and recognized by ER chaperones. Here we determined the crystal structures of the catalytic α subunit of glucosidase II (GIIα) complexed with two different glucosyl ligands containing the scissile bonds of first- and second-step reactions. Our structural data revealed that the nonreducing terminal disaccharide moieties of the two kinds of substrates can be accommodated in a gourd-shaped bilocular pocket, thereby providing a structural basis for substrate-binding specificity in the two-step deglucosylation catalyzed by this enzyme.
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14
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Sakono M, Seko A, Takeda Y, Hachisu M, Koizumi A, Fujikawa K, Seto H, Ito Y. Influence of high-mannose glycan whose glucose moiety is substituted with 5-thioglucose on calnexin/calreticulin cycle. RSC Adv 2016. [DOI: 10.1039/c6ra16476e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Our study first revealed that UDP-5-thioglucose functions as a glycosyl donor of UDP-glucose: glycoprotein glucosyltransferase to produce 5-thio-glucosylated Man9 (5S-G1M9).
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Affiliation(s)
- Masafumi Sakono
- Japan Science and Technology Agency (JST)
- ERATO Ito Glycotrilogy Project
- Wako
- Japan
- Department of Applied Chemistry
| | - Akira Seko
- Japan Science and Technology Agency (JST)
- ERATO Ito Glycotrilogy Project
- Wako
- Japan
| | - Yoichi Takeda
- Japan Science and Technology Agency (JST)
- ERATO Ito Glycotrilogy Project
- Wako
- Japan
- Department of Biotechnology
| | - Masakazu Hachisu
- Japan Science and Technology Agency (JST)
- ERATO Ito Glycotrilogy Project
- Wako
- Japan
- Department of Biological Science and Technology
| | - Akihiko Koizumi
- Japan Science and Technology Agency (JST)
- ERATO Ito Glycotrilogy Project
- Wako
- Japan
- Faculty of Pharmaceutical Sciences
| | - Kohki Fujikawa
- Japan Science and Technology Agency (JST)
- ERATO Ito Glycotrilogy Project
- Wako
- Japan
- SUNTORY Foundation for Life Sciences
| | - Hideharu Seto
- Synthetic Cellular Chemistry Laboratory
- RIKEN
- Wako
- Japan
| | - Yukishige Ito
- Japan Science and Technology Agency (JST)
- ERATO Ito Glycotrilogy Project
- Wako
- Japan
- Synthetic Cellular Chemistry Laboratory
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15
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Zhu T, Yamaguchi T, Satoh T, Kato K. A Hybrid Strategy for the Preparation of 13C-labeled High-mannose-type Oligosaccharides with Terminal Glucosylation for NMR Study. CHEM LETT 2015. [DOI: 10.1246/cl.150898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tong Zhu
- School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies)
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Takumi Yamaguchi
- School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies)
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- JST, PRESTO
| | - Koichi Kato
- School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies)
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- Medical and Biological Laboratories Co., Ltd
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16
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Glinschert A, Oscarson S. Synthesis of four (4″-, 2″-, 2′-, and 6-) monodeoxy analogs of the trisaccharide α-d-Glcp-(1→3)-α-d-Manp-(1→2)-α-d-ManpOMe recognized by Calreticulin/Calnexin. Carbohydr Res 2015; 414:65-71. [DOI: 10.1016/j.carres.2015.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/17/2015] [Accepted: 07/10/2015] [Indexed: 10/23/2022]
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17
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Olson LJ, Orsi R, Peterson FC, Parodi AJ, Kim JJP, D'Alessio C, Dahms NM. Crystal Structure and Functional Analyses of the Lectin Domain of Glucosidase II: Insights into Oligomannose Recognition. Biochemistry 2015; 54:4097-111. [PMID: 26062005 DOI: 10.1021/acs.biochem.5b00256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-Glycans are modified as part of a quality control mechanism during glycoprotein folding in the endoplasmic reticulum (ER). Glucosidase II (GII) plays a critical role by generating monoglucosylated glycans that are recognized by lectin chaperones, calnexin and calreticulin. To understand how the hydrolytic activity of GIIα is enhanced by the mannose 6-phosphate receptor (MPR) homology domain (MRH domain) of its β subunit, we now report a 1.6 Å resolution crystal structure of the MRH domain of GIIβ bound to mannose. A comparison of ligand-bound and unbound structures reveals no major difference in their overall fold, but rather a repositioning of side chains throughout the binding pocket, including Y372. Mutation of Y372 inhibits GII activity, demonstrating an important role for Y372 in regulating GII activity. Comparison of the MRH domains of GIIβ, MPRs, and the ER lectin OS-9 identified conserved residues that are critical for the structural integrity and architecture of the carbohydrate binding pocket. As shown by nuclear magnetic resonance spectroscopy, mutations of the primary binding pocket residues and adjacent W409, all of which inhibit the activity of GII both in vitro and in vivo, do not cause a significant change in the overall fold of the GIIβ MRH domain but impact locally the stability of the binding pocket. W409 does not directly contact mannose; rather, its indole ring is stabilized by binding into a hydrophobic pocket of an adjacent crystallographic neighbor. This suggests that W409 interacts with a hydrophobic region of the GIIβ or GIIα subunit to modulate its effect on GII activity.
