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Abstract
Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of─among others─biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein-ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Maurits A. den Boer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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2
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St-Gelais J, Denavit V, Giguère D. Efficient synthesis of a galectin inhibitor clinical candidate (TD139) using a Payne rearrangement/azidation reaction cascade. Org Biomol Chem 2021; 18:3903-3907. [PMID: 32400847 DOI: 10.1039/d0ob00910e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Selective galectin inhibitors are valuable research tools and could also be used as drug candidates. In that context, TD139, a thiodigalactoside galectin-3 inhibitor, is currently being evaluated clinically for the treatment of idiopathic pulmonary fibrosis. Herein, we describe a new strategy for the preparation of TD139. Starting from inexpensive levoglucosan, we used a rarely employed reaction cascade: Payne rearrangement/azidation process leading to 3-azido-galactopyranose. The latter intermediate was efficiently converted into TD139 in a few simple and practical steps.
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Affiliation(s)
- Jacob St-Gelais
- Département de Chimie, 1045 av. De la Médecine, Université Laval, GlycoNet, Québec City, Qc, Canada G1V 0A6.
| | - Vincent Denavit
- Département de Chimie, 1045 av. De la Médecine, Université Laval, GlycoNet, Québec City, Qc, Canada G1V 0A6.
| | - Denis Giguère
- Département de Chimie, 1045 av. De la Médecine, Université Laval, GlycoNet, Québec City, Qc, Canada G1V 0A6.
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3
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Flügge F, Peters T. Insights into Allosteric Control of Human Blood Group A and B Glycosyltransferases from Dynamic NMR. ChemistryOpen 2019; 8:760-769. [PMID: 31289712 PMCID: PMC6591795 DOI: 10.1002/open.201900116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/03/2019] [Indexed: 12/25/2022] Open
Abstract
Human blood group A and B glycosyltransferases (GTA, GTB) are retaining glycosyltransferases, requiring a catalytic mechanism that conserves the anomeric configuration of the hexopyranose moiety of the donor substrate (UDP-GalNAc, UDP-Gal). Previous studies have shown that GTA and GTB cycle through structurally distinct states during catalysis. Here, we link binding and release of substrates, substrate-analogs, and products to transitions between open, semi-closed, and closed states of the enzymes. Methyl TROSY based titration experiments in combination with zz-exchange experiments uncover dramatic changes of binding kinetics associated with allosteric interactions between donor-type and acceptor-type ligands. Taken together, this highlights how allosteric control of on- and off-rates correlates with conformational changes, driving catalysis to completion.
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Affiliation(s)
- Friedemann Flügge
- Institute of Chemistry and MetabolomicsUniversity of Lübeck23562LübeckGermany
| | - Thomas Peters
- Institute of Chemistry and MetabolomicsUniversity of Lübeck23562LübeckGermany
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4
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Gagnon SML, Legg MSG, Sindhuwinata N, Letts JA, Johal AR, Schuman B, Borisova SN, Palcic MM, Peters T, Evans SV. High-resolution crystal structures and STD NMR mapping of human ABO(H) blood group glycosyltransferases in complex with trisaccharide reaction products suggest a molecular basis for product release. Glycobiology 2018; 27:966-977. [PMID: 28575295 DOI: 10.1093/glycob/cwx053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/31/2017] [Indexed: 11/12/2022] Open
Abstract
The human ABO(H) blood group A- and B-synthesizing glycosyltransferases GTA and GTB have been structurally characterized to high resolution in complex with their respective trisaccharide antigen products. These findings are particularly timely and relevant given the dearth of glycosyltransferase structures collected in complex with their saccharide reaction products. GTA and GTB utilize the same acceptor substrates, oligosaccharides terminating with α-l-Fucp-(1→2)-β-d-Galp-OR (where R is a glycolipid or glycoprotein), but use distinct UDP donor sugars, UDP-N-acetylgalactosamine and UDP-galactose, to generate the blood group A (α-l-Fucp-(1→2)[α-d-GalNAcp-(1→3)]-β-d-Galp-OR) and blood group B (α-l-Fucp-(1→2)[α-d-Galp-(1→3)]-β-d-Galp-OR) determinant structures, respectively. Structures of GTA and GTB in complex with their respective trisaccharide products reveal a conflict between the transferred sugar monosaccharide and the β-phosphate of the UDP donor. Mapping of the binding epitopes by saturation transfer difference NMR measurements yielded data consistent with the X-ray structural results. Taken together these data suggest a mechanism of product release where monosaccharide transfer to the H-antigen acceptor induces active site disorder and ejection of the UDP leaving group prior to trisaccharide egress.
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Affiliation(s)
- Susannah M L Gagnon
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Max S G Legg
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Nora Sindhuwinata
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - James A Letts
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Asha R Johal
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Brock Schuman
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Svetlana N Borisova
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Monica M Palcic
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6.,Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Thomas Peters
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Stephen V Evans
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
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5
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Weissbach S, Flügge F, Peters T. Substrate Binding Drives Active-Site Closing of Human Blood Group B Galactosyltransferase as Revealed by Hot-Spot Labeling and NMR Spectroscopy Experiments. Chembiochem 2018; 19:970-978. [PMID: 29457687 DOI: 10.1002/cbic.201800019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Indexed: 11/05/2022]
Abstract
Crystallography has shown that human blood group A (GTA) and B (GTB) glycosyltransferases undergo transitions between "open", "semiclosed", and "closed" conformations upon substrate binding. However, the timescales of the corresponding conformational reorientations are unknown. Crystal structures show that the Trp and Met residues are located at "conformational hot spots" of the enzymes. Therefore, we utilized 15 N side-chain labeling of Trp residues and 13 C-methyl labeling of Met residues to study substrate-induced conformational transitions of GTB. Chemical-shift perturbations (CSPs) of Met and Trp residues in direct contact with substrate ligands reflect binding kinetics, whereas the CSPs of Met and Trp residues at remote sites reflect conformational changes of the enzyme upon substrate binding. Acceptor binding is fast on the chemical-shift timescale with rather small CSPs in the range of less than approximately 20 Hz. Donor binding matches the intermediate exchange regime to yield an estimate for exchange rate constants of approximately 200-300 Hz. Donor or acceptor binding to GTB saturated with acceptor or donor substrate, respectively, is slow (<10 Hz), as are coupled protein motions, reflecting mutual allosteric control of donor and acceptor binding. Remote CSPs suggest that substrate binding drives the enzyme into the closed state required for catalysis. These findings should contribute to better understanding of the mechanism of glycosyl transfer of GTA and GTB.
