1
|
Xu Y, Wagner GK. A cell-permeable probe for the labelling of a bacterial glycosyltransferase and virulence factor. RSC Chem Biol 2024; 5:55-62. [PMID: 38179196 PMCID: PMC10763556 DOI: 10.1039/d3cb00092c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/18/2023] [Indexed: 01/06/2024] Open
Abstract
Chemical probes for bacterial glycosyltransferases are of interest for applications such as tracking of expression levels, and strain profiling and identification. Existing probes for glycosyltransferases are typically based on sugar-nucleotides, whose charged nature limits their applicability in intact cells. We report the development of an uncharged covalent probe for the bacterial galactosyltransferase LgtC, and its application for the fluorescent labelling of this enzyme in recombinant form, cell lysates, and intact cells. The probe was designed by equipping a previously reported covalent LgtC inhibitor based on a pyrazol-3-one scaffold with a 7-hydroxycoumarin fluorophore. We show that this pyrazol-3-ones scaffold is surprisingly stable in aqueous media, which may have wider implications for the use of pyrazol-3-ones as chemical probes. We also show that the 7-hydroxycoumarin fluorophore leads to an unexpected improvement in activity, which could be exploited for the development of second generation analogues. These results will provide a basis for the development of LgtC-specific probes for the detection of LgtC-expressing bacterial strains.
Collapse
Affiliation(s)
- Yong Xu
- Department of Chemistry, King's College London UK
| | - Gerd K Wagner
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road Belfast BT9 7BL UK
| |
Collapse
|
2
|
Enzymatic Glyco-Modification of Synthetic Membrane Systems. Biomolecules 2023; 13:biom13020335. [PMID: 36830704 PMCID: PMC9952996 DOI: 10.3390/biom13020335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
The present report assesses the capability of a soluble glycosyltransferase to modify glycolipids organized in two synthetic membrane systems that are attractive models to mimic cell membranes: giant unilamellar vesicles (GUVs) and supported lipid bilayers (SLBs). The objective was to synthesize the Gb3 antigen (Galα1,4Galβ1,4Glcβ-Cer), a cancer biomarker, at the surface of these membrane models. A soluble form of LgtC that adds a galactose residue from UDP-Gal to lactose-containing acceptors was selected. Although less efficient than with lactose, the ability of LgtC to utilize lactosyl-ceramide as an acceptor was demonstrated on GUVs and SLBs. The reaction was monitored using the B-subunit of Shiga toxin as Gb3-binding lectin. Quartz crystal microbalance with dissipation analysis showed that transient binding of LgtC at the membrane surface was sufficient for a productive conversion of LacCer to Gb3. Molecular dynamics simulations provided structural elements to help rationalize experimental data.
Collapse
|
3
|
Sharyan A, Gonzalez C, Ukaegbu O, Powell K, McCarthy PC. Determination of the binding affinities of Neisseria meningitidis serogroup W capsule polymerase with two nucleotide sugar substrates. BMC Res Notes 2018; 11:482. [PMID: 30012207 PMCID: PMC6048754 DOI: 10.1186/s13104-018-3596-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/12/2018] [Indexed: 01/22/2023] Open
Abstract
Objective Meningococcal meningitis is a public health burden. Immunization strategies have reduced global incidence of the disease. Glycoconjugate vaccines are the most effective type of vaccine to combat most causes of meningococcal meningitis. These vaccines contain capsular polysaccharide fragments from disease-causing serogroups of Neisseria meningitidis that are chemically attached to a carrier protein. The enzymes responsible for capsular polysaccharide synthesis can serve as tools to make these critical vaccine components. One such enzyme is the N. meningitidis serogroup W capsule polymerase. This enzyme is responsible for creating the galactose-sialic acid containing capsular polysaccharide of this serogroup. Our aim in this study was to determine the binding affinities of nucleotide sugar donors CMP-sialic acid and UDP-galactose using a coupled transferase assay to inform future work to modulate polysaccharide synthesis by this enzyme. Results We determined a Km of 66.8 µM for CMP-sialic acid and a Km for UDP-galactose of 3.9 µM. These values are lower than reported values for other retaining galactosyltransferases and inverting sialyltransferases respectively. There were difficulties obtaining reliable data for galactosyltransferase activity. An alternate strategy is needed to assess kinetic parameters of the separate transferase activities for this enzyme. Electronic supplementary material The online version of this article (10.1186/s13104-018-3596-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Abeer Sharyan
- Department of Chemistry, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD, 21251, USA
| | - Cendy Gonzalez
- Department of Biology, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD, 21251, USA
| | - Ophelia Ukaegbu
- Department of Chemistry, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD, 21251, USA
| | - Kayla Powell
- Department of Chemistry, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD, 21251, USA
| | - Pumtiwitt C McCarthy
- Department of Chemistry, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD, 21251, USA.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Salinas SR, Petruk AA, Brukman NG, Bianco MI, Jacobs M, Marti MA, Ielpi L. Binding of the substrate UDP-glucuronic acid induces conformational changes in the xanthan gum glucuronosyltransferase. Protein Eng Des Sel 2016; 29:197-207. [PMID: 27099353 DOI: 10.1093/protein/gzw007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/02/2016] [Indexed: 01/24/2023] Open
Abstract
GumK is a membrane-associated glucuronosyltransferase of Xanthomonas campestris that is involved in xanthan gum biosynthesis. GumK belongs to the inverting GT-B superfamily and catalyzes the transfer of a glucuronic acid (GlcA) residue from uridine diphosphate (UDP)-GlcA (UDP-GlcA) to a lipid-PP-trisaccharide embedded in the membrane of the bacteria. The structure of GumK was previously described in its apo- and UDP-bound forms, with no significant conformational differences being observed. Here, we study the behavior of GumK toward its donor substrate UDP-GlcA. Turbidity measurements revealed that the interaction of GumK with UDP-GlcA produces aggregation of protein molecules under specific conditions. Moreover, limited proteolysis assays demonstrated protection of enzymatic digestion when UDP-GlcA is present, and this protection is promoted by substrate binding. Circular dichroism spectroscopy also revealed changes in the GumK tertiary structure after UDP-GlcA addition. According to the obtained emission fluorescence results, we suggest the possibility of exposure of hydrophobic residues upon UDP-GlcA binding. We present in silico-built models of GumK complexed with UDP-GlcA as well as its analogs UDP-glucose and UDP-galacturonic acid. Through molecular dynamics simulations, we also show that a relative movement between the domains appears to be specific and to be triggered by UDP-GlcA. The results presented here strongly suggest that GumK undergoes a conformational change upon donor substrate binding, likely bringing the two Rossmann fold domains closer together and triggering a change in the N-terminal domain, with consequent generation of the acceptor substrate binding site.