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Affiliation(s)
- Linda J Olson
- †Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Ramiro Orsi
- ‡Laboratory of Glycobiology, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina
| | - Francis C Peterson
- †Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Armando J Parodi
- ‡Laboratory of Glycobiology, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina
| | - Jung-Ja P Kim
- †Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Cecilia D'Alessio
- ‡Laboratory of Glycobiology, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires, Argentina.,§School of Sciences, University of Buenos Aires, Buenos Aires, Argentina
| | - Nancy M Dahms
- †Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
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18
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Izumi M, Dedola S, Ito Y, Kajihara Y. Chemical Synthesis of Homogeneous Glycoproteins for the Study of Glycoprotein Quality Control System. Isr J Chem 2015. [DOI: 10.1002/ijch.201400154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Wang LX, Amin MN. Chemical and chemoenzymatic synthesis of glycoproteins for deciphering functions. ACTA ACUST UNITED AC 2015; 21:51-66. [PMID: 24439206 DOI: 10.1016/j.chembiol.2014.01.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 12/31/2013] [Accepted: 01/02/2014] [Indexed: 12/11/2022]
Abstract
Glycoproteins are an important class of biomolecules involved in a number of biological recognition processes. However, natural and recombinant glycoproteins are usually produced as mixtures of glycoforms that differ in the structures of the pendent glycans, which are difficult to separate in pure glycoforms. As a result, synthetic homogeneous glycopeptides and glycoproteins have become indispensable probes for detailed structural and functional studies. A number of elegant chemical and biological strategies have been developed for synthetic construction of tailor-made, full-size glycoproteins to address specific biological problems. In this review, we highlight recent advances in chemical and chemoenzymatic synthesis of homogeneous glycoproteins. Selected examples are given to demonstrate the applications of tailor-made, glycan-defined glycoproteins for deciphering glycosylation functions.
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Affiliation(s)
- Lai-Xi Wang
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Mohammed N Amin
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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20
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Analytical method for determining relative chaperone activity using an ovalbumin-conjugated column. Biochem Biophys Res Commun 2015; 456:333-8. [DOI: 10.1016/j.bbrc.2014.11.081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 11/22/2014] [Indexed: 11/16/2022]
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21
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Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 842:217-30. [PMID: 25408346 DOI: 10.1007/978-3-319-11280-0_14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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22
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Structural insight into substrate recognition by the endoplasmic reticulum folding-sensor enzyme: crystal structure of third thioredoxin-like domain of UDP-glucose:glycoprotein glucosyltransferase. Sci Rep 2014; 4:7322. [PMID: 25471383 PMCID: PMC4255179 DOI: 10.1038/srep07322] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/18/2014] [Indexed: 02/07/2023] Open
Abstract
The endoplasmic reticulum (ER) possesses a protein quality control system that supports the efficient folding of newly synthesized glycoproteins. In this system, a series of N-linked glycan intermediates displayed on proteins serve as quality tags. The ER folding-sensor enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) operates as the gatekeeper for ER quality control by specifically transferring monoglucose residues to incompletely folded glycoproteins, thereby allowing them to interact with lectin chaperone complexes to facilitate their folding. Despite its functional importance, no structural information is available for this key enzyme to date. To elucidate the folding-sensor mechanism in the ER, we performed a structural study of UGGT. Based on bioinformatics analyses, the folding-sensor region of UGGT was predicted to harbour three tandem thioredoxin (Trx)-like domains, which are often found in proteins involved in ER quality control. Furthermore, we determined the three-dimensional structure of the third Trx-like domain, which exhibits an extensive hydrophobic patch concealed by its flexible C-terminal helix. Our structural data suggest that this hydrophobic patch is involved in intermolecular interactions, thereby contributing to the folding-sensor mechanism of UGGT.