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Affiliation(s)
- Sophie Weissbach
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Friedemann Flügge
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Thomas Peters
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
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6
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Flügge F, Peters T. Complete assignment of Ala, Ile, Leu, Met and Val methyl groups of human blood group A and B glycosyltransferases using lanthanide-induced pseudocontact shifts and methyl-methyl NOESY. JOURNAL OF BIOMOLECULAR NMR 2018; 70:245-259. [PMID: 29700756 DOI: 10.1007/s10858-018-0183-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/21/2018] [Indexed: 05/05/2023]
Abstract
Human blood group A and B glycosyltransferases (GTA, GTB) are highly homologous glycosyltransferases. A number of high-resolution crystal structures is available showing that these enzymes convert from an open conformation into a catalytically active closed conformation upon substrate binding. However, the mechanism of glycosyltransfer is still under debate, and the precise nature as well as the time scales of conformational transitions are unknown. NMR offers a variety of experiments to shine more light on these unresolved questions. Therefore, in a first step we have assigned all methyl resonance signals in MILVA labeled samples of GTA and GTB, still a challenging task for 70 kDa homodimeric proteins. Assignments were obtained from methyl-methyl NOESY experiments, and from measurements of lanthanide-induced pseudocontact shifts (PCS) using high resolution crystal structures as templates. PCSs and chemical shift perturbations, induced by substrate analogue binding, suggest that the fully closed state is not adopted in the presence of lanthanide ions.
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Affiliation(s)
- Friedemann Flügge
- Institute for Chemistry and Metabolomics, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Thomas Peters
- Institute for Chemistry and Metabolomics, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
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7
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Grimm LL, Weissbach S, Flügge F, Begemann N, Palcic MM, Peters T. Protein NMR Studies of Substrate Binding to Human Blood Group A and B Glycosyltransferases. Chembiochem 2017; 18:1260-1269. [PMID: 28256109 DOI: 10.1002/cbic.201700025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Indexed: 12/31/2022]
Abstract
Donor and acceptor substrate binding to human blood group A and B glycosyltransferases (GTA, GTB) has been studied by a variety of protein NMR experiments. Prior crystallographic studies had shown these enzymes to adopt an open conformation in the absence of substrates. Binding either of the donor substrate UDP-Gal or of UDP induces a semiclosed conformation. In the presence of both donor and acceptor substrates, the enzymes shift towards a closed conformation with ordering of an internal loop and the C-terminal residues, which then completely cover the donor-binding pocket. Chemical-shift titrations of uniformly 2 H,15 N-labeled GTA or GTB with UDP affected about 20 % of all crosspeaks in 1 H,15 N TROSY-HSQC spectra, reflecting substantial plasticity of the enzymes. On the other hand, it is this conformational flexibility that impedes NH backbone assignments. Chemical-shift-perturbation experiments with δ1-[13 C]methyl-Ile-labeled samples revealed two Ile residues-Ile123 at the bottom of the UDP binding pocket, and Ile192 as part of the internal loop-that were significantly disturbed upon stepwise addition of UDP and H-disaccharide, also revealing long-range perturbations. Finally, methyl TROSY-based relaxation dispersion experiments do not reveal micro- to millisecond timescale motions. Although this study reveals substantial conformational plasticity of GTA and GTB, the matter of how binding of substrates shifts the enzymes into catalytically competent states remains enigmatic.
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Affiliation(s)
- Lena Lisbeth Grimm
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Sophie Weissbach
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Friedemann Flügge
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Nora Begemann
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Monica M Palcic
- Department of Biochemistry and Microbiology, University of Victoria, P. O. Box 3800, STN CSC, Victoria, BC, V8W 3P6, Canada
| | - Thomas Peters
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
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8
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Arend P. ABO (histo) blood group phenotype development and human reproduction as they relate to ancestral IgM formation: A hypothesis. Immunobiology 2016; 221:116-27. [DOI: 10.1016/j.imbio.2015.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 03/18/2015] [Accepted: 07/07/2015] [Indexed: 10/23/2022]
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9
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Wagner GK, Pesnot T, Palcic MM, Jørgensen R. Novel UDP-GalNAc Derivative Structures Provide Insight into the Donor Specificity of Human Blood Group Glycosyltransferase. J Biol Chem 2015; 290:31162-72. [PMID: 26527682 PMCID: PMC4692239 DOI: 10.1074/jbc.m115.681262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Indexed: 01/17/2023] Open
Abstract
Two closely related glycosyltransferases are responsible for the final step of the biosynthesis of ABO(H) human blood group A and B antigens. The two enzymes differ by only four amino acid residues, which determine whether the enzymes transfer GalNAc from UDP-GalNAc or Gal from UDP-Gal to the H-antigen acceptor. The enzymes belong to the class of GT-A folded enzymes, grouped as GT6 in the CAZy database, and are characterized by a single domain with a metal dependent retaining reaction mechanism. However, the exact role of the four amino acid residues in the specificity of the enzymes is still unresolved. In this study, we report the first structural information of a dual specificity cis-AB blood group glycosyltransferase in complex with a synthetic UDP-GalNAc derivative. Interestingly, the GalNAc moiety adopts an unusual yet catalytically productive conformation in the binding pocket, which is different from the "tucked under" conformation previously observed for the UDP-Gal donor. In addition, we show that this UDP-GalNAc derivative in complex with the H-antigen acceptor provokes the same unusual binding pocket closure as seen for the corresponding UDP-Gal derivative. Despite this, the two derivatives show vastly different kinetic properties. Our results provide a important structural insight into the donor substrate specificity and utilization in blood group biosynthesis, which can very likely be exploited for the development of new glycosyltransferase inhibitors and probes.