Collapse
Affiliation(s)
- S R Salinas
- Laboratory of Bacterial Genetics, Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - A A Petruk
- Departamento de Química Inorgánica, Analítica, y Química Física/INQUIMAE CONICET, Córdoba, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - N G Brukman
- Laboratory of Bacterial Genetics, Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - M I Bianco
- Laboratory of Bacterial Genetics, Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - M Jacobs
- Laboratory of Bacterial Genetics, Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - M A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - L Ielpi
- Laboratory of Bacterial Genetics, Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| |
Collapse
|
6
|
Crublet E, Kerfah R, Mas G, Noirclerc-Savoye M, Lantez V, Vernet T, Boisbouvier J. A cost-effective protocol for the parallel production of libraries of 13CH3-specifically labeled mutants for NMR studies of high molecular weight proteins. Methods Mol Biol 2014; 1091:229-244. [PMID: 24203337 DOI: 10.1007/978-1-62703-691-7_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
There is increasing interest in applying NMR spectroscopy to the study of large protein assemblies. Development of methyl-specific labeling protocols combined with improved NMR spectroscopy enable nowadays studies of proteins complexes up to 1 MDa. For such large complexes, the major interest lies in obtaining structural, dynamic and interaction information in solution, which requires sequence-specific resonance assignment of NMR signals. While such analysis is quite standard for small proteins, it remains one of the major bottlenecks when the size of the protein increases. Here, we describe implementation and latest improvements of SeSAM, a fast and user-friendly approach for assignment of methyl resonances in large proteins using mutagenesis. We have improved culture medium to boost the production of methyl-specifically labeled proteins, allowing us to perform small-scale parallel production and purification of a library of (13)CH3-specifically labeled mutants. This optimized protocol is illustrated by assignment of Alanine, Isoleucine, and Valine methyl groups of the homododecameric aminopeptidase PhTET2. We estimated that this improved method allows assignment of ca. 100 methyl cross-peaks in 2 weeks, including 4 days of NMR time and less than 2 k€ of isotopic materials.
Collapse
Affiliation(s)
- Elodie Crublet
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA, Grenoble, France
| | | | | | | | | | | | | |
Collapse
|
7
|
Sinha K, Jen-Jacobson L, Rule GS. Divide and conquer is always best: sensitivity of methyl correlation experiments. JOURNAL OF BIOMOLECULAR NMR 2013; 56:331-5. [PMID: 23771591 PMCID: PMC3758368 DOI: 10.1007/s10858-013-9751-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 06/08/2013] [Indexed: 05/03/2023]
Abstract
The HMCM [CG]CBCA experiment (Tugarinov and Kay in J Am Chem Soc 125:13868-13878, 2003) correlates methyl carbon and proton shifts to Cγ, Cβ, and Cα resonances for the purpose of resonance assignments. The relative sensitivity of the HMCM[CG]CBCA sequence experiment is compared to a divide-and-conquer approach to assess whether it is best to collect all of the methyl correlations at once, or to perform separate experiments for each correlation. A straightforward analysis shows that the divide-and-conquer approach is intrinsically more sensitive, and should always be used to obtain methyl-Cγ, Cβ, and Cα correlations. The improvement in signal-to-noise associated with separate experiments is illustrated by the detection of methyl-aliphatic correlations in a 65 kDa protein-DNA complex.
Collapse
Affiliation(s)
- Kaustubh Sinha
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | | |
Collapse
|
8
|
Chan PHW, Cheung AH, Okon M, Chen HM, Withers SG, McIntosh LP. Investigating the Structural Dynamics of α-1,4-Galactosyltransferase C from Neisseria meningitidis by Nuclear Magnetic Resonance Spectroscopy. Biochemistry 2013; 52:320-32. [DOI: 10.1021/bi301317d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Patrick H. W. Chan
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for High-throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4,
Canada
| | - Adrienne H. Cheung
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Mark Okon
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1,
Canada
| | - Hong-Ming Chen
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1,
Canada
| | - Stephen G. Withers
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for High-throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4,
Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1,
Canada
| | - Lawrence P. McIntosh
- Department of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Centre for High-throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4,
Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1,
Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4,
Canada
| |
Collapse
|