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23
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Glycan specificity of a testis-specific lectin chaperone calmegin and effects of hydrophobic interactions. Biochim Biophys Acta Gen Subj 2014; 1840:2904-13. [DOI: 10.1016/j.bbagen.2014.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 03/19/2014] [Accepted: 04/14/2014] [Indexed: 01/29/2023]
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24
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Kamiya Y, Satoh T, Kato K. Recent advances in glycoprotein production for structural biology: toward tailored design of glycoforms. Curr Opin Struct Biol 2014; 26:44-53. [PMID: 24841384 DOI: 10.1016/j.sbi.2014.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 03/20/2014] [Accepted: 03/25/2014] [Indexed: 01/01/2023]
Abstract
Because of the complexity, heterogeneity, and flexibility of the glycans, the structural analysis of glycoproteins has been eschewed until recently, with a few prominent exceptions. This aversion may have branded structural biologists as glycophobics. However, recent technological advancements in glycoprotein expression systems, employing genetically engineered production vehicles derived from mammalian, insect, yeast, and even bacterial cells, have yielded encouraging breakthroughs. The major advance is the active control of glycoform expression of target glycoproteins based on the genetic manipulation of glycan biogenetic pathways, which was previously overlooked, abolished, or considered unmanageable. Moreover, synthetic and/or chemoenzymatic approaches now enable the preparation of glycoproteins with uniform glycoforms designed in a tailored fashion.
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Affiliation(s)
- Yukiko Kamiya
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; The Glycoscience Institute, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan; GLYENCE Co., Ltd., 2-22-8 Chikusa, Chikusa-ku, Nagoya 464-0858, Japan.
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25
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Aikawa JI, Takeda Y, Matsuo I, Ito Y. Trimming of glucosylated N-glycans by human ER α1,2-mannosidase I. ACTA ACUST UNITED AC 2014; 155:375-84. [DOI: 10.1093/jb/mvu008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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26
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Satoh T, Suzuki K, Yamaguchi T, Kato K. Structural basis for disparate sugar-binding specificities in the homologous cargo receptors ERGIC-53 and VIP36. PLoS One 2014; 9:e87963. [PMID: 24498414 PMCID: PMC3912170 DOI: 10.1371/journal.pone.0087963] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 12/30/2013] [Indexed: 12/19/2022] Open
Abstract
ERGIC-53 and VIP36 are categorized as leguminous type (L-type) lectins, and they function as cargo receptors for trafficking certain N-linked glycoproteins in the secretory pathway in animal cells. They share structural similarities in their carbohydrate recognition domains (CRDs) but exhibit distinct sugar-binding specificities and affinities. VIP36 specifically interacts with the α1,2-linked D1 mannosyl arm without terminal glucosylation, while ERGIC-53 shows a broader specificity and lower binding affinity to the high-mannose-type oligosaccharides, irrespective of the presence or absence of the non-reducing terminal glucose residue at the D1 arm. In this study, we determined the crystal structure of ERGIC-53-CRD in complex with their binding partner, MCFD2 and the α1,2 mannotriose which corresponds to the trisaccharide of the D1 arm of high-mannose-type glycans. ERGIC-53 can interact with the D1 trimannosyl arm in two alternative modes, one of which is similar but distinct from that previously observed for VIP36. ERGIC-53 has a shallower sugar-binding pocket than VIP36 because of the single amino acid substitution, Asp-to-Gly. This enables ERGIC-53 to accommodate the non-reducing terminal glucose of the D1 arm in its CRD. In the other interaction mode, the 3-OH group of the terminal mannose was situated outward with respect to the sugar binding pocket, also enabling the Glcα1-3 linkage formation without steric hindrance. Our findings thus provide a structural basis for the broad sugar-binding specificity of the ERGIC-53/MCFD2 cargo receptor complex.