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Affiliation(s)
- Gerd K Wagner
- From the Department of Chemistry, King's College London, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Thomas Pesnot
- the University of East Anglia, School of Pharmacy, Norwich NR47TJ, England, and
| | - Monica M Palcic
- the Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
| | - Rene Jørgensen
- the Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
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10
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Gagnon SML, Meloncelli PJ, Zheng RB, Haji-Ghassemi O, Johal AR, Borisova SN, Lowary TL, Evans SV. High Resolution Structures of the Human ABO(H) Blood Group Enzymes in Complex with Donor Analogs Reveal That the Enzymes Utilize Multiple Donor Conformations to Bind Substrates in a Stepwise Manner. J Biol Chem 2015; 290:27040-27052. [PMID: 26374898 DOI: 10.1074/jbc.m115.682401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Indexed: 11/06/2022] Open
Abstract
Homologous glycosyltransferases α-(1→3)-N-acetylgalactosaminyltransferase (GTA) and α-(1→3)-galactosyltransferase (GTB) catalyze the final step in ABO(H) blood group A and B antigen synthesis through sugar transfer from activated donor to the H antigen acceptor. These enzymes have a GT-A fold type with characteristic mobile polypeptide loops that cover the active site upon substrate binding and, despite intense investigation, many aspects of substrate specificity and catalysis remain unclear. The structures of GTA, GTB, and their chimeras have been determined to between 1.55 and 1.39 Å resolution in complex with natural donors UDP-Gal, UDP-Glc and, in an attempt to overcome one of the common problems associated with three-dimensional studies, the non-hydrolyzable donor analog UDP-phosphono-galactose (UDP-C-Gal). Whereas the uracil moieties of the donors are observed to maintain a constant location, the sugar moieties lie in four distinct conformations, varying from extended to the "tucked under" conformation associated with catalysis, each stabilized by different hydrogen bonding partners with the enzyme. Further, several structures show clear evidence that the donor sugar is disordered over two of the observed conformations and so provide evidence for stepwise insertion into the active site. Although the natural donors can both assume the tucked under conformation in complex with enzyme, UDP-C-Gal cannot. Whereas UDP-C-Gal was designed to be "isosteric" with natural donor, the small differences in structure imposed by changing the epimeric oxygen atom to carbon appear to render the enzyme incapable of binding the analog in the active conformation and so preclude its use as a substrate mimic in GTA and GTB.
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Affiliation(s)
- Susannah M L Gagnon
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Peter J Meloncelli
- the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ruixiang B Zheng
- the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Omid Haji-Ghassemi
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Asha R Johal
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Svetlana N Borisova
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Todd L Lowary
- the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Stephen V Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and.
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Kitova EN, El-Hawiet A, Klassen JS. Screening carbohydrate libraries for protein interactions using the direct ESI-MS assay. Applications to libraries of unknown concentration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1908-16. [PMID: 25135608 DOI: 10.1007/s13361-014-0964-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/02/2014] [Accepted: 07/04/2014] [Indexed: 05/22/2023]
Abstract
A semiquantitative electrospray ionization mass spectrometry (ESI-MS) binding assay suitable for analyzing mixtures of oligosaccharides, at unknown concentrations, for interactions with target proteins is described. The assay relies on the differences in the ratio of the relative abundances of the ligand-bound and free protein ions measured by ESI-MS at two or more initial protein concentrations to distinguish low affinity (≤10(3) M(-1)) ligands from moderate and high affinity (>10(5) M(-1)) ligands present in the library and to rank their affinities. Control experiments were performed on solutions of a single chain antibody and a mixture of synthetic oligosaccharides, with known affinities, in the absence and presence of a 40-component carbohydrate library to demonstrate the implementation and reliability of the assay. The application of the assay for screening natural libraries of carbohydrates against proteins is also demonstrated using mixtures of human milk oligosaccharides, isolated from breast milk, and fragments of a bacterial toxin and human galectin 3.
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Affiliation(s)
- Elena N Kitova
- Alberta Glycomics Center and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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12
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Brockhausen I. Crossroads between Bacterial and Mammalian Glycosyltransferases. Front Immunol 2014; 5:492. [PMID: 25368613 PMCID: PMC4202792 DOI: 10.3389/fimmu.2014.00492] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/23/2014] [Indexed: 11/26/2022] Open
Abstract
Bacterial glycosyltransferases (GT) often synthesize the same glycan linkages as mammalian GT; yet, they usually have very little sequence identity. Nevertheless, enzymatic properties, folding, substrate specificities, and catalytic mechanisms of these enzyme proteins may have significant similarity. Thus, bacterial GT can be utilized for the enzymatic synthesis of both bacterial and mammalian types of complex glycan structures. A comparison is made here between mammalian and bacterial enzymes that synthesize epitopes found in mammalian glycoproteins, and those found in the O antigens of Gram-negative bacteria. These epitopes include Thomsen–Friedenreich (TF or T) antigen, blood group O, A, and B, type 1 and 2 chains, Lewis antigens, sialylated and fucosylated structures, and polysialic acids. Many different approaches can be taken to investigate the substrate binding and catalytic mechanisms of GT, including crystal structure analyses, mutations, comparison of amino acid sequences, NMR, and mass spectrometry. Knowledge of the protein structures and functions helps to design GT for specific glycan synthesis and to develop inhibitors. The goals are to develop new strategies to reduce bacterial virulence and to synthesize vaccines and other biologically active glycan structures.
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Affiliation(s)
- Inka Brockhausen
- Department of Medicine, Queen's University , Kingston, ON , Canada ; Department of Biomedical and Molecular Sciences, Queen's University , Kingston, ON , Canada
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13
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Han L, Kitova EN, Tan M, Jiang X, Pluvinage B, Boraston AB, Klassen JS. Affinities of human histo-blood group antigens for norovirus capsid protein complexes. Glycobiology 2014; 25:170-80. [PMID: 25395406 DOI: 10.1093/glycob/cwu100] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The binding profiles of many human noroviruses (huNoVs) for human histo-blood group antigens have been characterized. However, quantitative-binding data for these important virus-host interactions are lacking. Here, we report on the intrinsic (per binding site) affinities of HBGA oligosaccharides for the huNoV VA387 virus-like particles (VLPs) and the associated subviral P particles measured using electrospray ionization mass spectrometry. The affinities of 13 HBGA oligosaccharides, containing A, B and H epitopes, with variable sizes (disaccharide to tetrasaccharide) and different precursor chain types (types 1, 2, 3, 5 and 6), were measured for the P particle, while the affinities of the A and B trisaccharides and A and B type 6 tetrasaccharides for the VLP were determined. The intrinsic affinities of the HBGA oligosaccharides for the P particle range from 500 to 2300 M(-1), while those of the A and B trisaccharides and the A and B type 6 tetrasaccharides for the VLP range from 1000 to 4000 M(-1). Comparison of these binding data with those measured previously for the corresponding P dimer reveals that the HBGA oligosaccharides tested exhibit similar intrinsic affinities for the P dimer and P particle. The intrinsic affinities for the VLP are consistently higher than those measured for the P particle, but within a factor of three. While the cause of the subtle differences in HBGA oligosaccharide affinities for the P dimer and P particle and those for the VLP remains unknown, the present data support the use of P dimers or P particles as surrogates to the VLP for huNoV-receptor-binding studies.