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Affiliation(s)
- Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Japan
- JST, PRESTO, Mizuho-ku, Nagoya, Japan
| | - Kousuke Suzuki
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Japan
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
| | - Takumi Yamaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Japan
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Japan
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan
- * E-mail:
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27
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Fernández-Álvarez A, Elías-Villalobos A, Jiménez-Martín A, Marín-Menguiano M, Ibeas JI. Endoplasmic reticulum glucosidases and protein quality control factors cooperate to establish biotrophy in Ustilago maydis. THE PLANT CELL 2013; 25:4676-90. [PMID: 24280385 PMCID: PMC3875743 DOI: 10.1105/tpc.113.115691] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/04/2013] [Accepted: 11/04/2013] [Indexed: 05/21/2023]
Abstract
Secreted fungal effectors mediate plant-fungus pathogenic interactions. These proteins are typically N-glycosylated, a common posttranslational modification affecting their location and function. N-glycosylation consists of the addition, and subsequent maturation, of an oligosaccharide core in the endoplasmic reticulum (ER) and Golgi apparatus. In this article, we show that two enzymes catalyzing specific stages of this pathway in maize smut (Ustilago maydis), glucosidase I (Gls1) and glucosidase II β-subunit (Gas2), are essential for its pathogenic interaction with maize (Zea mays). Gls1 is required for the initial stages of infection following appressorium penetration, and Gas2 is required for efficient fungal spreading inside infected tissues. While U. maydis Δgls1 cells induce strong plant defense responses, Δgas2 hyphae are able to repress them, showing that slight differences in the N-glycoprotein processing can determine the extent of plant-fungus interactions. Interestingly, the calnexin protein, a central element of the ER quality control system for N-glycoproteins in eukaryotic cells, is essential for avoiding plant defense responses in cells with defective N-glycoproteins processing. Thus, N-glycoprotein maturation and this conserved checkpoint appear to play an important role in the establishment of an initial biotrophic state with the plant, which allows subsequent colonization.
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28
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Abstract
In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray-based technology has been widely employed for rapid analysis of the glycan binding properties of lectins and antibodies, the quantitative measurements of glycan-protein interactions, detection of cells and pathogens, identification of disease-related anti-glycan antibodies for diagnosis, and fast assessment of substrate specificities of glycosyltransferases. This review covers the construction of carbohydrate microarrays, detection methods of carbohydrate microarrays and their applications in biological and biomedical research.
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Affiliation(s)
- Sungjin Park
- National Creative Research Initiative Center for Biofunctional Molecules, Department of Chemistry, Yonsei University, Seoul 120-749, Korea
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29
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Matsushima H, Hirano M, Ito Y, Totani K. Diverse Effects of Macromolecular Crowding on the Sequential Glycan-Processing Pathway Involved in Glycoprotein Quality Control. Chembiochem 2013; 14:753-8. [DOI: 10.1002/cbic.201300028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Indexed: 12/20/2022]
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30
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Izumi M, Kiuchi T, Ito Y, Kajihara Y. Misfolded Glycoproteins as Probes for Analysis of Folding Sensor Enzyme UDP-Glucose. TRENDS GLYCOSCI GLYC 2013. [DOI: 10.4052/tigg.25.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Iwamoto S, Isoyama M, Hirano M, Yamaya K, Ito Y, Matsuo I, Totani K. Reconstructed glycan profile for evaluation of operating status of the endoplasmic reticulum glycoprotein quality control. Glycobiology 2012; 23:121-31. [DOI: 10.1093/glycob/cws130] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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32
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Sakono M, Seko A, Takeda Y, Hachisu M, Ito Y. Biophysical properties of UDP-glucose:glycoprotein glucosyltransferase, a folding sensor enzyme in the ER, delineated by synthetic probes. Biochem Biophys Res Commun 2012; 426:504-10. [PMID: 22960071 DOI: 10.1016/j.bbrc.2012.08.112] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 08/23/2012] [Indexed: 12/19/2022]
Abstract
UDP-glucose:glycoprotein glucosyltransferase plays a key role in glycoprotein quality control in the endoplasmic reticulum, by virtue of its ability to discriminate folding states. Although lines of evidence have clarified the ability of UGGT to recognize a partially unfolded protein, its mechanistic rationale has been obscure. In this study, the substrate recognition mechanism of UGGT was studied using synthetic substrate of UGGT. Although UGGT has high extent of surface hydrophobicity, it clearly lacks property of typical molecular chaperones. Furthermore, it was revealed that the addition of the substrate caused secondary structure change of UGGT in a dose-dependent manner, resulting that the K(d) value of the UGGT-substrate interaction was estimated from theoretical formula based on 1:1 complexation between UGGT and the acceptor substrate. Moreover, the kinetic analysis of glucosyltransferase activity of UGGT elucidated Michaelis constant K(m) correctly.
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Affiliation(s)
- Masafumi Sakono
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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33
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Izumi M, Makimura Y, Dedola S, Seko A, Kanamori A, Sakono M, Ito Y, Kajihara Y. Chemical synthesis of intentionally misfolded homogeneous glycoprotein: a unique approach for the study of glycoprotein quality control. J Am Chem Soc 2012; 134:7238-41. [PMID: 22497239 DOI: 10.1021/ja3013177] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biosynthesis of glycoproteins in the endoplasmic reticulum employs a quality control system, which discriminates and excludes misfolded malfunctional glycoproteins from a correctly folded one. As chemical tools to study the glycoprotein quality control system, we systematically synthesized misfolded homogeneous glycoproteins bearing a high-mannose type oligosaccharide via oxidative misfolding of a chemically synthesized homogeneous glycopeptide. The endoplasmic reticulum folding sensor enzyme, UDP-glucose:glycoprotein glucosyltransferase (UGGT), recognizes a specific folding intermediate, which exhibits a molten globule-like hydrophobic nature.
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Affiliation(s)
- Masayuki Izumi
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043 Japan
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Kamiya Y, Satoh T, Kato K. Molecular and structural basis for N-glycan-dependent determination of glycoprotein fates in cells. Biochim Biophys Acta Gen Subj 2012; 1820:1327-37. [PMID: 22240168 DOI: 10.1016/j.bbagen.2011.12.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 12/27/2011] [Accepted: 12/27/2011] [Indexed: 11/18/2022]
Abstract
BACKGROUND N-linked oligosaccharides operate as tags for protein quality control, consigning glycoproteins to different fates, i.e. folding in the endoplasmic reticulum (ER), vesicular transport between the ER and the Golgi complex, and ER-associated degradation of glycoproteins, by interacting with a panel of intracellular lectins in the early secretory pathway. SCOPE OF REVIEW This review summarizes the current state of knowledge regarding the molecular and structural basis for glycoprotein-fate determination in cells that is achieved through the actions of the intracellular lectins and its partner proteins. MAJOR CONCLUSIONS Cumulative frontal affinity chromatography (FAC) data demonstrated that the intracellular lectins exhibit distinct sugar-binding specificity profiles. The glycotopes recognized by these lectins as fate determinants are embedded in the triantennary structures of the high-mannose-type oligosaccharides and are exposed upon trimming of the outer glucose and mannose residues during the N-glycan processing pathway. Furthermore, recently emerged 3D structural data offer mechanistic insights into functional interplay between an intracellular lectin and its binding partner in the early secretory pathway. GENERAL SIGNIFICANCE Structural biology approaches in conjunction with FAC methods provide atomic pictures of the mechanisms behind the glycoprotein-fate determination in cells. This article is a part of a Special issue entitled: Glycoproteomics.