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Affiliation(s)
- Ling Han
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Elena N Kitova
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Ming Tan
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Xi Jiang
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Benjamin Pluvinage
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6
| | - John S Klassen
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2
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14
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Storry JR, Condon J, Hult AK, Harrison A, Jørgensen R, Olsson ML. An age-dependent ABO discrepancy between mother and baby reveals a novelAweakallele. Transfusion 2014; 55:422-6. [DOI: 10.1111/trf.12840] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Jill R. Storry
- Division of Hematology and Transfusion Medicine; Department of Laboratory Medicine; Lund University; Lund Sweden
- Clinical Immunology and Transfusion Medicine; Laboratory Medicine; Office of Medical Services; Lund Sweden
| | - Jennifer Condon
- Australian Red Cross Blood Service; Melbourne Victoria Australia
| | - Annika K. Hult
- Division of Hematology and Transfusion Medicine; Department of Laboratory Medicine; Lund University; Lund Sweden
- Clinical Immunology and Transfusion Medicine; Laboratory Medicine; Office of Medical Services; Lund Sweden
| | | | | | - Martin L. Olsson
- Division of Hematology and Transfusion Medicine; Department of Laboratory Medicine; Lund University; Lund Sweden
- Clinical Immunology and Transfusion Medicine; Laboratory Medicine; Office of Medical Services; Lund Sweden
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15
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Naegeli A, Michaud G, Schubert M, Lin CW, Lizak C, Darbre T, Reymond JL, Aebi M. Substrate specificity of cytoplasmic N-glycosyltransferase. J Biol Chem 2014; 289:24521-32. [PMID: 24962585 DOI: 10.1074/jbc.m114.579326] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
N-Linked protein glycosylation is a very common post-translational modification that can be found in all kingdoms of life. The classical, highly conserved pathway entails the assembly of a lipid-linked oligosaccharide and its transfer to an asparagine residue in the sequon NX(S/T) of a secreted protein by the integral membrane protein oligosaccharyltransferase. A few species in the class of γ-proteobacteria encode a cytoplasmic N-glycosylation system mediated by a soluble N-glycosyltransferase (NGT). This enzyme uses nucleotide-activated sugars to modify asparagine residues with single monosaccharides. As these enzymes are not related to oligosaccharyltransferase, NGTs constitute a novel class of N-glycosylation catalyzing enzymes. To characterize the NGT-catalyzed reaction, we developed a sensitive and quantitative in vitro assay based on HPLC separation and quantification of fluorescently labeled substrate peptides. With this assay we were able to directly quantify glycopeptide formation by Actinobacillus pleuropneumoniae NGT and determine its substrate specificities: NGT turns over a number of different sugar donor substrates and allows for activation by both UDP and GDP. Quantitative analysis of peptide substrate turnover demonstrated a strikingly similar specificity as the classical, oligosaccharyltransferase-catalyzed N-glycosylation, with NX(S/T) sequons being the optimal NGT substrates.
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Affiliation(s)
- Andreas Naegeli
- From the Department of Biology, Institute of Microbiology, ETH Zurich, CH-8093 Zurich
| | - Gaëlle Michaud
- the Department of Chemistry and Biochemistry, University of Berne, 3012 Berne, and
| | - Mario Schubert
- the Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Chia-Wei Lin
- From the Department of Biology, Institute of Microbiology, ETH Zurich, CH-8093 Zurich
| | - Christian Lizak
- the Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Tamis Darbre
- the Department of Chemistry and Biochemistry, University of Berne, 3012 Berne, and
| | - Jean-Louis Reymond
- the Department of Chemistry and Biochemistry, University of Berne, 3012 Berne, and
| | - Markus Aebi
- From the Department of Biology, Institute of Microbiology, ETH Zurich, CH-8093 Zurich,
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16
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Lin H, Kitova EN, Klassen JS. Measuring positive cooperativity using the direct ESI-MS assay. Cholera toxin B subunit homopentamer binding to GM1 pentasaccharide. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:104-110. [PMID: 24122305 DOI: 10.1007/s13361-013-0751-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
Direct electrospray ionization mass spectrometry (ESI-MS) assay was used to investigate the stepwise binding of the GM1 pentasaccharide β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp (GM1os) to the cholera toxin B subunit homopentamer (CTB5) and to establish conclusively whether GM1os binding is cooperative. Apparent association constants were measured for the stepwise addition of one to five GM1os to CTB5 at pH 6.9 and 22 °C. The intrinsic association constant, which was established from the apparent association constant for the addition of a single GM1os to CTB5, was found to be (3.2 ± 0.2) × 106 M(–1). This is in reasonable agreement with the reported value of (6.4 ± 0.3) × 106 M(–1), which was measured at pH 7.4 and 25 °C using isothermal titration calorimetry (ITC). Analysis of the apparent association constants provides direct and unambiguous evidence that GM1os binding exhibits small positive cooperativity. Binding was found to be sensitive to the number of ligand-bound nearest neighbor subunits, with the affinities enhanced by a factor of 1.7 and 2.9 when binding occurs next to one or two ligand-bound subunits, respectively. These findings, which provide quantitative support for the binding model proposed by Homans and coworkers [14], highlight the unique strengths of the direct ESI-MS assay for measuring cooperative ligand binding.