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Affiliation(s)
- Yukiko Kamiya
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
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Fukase K, Fujimoto Y, Shimoyama A, Tanaka K. Synthesis of Bacterial Glycoconjugates and Their Bio-functional Studies in Innate Immunity. J SYN ORG CHEM JPN 2012. [DOI: 10.5059/yukigoseikyokaishi.70.113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Aikawa JI, Matsuo I, Ito Y. In vitro mannose trimming property of human ER α-1,2 mannosidase I. Glycoconj J 2011; 29:35-45. [PMID: 22160784 DOI: 10.1007/s10719-011-9362-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 11/13/2011] [Accepted: 11/16/2011] [Indexed: 12/31/2022]
Abstract
Endoplasmic reticulum α-1,2 mannosidase I (ERManI) is an enzyme, which removes α(1-2) linked mannoses from asparagine-linked oligosaccharides on glycoproteins in the endoplasmic reticulum (ER). ERManI preferentially removes one α(1-2) linked mannose from B-chain of Man(9)GlcNAc(2). When glycoproteins fail to achieve properly folding, increased removal of α(1-2) linked mannoses on their oligosaccharides is induced and leads them to be disposed and degraded by ER-associated degradation pathway. However, it is still inconclusive whether accelerated removal of α(1-2) linked mannoses on those glycoproteins is catalyzed by the α-1,2 mannosidase I, proteins similar to mannosidase I [e.g. ER degradation-enhancing α-1,2 mannosidase-like protein (EDEM)], or both of them. Therefore, to approach this issue, we have investigated its in vitro activities using various oligosaccharides and glycoproteins as substrates. A recombinant form of human ERManI (hERManI) was prepared by using Escherichia coli. First, the enzyme generated Man(6)GlcNAc(2)-PA and Man(5)GlcNAc(2)-PA from 100 μM Man(9)GlcNAc(2)-PA after a one-hour reaction. Second, we have exposed bovine thyroglobulin and soybean agglutinin to denaturing conditions, e.g. 8 M urea, and used those glycoproteins as substrates. Sugar moieties were released from the reactant by PNGase F and their structures and amounts were elucidated by HPLC analysis. Intriguingly, the enzyme was shown to remove mannoses from bovine thyroglobulin and soybean agglutinin to larger extents when they were exposed to a denaturant. Therefore, our results suggested that hERManI could recognize tertiary and/or quaternary structures of glycoproteins and remove more α-1,2 linked mannoses from misfolded glycoproteins in living cells.
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Affiliation(s)
- Jun-ichi Aikawa
- RIKEN Advanced Science Institute, Hirosawa, Wako, Saitama, Japan.
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Amin MN, Huang W, Mizanur RM, Wang LX. Convergent synthesis of homogeneous Glc1Man9GlcNAc2-protein and derivatives as ligands of molecular chaperones in protein quality control. J Am Chem Soc 2011; 133:14404-17. [PMID: 21819116 DOI: 10.1021/ja204831z] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A detailed understanding of the molecular mechanism of chaperone-assisted protein quality control is often hampered by the lack of well-defined homogeneous glycoprotein probes. We describe here a highly convergent chemoenzymatic synthesis of the monoglucosylated glycoforms of bovine ribonuclease (RNase) as specific ligands of lectin-like chaperones calnexin (CNX) and calreticulin (CRT) that are known to recognize the monoglucosylated high-mannose oligosaccharide component of glycoproteins in protein folding. The synthesis of a selectively modified glycoform Gal(1)Glc(1)Man(9)GlcNAc(2)-RNase was accomplished by chemical synthesis of a large N-glycan oxazoline and its subsequent enzymatic ligation to GlcNAc-RNase under the catalysis of a glycosynthase. Selective removal of the terminal galactose by a β-galactosidase gave the Glc(1)Man(9)GlcNAc(2)-RNase glycoform in excellent yield. CD spectroscopic analysis and RNA-hydrolyzing assay indicated that the synthetic RNase glycoforms maintained essentially the same global conformations and were fully active as the natural bovine ribonuclease B. SPR binding studies revealed that the Glc(1)Man(9)GlcNAc(2)-RNase had high affinity to lectin CRT, while the synthetic Man(9)GlcNAc(2)-RNase glycoform and natural RNase B did not show CRT-binding activity. These results confirmed the essential role of the glucose moiety in the chaperone molecular recognition. Interestingly, the galactose-masked glycoform Gal(1)Glc(1)Man(9)GlcNAc(2)-RNase also showed significant affinity to lectin CRT, suggesting that a galactose β-1,4-linked to the key glucose moiety does not significantly block the lectin binding. These synthetic homogeneous glycoprotein probes should be valuable for a detailed mechanistic study on how molecular chaperones work in concert to distinguish between misfolded and folded glycoproteins in the protein quality control cycle.
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Affiliation(s)
- Mohammed N Amin
- Institute of Human Virology, Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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Wang LX. The Amazing Transglycosylation Activity of Endo-β-N-acetylglucosaminidases. TRENDS GLYCOSCI GLYC 2011; 23:33-52. [PMID: 25309039 DOI: 10.4052/tigg.23.33] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Major advances have been made in exploring the transglycosylation activity of endo-β-N-acetylglucosaminidases (ENGases) for synthetic purpose. The exploration of synthetic sugar oxazolines as donor substrates for the ENGase-catalyzed transglycosylation has expanded the substrate availability and significantly enhanced the overall transglycosylation efficiency. On the other hand, site-directed mutagenesis in combination with activity screening has led to the discovery of the first generation ENGase-based glycosynthases that can use highly active sugar oxazolines as substrates for transglycosylation but lack hydrolytic activity on the ground-state products. ENGases have shown amazing flexibility in transglycosylation and possess much broader substrate specificity than previously thought. Now the ENGase-based chemoenzymatic method has been extended to the synthesis of a range of complex carbohydrates, including homogeneous glycopeptides, glycoproteins carrying well-defined glycans, novel oligosaccharide clusters, unusually glycosylated natural products, and even polysaccharides. This article highlights recent advances related to ENGase-catalyzed transglycosylation with a focus on their synthetic potential.
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Affiliation(s)
- Lai-Xi Wang
- Institute of Human Virology and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA, Tel: 410-706-4982
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Li Y, Roy B, Liu X. New insight on 2-naphthylmethyl (NAP) ether as a protecting group in carbohydrate synthesis: a divergent approach towards a high-mannose type oligosaccharide library. Chem Commun (Camb) 2011; 47:8952-4. [DOI: 10.1039/c1cc13264d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Miyagawa A, Totani K, Matsuo I, Ito Y. Promiscuous activity of ER glucosidase II discovered through donor specificity analysis of UGGT. Biochem Biophys Res Commun 2010; 403:322-8. [PMID: 21075077 DOI: 10.1016/j.bbrc.2010.11.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Abstract
In glycoprotein quality control system in the endoplasmic reticulum (ER), UGGT (UDP-glucose:glycoprotein glucosyltransferase) and glucosidase II (G-II) play key roles. UGGT serves as a glycoprotein folding sensor by virtue of its unique specificity to glucosylate glycoproteins at incompletely folded stage. By using various UDP-Glc analogues, we first analyzed donor specificity of UGGT, which was proven to be rather narrow. However, marginal activity was observed with UDP-galactose and UDP-glucuronic acid as well as with 3-, 4- and 6-deoxy glucose analogues to give corresponding transfer products. Intriguingly, G-II smoothly converted all of them back to Man(9)GlcNAc(2), providing an indication that G-II has a promiscuous activity as a broad specificity hexosidase.
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Affiliation(s)
- Atsushi Miyagawa
- RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan.
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Ishiwata A, Lee YJ, Ito Y. Recent advances in stereoselective glycosylation through intramolecular aglycon delivery. Org Biomol Chem 2010; 8:3596-608. [DOI: 10.1039/c004281a] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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