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17
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Johal AR, Blackler RJ, Alfaro JA, Schuman B, Borisova S, Evans SV. pH-induced conformational changes in human ABO(H) blood group glycosyltransferases confirm the importance of electrostatic interactions in the formation of the semi-closed state. Glycobiology 2013; 24:237-46. [PMID: 24265507 DOI: 10.1093/glycob/cwt098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The homologous human ABO(H) A and B blood group glycosyltransferases GTA and GTB have two mobile polypeptide loops surrounding their active sites that serve to allow substrate access and product egress and to recognize and sequester substrates for catalysis. Previous studies have established that these enzymes can move from the "open" state to the "semi-closed" then "closed" states in response to addition of a substrate. The contribution of electrostatic interactions to these conformational changes has now been demonstrated by the determination at various pH of the structures of GTA, GTB and the chimeric enzyme ABBA. At near-neutral pH, GTA displays the closed state in which both mobile loops order around the active site, whereas ABBA and GTB display the open state. At low pH, the apparent protonation of the DXD motif in GTA leads to the expulsion of the donor analog to yield the open state, whereas at high pH, both ABBA and GTB form the semi-closed state in which the first mobile loop becomes an ordered α-helix. Step-wise deprotonation of GTB in increments of 0.5 between pH 6.5 and 10.0 shows that helix ordering is gradual, which indicates that the formation of the semi-closed state is dependent on electrostatic forces consistent with the binding of substrate. Spectropolarimetric studies of the corresponding stand-alone peptide in solution reveal no tendency toward helix formation from pH 7.0 to 10.0, which shows that pH-dependent stability is a product of the larger protein environment and underlines the importance of substrate in active site ordering.
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Affiliation(s)
- Asha R Johal
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6
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18
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Fiebig T, Berti F, Freiberger F, Pinto V, Claus H, Romano MR, Proietti D, Brogioni B, Stummeyer K, Berger M, Vogel U, Costantino P, Gerardy-Schahn R. Functional expression of the capsule polymerase of Neisseria meningitidis serogroup X: a new perspective for vaccine development. Glycobiology 2013; 24:150-8. [PMID: 24259400 DOI: 10.1093/glycob/cwt102] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Neisseria meningitidis (Nm) is a leading cause of bacterial meningitis and sepsis. A key feature in pathogenicity is the capsular polysaccharide (CPS) that prevents complement activation and thus supports bacterial survival in the host. Twelve serogroups characterized by immunologically and structurally different CPSs have been identified. Meningococcal CPSs elicit bactericidal antibodies and consequently are used for the development of vaccines. Vaccination against the epidemiologically most relevant serogroups was initially carried out with purified CPS and later followed by conjugate vaccines which consist of CPS covalently linked to a carrier protein. Of increasing importance in the African meningitis belt is NmX for which no vaccine is currently available. Here, we describe the molecular cloning, recombinant expression and purification of the capsule polymerase (CP) of NmX called CsxA. The protein expressed with N- and/or C-terminal epitope tags was soluble and could be purified to near homogeneity. With short oligosaccharide primers derived from the NmX capsular polysaccharide (CPSX), recombinant CsxA produced long polymer chains in vitro that in immunoblots were detected with NmX-specific antibodies. Moreover, the chemical identity of in vitro produced NmX polysaccharides was confirmed by NMR. Besides the demonstration that the previously identified gene csxA encodes the NmX CP CsxA, the data presented in this study pave the way for the use of the recombinant CP as a safe and economic way to generate the CPSX in vaccine developmental programs.
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Affiliation(s)
- Timm Fiebig
- Institute for Cellular Chemistry, Hannover Medical School, Carl-Neuberg Str. 1, 30625 Hannover, Germany
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19
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Lin H, Kitova EN, Klassen JS. Quantifying Protein–Ligand Interactions by Direct Electrospray Ionization-MS Analysis: Evidence of Nonuniform Response Factors Induced by High Molecular Weight Molecules and Complexes. Anal Chem 2013; 85:8919-22. [DOI: 10.1021/ac401936x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hong Lin
- Department
of Chemistry and
Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Elena N. Kitova
- Department
of Chemistry and
Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - John S. Klassen
- Department
of Chemistry and
Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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20
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Sindhuwinata N, Grimm LL, Weißbach S, Zinn S, Munoz E, Palcic MM, Peters T. Thermodynamic Signature of Substrates and Substrate Analogs Binding to Human Blood Group B Galactosyltransferase from Isothermal Titration Calorimetry Experiments. Biopolymers 2013; 99:784-95. [DOI: 10.1002/bip.22297] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 05/26/2013] [Accepted: 05/28/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Nora Sindhuwinata
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Luebeck; Ratzeburger Allee 160; 23562; Luebeck; Germany
| | - Lena L. Grimm
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Luebeck; Ratzeburger Allee 160; 23562; Luebeck; Germany
| | - Sophie Weißbach
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Luebeck; Ratzeburger Allee 160; 23562; Luebeck; Germany
| | - Sabrina Zinn
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Luebeck; Ratzeburger Allee 160; 23562; Luebeck; Germany
| | - Eva Munoz
- Department of Organic Chemistry; University of Santiago de Compostela, Avenida de las Ciencias; S.N. 15782; Santiago de Compostela; Spain
| | - Monica M. Palcic
- Carlsberg Laboratory; Gamle Carlsberg Vej10; DK-1799; Copenhagen V.; Denmark
| | - Thomas Peters
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Luebeck; Ratzeburger Allee 160; 23562; Luebeck; Germany
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21
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Gómez H, Lluch JM, Masgrau L. Substrate-Assisted and Nucleophilically Assisted Catalysis in Bovine α1,3-Galactosyltransferase. Mechanistic Implications for Retaining Glycosyltransferases. J Am Chem Soc 2013; 135:7053-63. [DOI: 10.1021/ja4024447] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hansel Gómez
- Institut
de Biotecnologia i de Biomedicina and †Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - José M. Lluch
- Institut
de Biotecnologia i de Biomedicina and †Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Laura Masgrau
- Institut
de Biotecnologia i de Biomedicina and †Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
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22
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Sugiarto G, Lau K, Qu J, Li Y, Lim S, Mu S, Ames JB, Fisher AJ, Chen X. A sialyltransferase mutant with decreased donor hydrolysis and reduced sialidase activities for directly sialylating LewisX. ACS Chem Biol 2012; 7:1232-40. [PMID: 22583967 DOI: 10.1021/cb300125k] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Glycosyltransferases are important catalysts for enzymatic and chemoenzymatic synthesis of complex carbohydrates and glycoconjugates. The glycosylation efficiencies of wild-type glycosyltransferases vary considerably when different acceptor substrates are used. Using a multifunctional Pasteurella multocida sialyltransferase 1 (PmST1) as an example, we show here that the sugar nucleotide donor hydrolysis activity of glycosyltransferases contributes significantly to the low yield of glycosylation when a poor acceptor substrate is used. With a protein crystal structure-based rational design, we generated a single mutant (PmST1 M144D) with decreased donor hydrolysis activity without significantly affecting its α2-3-sialylation activity when a poor fucose-containing acceptor substrate was used. The single mutant also has a drastically decreased α2-3-sialidase activity. X-ray and NMR structural studies revealed that unlike the wild-type PmST1, which changes to a closed conformation once a donor binds, the M144D mutant structure adopts an open conformation even in the presence of the donor substrate. The PmST1 M144D mutant with decreased donor hydrolysis and reduced sialidase activity has been used as a powerful catalyst for efficient chemoenzymatic synthesis of complex sialyl Lewis(x) antigens containing different sialic acid forms. This work sheds new light on the effect of donor hydrolysis activity of glycosyltransferases on glycosyltransferase-catalyzed reactions and provides a novel strategy to improve glycosyltransferase substrate promiscuity by decreasing its donor hydrolysis activity.
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Affiliation(s)
- Go Sugiarto
- Department
of Chemistry and ‡Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue,
Davis, California 95616, United States
| | - Kam Lau
- Department
of Chemistry and ‡Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue,
Davis, California 95616, United States
| | - Jingyao Qu
- Department
of Chemistry and ‡Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue,
Davis, California 95616, United States
| | - Yanhong Li
- Department
of Chemistry and ‡Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue,
Davis, California 95616, United States
| | - Sunghyuk Lim
- Department
of Chemistry and ‡Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue,
Davis, California 95616, United States
| | - Shengmao Mu
- Department
of Chemistry and ‡Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue,
Davis, California 95616, United States
| | - James B. Ames
- Department
of Chemistry and ‡Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue,
Davis, California 95616, United States
| | - Andrew J. Fisher
- Department
of Chemistry and ‡Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue,
Davis, California 95616, United States
| | - Xi Chen
- Department
of Chemistry and ‡Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue,
Davis, California 95616, United States
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23
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El-Hawiet A, Kitova EN, Klassen JS. Quantifying Carbohydrate–Protein Interactions by Electrospray Ionization Mass Spectrometry Analysis. Biochemistry 2012; 51:4244-53. [DOI: 10.1021/bi300436x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amr El-Hawiet
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
| | - Elena N. Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
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24
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El-Hawiet A, Kitova EN, Arutyunov D, Simpson DJ, Szymanski CM, Klassen JS. Quantifying Ligand Binding to Large Protein Complexes Using Electrospray Ionization Mass Spectrometry. Anal Chem 2012; 84:3867-70. [DOI: 10.1021/ac3005082] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amr El-Hawiet
- Alberta
Glycomics Centre and †Department of Chemistry or §Department of Biological Sciences, University of Alberta, Edmonton, Alberta,
Canada T6G 2G2
| | - Elena N. Kitova
- Alberta
Glycomics Centre and †Department of Chemistry or §Department of Biological Sciences, University of Alberta, Edmonton, Alberta,
Canada T6G 2G2
| | - Denis Arutyunov
- Alberta
Glycomics Centre and †Department of Chemistry or §Department of Biological Sciences, University of Alberta, Edmonton, Alberta,
Canada T6G 2G2
| | - David J. Simpson
- Alberta
Glycomics Centre and †Department of Chemistry or §Department of Biological Sciences, University of Alberta, Edmonton, Alberta,
Canada T6G 2G2
| | - Christine M. Szymanski
- Alberta
Glycomics Centre and †Department of Chemistry or §Department of Biological Sciences, University of Alberta, Edmonton, Alberta,
Canada T6G 2G2
| | - John S. Klassen
- Alberta
Glycomics Centre and †Department of Chemistry or §Department of Biological Sciences, University of Alberta, Edmonton, Alberta,
Canada T6G 2G2
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25
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Kitova EN, El-Hawiet A, Schnier PD, Klassen JS. Reliable determinations of protein-ligand interactions by direct ESI-MS measurements. Are we there yet? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:431-41. [PMID: 22270873 DOI: 10.1007/s13361-011-0311-9] [Citation(s) in RCA: 188] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 11/25/2011] [Accepted: 11/29/2011] [Indexed: 05/11/2023]
Abstract
The association-dissociation of noncovalent interactions between protein and ligands, such as other proteins, carbohydrates, lipids, DNA, or small molecules, are critical events in many biological processes. The discovery and characterization of these interactions is essential to a complete understanding of biochemical reactions and pathways and to the design of novel therapeutic agents that may be used to treat a variety of diseases and infections. Over the last 20 y, electrospray ionization mass spectrometry (ESI-MS) has emerged as a versatile tool for the identification and quantification of protein-ligand interactions in vitro. Here, we describe the implementation of the direct ESI-MS assay for the determination of protein-ligand binding stoichiometry and affinity. Additionally, we outline common sources of error encountered with these measurements and various strategies to overcome them. Finally, we comment on some of the outstanding challenges associated with the implementation of the assay and highlight new areas where direct ESI-MS measurements are expected to make significant contributions in the future.
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Affiliation(s)
- Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
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26
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Schaefer K, Albers J, Sindhuwinata N, Peters T, Meyer B. A New Concept for Glycosyltransferase Inhibitors: Nonionic Mimics of the Nucleotide Donor of the Human Blood Group B Galactosyltransferase. Chembiochem 2012; 13:443-50. [DOI: 10.1002/cbic.201100642] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Indexed: 11/06/2022]
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27
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El-Hawiet A, Shoemaker GK, Daneshfar R, Kitova EN, Klassen JS. Applications of a catch and release electrospray ionization mass spectrometry assay for carbohydrate library screening. Anal Chem 2011; 84:50-8. [PMID: 22128847 DOI: 10.1021/ac202760e] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Applications of a catch and release electrospray ionization mass spectrometry (CaR-ESI-MS) assay for screening carbohydrate libraries against target proteins are described. Direct ESI-MS measurements were performed on solutions containing a target protein (a single chain antibody, an antigen binding fragment, or a fragment of a bacterial toxin) and a library of carbohydrates containing multiple specific ligands with affinities in the 10(3) to 10(6) M(-1) range. Ligands with moderate affinity (10(4) to 10(6) M(-1)) were successfully detected from mixtures containing >200 carbohydrates (at concentrations as low as 0.25 μM each). Additionally, the absolute affinities were estimated from the abundance of free and ligand-bound protein ions determined from the ESI mass spectrum. Multiple low affinity ligands (~10(3) M(-1)) were successfully detected in mixtures containing >20 carbohydrates (at concentrations of ~10 μM each). However, identification of specific interactions required the use of the reference protein method to correct the mass spectrum for the occurrence of nonspecific carbohydrate-protein binding during the ESI process. The release of the carbohydrate ligands, as ions, was successfully demonstrated using collision-induced dissociation performed on the deprotonated ions of the protein-carbohydrate complexes. The use of ion mobility separation, performed on deprotonated carbohydrate ions following their release from the complex, allowed for the positive identification of isomeric ligands.
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Affiliation(s)
- Amr El-Hawiet
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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28
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Dybvik AI, Norberg AL, Schute V, Soltwisch J, Peter-Katalinić J, Vårum KM, Eijsink VGH, Dreisewerd K, Mormann M, Sørlie M. Analysis of noncovalent chitinase-chito-oligosaccharide complexes by infrared-matrix assisted laser desorption ionization and nanoelectrospray ionization mass spectrometry. Anal Chem 2011; 83:4030-6. [PMID: 21473578 DOI: 10.1021/ac1031308] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transferring noncovalently bound complexes from the condensed phase into the gas phase represents a challenging task due to weak intermolecular bonds that have to be maintained during the phase transition. Currently, electrospray ionization (ESI) is the standard mass spectrometric (MS) technique to analyze noncovalent complexes. Although infrared matrix-assisted laser desorption ionization (IR-MALDI)-MS also provides particular soft desorption/ionization conditions, this method has so far hardly been applied for the analysis of noncovalent complexes. In this study, we employed IR-MALDI orthogonal time-of-flight (o-TOF)-MS in combination with the liquid matrix glycerol to characterize the specific complex formation of chito-oligosaccharide (CHOS) ligands with two variants of Chitinase A (ChiA) from Serratia marcescens, the inactive E315Q mutant and the active W167A mutant, respectively. The IR-MALDI-o-TOF-MS results were compared to those obtained using nano-ESI-quadrupole (q)-TOF-MS and ultraviolet (UV)-MALDI-o-TOF-MS. Using IR-MALDI-o-TOF-MS, specific noncovalent complexes between ChiA and CHOS were detected with distributions between enzymes with bound oligosaccharides vs free enzymes that were essentially identical to those obtained by nano-ESI-q-TOF-MS. Chitinase-CHOS complexes were not detected when UV-MALDI was employed for desorption/ionization. The results show that IR-MALDI-MS can be a valuable tool for fast and simple screening of noncovalent enzyme-ligand interactions.
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Affiliation(s)
- Anette I Dybvik
- Department of Biotechnology, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, N-7491 Trondheim, Norway
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29
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Liu L, Kitova EN, Klassen JS. Quantifying protein-fatty acid interactions using electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:310-318. [PMID: 21472590 DOI: 10.1007/s13361-010-0032-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 11/08/2010] [Indexed: 05/30/2023]
Abstract
The application of the direct electrospray ionization mass spectrometry (ESI-MS) assay to quantify interactions between bovine β-lactoglobulin (Lg) and a series of fatty acids (FA), CH(3)(CH(2))(x)COOH, where x=6 (caprylic acid, CpA), 8 (capric acid, CA), 10 (lauric acid, LA), 12 (myristic acid, MA), 14 (palmitic acid, PA) and 16 (stearic acid, SA), is described. Control ESI-MS binding measurements performed on the Lg-PA interaction revealed that both the protonated and deprotonated gas phase ions of the (Lg + PA) complex are prone to dissociate in the ion source, which leads to artificially small association constants (K (a)). The addition of imidazole, a stabilizing solution additive, at high concentration (10 mM) increased the relative abundance of (Lg + PA) complex measured by ESI-MS in both positive and negative ion modes. The K(a) value measured in negative ion mode and using sampling conditions that minimize in-source dissociation is in good agreement with a value determined using a competitive fluorescence assay. The K (a) values measured by ESI-MS for the Lg interactions with MA and SA are also consistent with values expected based on the fluorescence measurements. However, the K (a) values measured using optimal sampling conditions in positive ion mode are significantly lower than those measured in negative ion mode for all of the FAs investigated. It is concluded that the protonated gaseous ions of the (Lg + FA) complexes are kinetically less stable than the deprotonated ions. In-source dissociation was significant for the complexes of Lg with the shorter FAs (CpA, CA, and LA) in both modes and, in the case of CpA, no binding could be detected by ESI-MS. The affinities of Lg for CpA, CA, and LA determined using the reference ligand ESI-MS assay, a method for quantifying labile protein-ligand complexes that are prone to in-source dissociation, were found to be in good agreement with reported values.
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Affiliation(s)
- Lan Liu
- Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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30
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Soya N, Fang Y, Palcic MM, Klassen JS. Trapping and characterization of covalent intermediates of mutant retaining glycosyltransferases. Glycobiology 2010; 21:547-52. [PMID: 21098513 DOI: 10.1093/glycob/cwq190] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The enzymatic mechanism by which retaining glycosyltransferases (GTs) transfer monosaccharides with net retention of the anomeric configuration has, so far, resisted elucidation. Here, direct detection of covalent glycosyl-enzyme intermediates for mutants of two model retaining GTs, the human blood group synthesizing α-(1 → 3)-N-acetylgalactosaminyltransferase (GTA) and α-(1 → 3)-galactosyltransferase (GTB) mutants, by mass spectrometry (MS) is reported. Incubation of mutants of GTA or GTB, in which the putative catalytic nucleophile Glu(303) was replaced with Cys (i.e. GTA(E303C) and GTB(E303C)), with their respective donor substrate results in a covalent intermediate. Tandem MS analysis using collision-induced dissociation confirmed Cys(303) as the site of glycosylation. Exposure of the glycosyl-enzyme intermediates to a disaccharide acceptor results in the formation of the corresponding enzymatic trisaccharide products. These findings suggest that the GTA(E303C) and GTB(E303C) mutants may operate by a double-displacement mechanism.
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Affiliation(s)
- Naoto Soya
- Alberta Ingenuity Centre for Carbohydrate Science, Department of Chemistry, University of Alberta, Edmonton, Alta, Canada
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El-Hawiet A, Kitova EN, Liu L, Klassen JS. Quantifying labile protein-ligand interactions using electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1893-1899. [PMID: 20801056 DOI: 10.1016/j.jasms.2010.07.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 07/19/2010] [Accepted: 07/21/2010] [Indexed: 05/29/2023]
Abstract
A new electrospray ionization mass spectrometry (ES-MS) approach for quantifying protein-ligand complexes that are prone to in-source (gas-phase) dissociation is described. The method, referred to here as the reference ligand ES-MS method, is based on the direct ES-MS assay and competitive ligand binding. A reference ligand (L(ref)), which binds specifically to the protein (P), at the same binding site as the ligand (L) of interest, with known affinity and forms a stable protein-ligand complex in the gas phase, is added to the solution. The fraction of P bound to L(ref), which is determined directly from the ES mass spectrum, is sensitive to the fraction of P bound to L in solution and enables the affinity of P for L to be determined. A mathematical framework for the implementation of the method in cases where P has one or two specific ligand binding sites is given. Affinities of two carbohydrate-binding proteins, a single chain fragment of a monoclonal antibody and the lectin concanavalin A, for monosaccharide ligands are reported and the results are shown to agree with values obtained using isothermal titration calorimetry.
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Affiliation(s)
- Amr El-Hawiet
- Alberta Ingenuity Centre for Carbohydrate Science, Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Schuman B, Persson M, Landry RC, Polakowski R, Weadge JT, Seto NOL, Borisova SN, Palcic MM, Evans SV. Cysteine-to-serine mutants dramatically reorder the active site of human ABO(H) blood group B glycosyltransferase without affecting activity: structural insights into cooperative substrate binding. J Mol Biol 2010; 402:399-411. [PMID: 20655926 PMCID: PMC3069981 DOI: 10.1016/j.jmb.2010.07.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 07/15/2010] [Accepted: 07/18/2010] [Indexed: 11/29/2022]
Abstract
A common feature in the structures of GT-A-fold-type glycosyltransferases is a mobile polypeptide loop that has been observed to participate in substrate recognition and enclose the active site upon substrate binding. This is the case for the human ABO(H) blood group B glycosyltransferase GTB, where amino acid residues 177-195 display significantly higher levels of disorder in the unliganded state than in the fully liganded state. Structural studies of mutant enzymes GTB/C80S/C196S and GTB/C80S/C196S/C209S at resolutions ranging from 1.93 to 1.40 A display the opposite trend, where the unliganded structures show nearly complete ordering of the mobile loop residues that is lost upon substrate binding. In the liganded states of the mutant structures, while the UDP moiety of the donor molecule is observed to bind in the expected location, the galactose moiety is observed to bind in a conformation significantly different from that observed for the wild-type chimeric structures. Although this would be expected to impede catalytic turnover, the kinetics of the transfer reaction are largely unaffected. These structures demonstrate that the enzymes bind the donor in a conformation more similar to the dominant solution rotamer and facilitate its gyration into the catalytically competent form. Further, by preventing active-site closure, these structures provide a basis for recently observed cooperativity in substrate binding. Finally, the mutation of C80S introduces a fully occupied UDP binding site at the enzyme dimer interface that is observed to be dependent on the binding of H antigen acceptor analog.
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Affiliation(s)
- Brock Schuman
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Petch Building, Victoria, BC, Canada V8W 3P6
| | - Mattias Persson
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-200 Valby, Denmark
| | - Roxanne C. Landry
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Robert Polakowski
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Joel T. Weadge
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-200 Valby, Denmark
| | - Nina O. L. Seto
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Petch Building, Victoria, BC, Canada V8W 3P6
- Institute for Biological Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Svetlana N. Borisova
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Petch Building, Victoria, BC, Canada V8W 3P6
| | - Monica M. Palcic
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-200 Valby, Denmark
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Stephen V. Evans
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Petch Building, Victoria, BC, Canada V8W 3P6
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
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Adlercreutz D, Weadge JT, Petersen BO, Duus JØ, Dovichi NJ, Palcic MM. Enzymatic synthesis of Gb3 and iGb3 ceramides. Carbohydr Res 2010; 345:1384-8. [PMID: 20206917 PMCID: PMC3282984 DOI: 10.1016/j.carres.2010.02.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 02/04/2010] [Accepted: 02/05/2010] [Indexed: 11/16/2022]
Abstract
Gb3 and iGb3 are physiologically important trihexosylceramides with a terminal alpha-d-Galp-(1-->4)-beta-d-Galp- and alpha-d-Galp-(1-->3)-beta-d-Galp sequence, respectively. In particular iGb3 is attracting considerable attention as it is believed to serve as a ligand for natural killer T cells. Whether or not iGb3 is present in humans and which enzyme might be responsible for its synthesis is at present a matter of lively debate. In the current investigation we evaluated human blood group B galactosyltransferase (GTB) for its ability to catalyze the formation of iGb3 from lactosylceramide and UDP-Galp. GTB is a retaining glycosyltransferase that in vivo catalyzes the transfer of galactose from UDP-Galp donors to OH-3 of Galp on the H-antigen (alpha-l-Fucp-(1-->2)-beta-d-Galp) acceptor forming the blood group B antigen. GTB tolerates modifications in donor and acceptor substrates and its ability to accept lactosides as acceptors makes it a possible candidate for iGb3 production in humans. For comparison iGb3 and Gb3 were also synthesized from the same acceptor using an alpha-(1-->3)- and alpha-(1-->4)-specific galactosyltransferase, respectively. All the enzymes tested catalyzed the desired reactions. Product characterization by NMR analysis clearly differentiated between the alpha-Galp-(1-->3)-Galp and alpha-Galp-(1-->4)-Galp product, with the GTB product being identical to that of the alpha-(1-->3)-GalT-catalyzed reaction. The rate of transfer by GTB however was very low, only 0.001% of the rate obtained with a good substrate, H antigen disaccharide (octyl alpha-l-Fucp-(1-->2)-beta-d-Galp). This is too low to account for the possible formation of the iGb3 structure in humans in vivo.
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