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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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Rajakumara E, Abhishek S, Nitin K, Saniya D, Bajaj P, Schwaneberg U, Davari MD. Structure and Cooperativity in Substrate-Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design. ACS Chem Biol 2022; 17:266-280. [PMID: 35041385 DOI: 10.1021/acschembio.1c00500] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzyme-based synthetic chemistry provides a green way to synthesize industrially important chemical scaffolds and provides incomparable substrate specificity and unmatched stereo-, regio-, and chemoselective product formation. However, using biocatalysts at an industrial scale has its challenges, like their narrow substrate scope, limited stability in large-scale one-pot reactions, and low expression levels. These limitations can be overcome by engineering and fine-tuning these biocatalysts using advanced protein engineering methods. A detailed understanding of the enzyme structure and catalytic mechanism and its structure-function relationship, cooperativity in binding of substrates, and dynamics of substrate-enzyme-cofactor complexes is essential for rational enzyme engineering for a specific purpose. This Review covers all these aspects along with an in-depth categorization of various industrially and pharmaceutically crucial bisubstrate enzymes based on their reaction mechanisms and their active site and substrate/cofactor-binding site structures. As the bisubstrate enzymes constitute around 60% of the known industrially important enzymes, studying their mechanism of actions and structure-activity relationship gives significant insight into deciding the targets for protein engineering for developing industrial biocatalysts. Thus, this Review is focused on providing a comprehensive knowledge of the bisubstrate enzymes' structure, their mechanisms, and protein engineering approaches to develop them into industrial biocatalysts.
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Affiliation(s)
- Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Kulhar Nitin
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Dubey Saniya
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Priyanka Bajaj
- National Institute of Pharmaceutical Education and Research (NIPER), NH-44, Balanagar, Hyderabad 500037, India
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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Thines L, Stribny J, Morsomme P. From the Uncharacterized Protein Family 0016 to the GDT1 family: Molecular insights into a newly-characterized family of cation secondary transporters. MICROBIAL CELL 2020; 7:202-214. [PMID: 32743000 PMCID: PMC7380456 DOI: 10.15698/mic2020.08.725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Uncharacterized Protein Family 0016 (UPF0016) gathers poorly studied membrane proteins well conserved through evolution that possess one or two copies of the consensus motif Glu-x-Gly-Asp-(Arg/Lys)-(Ser/Thr). Members are found in many eukaryotes, bacteria and archaea. The interest for this protein family arose in 2012 when its human member TMEM165 was linked to the occurrence of Congenital Disorders of Glycosylation (CDGs) when harbouring specific mutations. Study of the UPF0016 family is undergone through the characterization of the bacterium Vibrio cholerae (MneA), cyanobacterium Synechocystis (SynPAM71), yeast Saccharomyces cerevisiae (Gdt1p), plant Arabidopsis thaliana (PAM71 and CMT1), and human (TMEM165) members. These proteins have all been identified as transporters of cations, more precisely of Mn2+, with an extra reported function in Ca2+ and/or H+ transport for some of them. Apart from glycosylation in humans, the UPF0016 members are required for lactation in humans, photosynthesis in plants and cyanobacteria, Ca2+ signaling in yeast, and Mn2+ homeostasis in the five aforementioned species. The requirement of the UPF0016 members for key physiological processes most likely derives from their transport activity at the Golgi membrane in human and yeast, the chloroplasts membranes in plants, the thylakoid and plasma membranes in cyanobacteria, and the cell membrane in bacteria. In the light of these studies on various UPF0016 members, this family is not considered as uncharacterized anymore and has been renamed the Gdt1 family according to the name of its S. cerevisiae member. This review aims at assembling and confronting the current knowledge in order to identify shared and distinct features in terms of transported molecules, mode of action, structure, etc., as well as to better understand their corresponding physiological roles.
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Affiliation(s)
- Louise Thines
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Jiri Stribny
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
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Kaltashov IA, Bobst CE, Pawlowski J, Wang G. Mass spectrometry-based methods in characterization of the higher order structure of protein therapeutics. J Pharm Biomed Anal 2020; 184:113169. [PMID: 32092629 DOI: 10.1016/j.jpba.2020.113169] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/31/2022]
Abstract
Higher order structure of protein therapeutics is an important quality attribute, which dictates both potency and safety. While modern experimental biophysics offers an impressive arsenal of state-of-the-art tools that can be used for the characterization of higher order structure, many of them are poorly suited for the characterization of biopharmaceutical products. As a result, these analyses were traditionally carried out using classical techniques that provide relatively low information content. Over the past decade, mass spectrometry made a dramatic debut in this field, enabling the characterization of higher order structure of biopharmaceuticals as complex as monoclonal antibodies at a level of detail that was previously unattainable. At present, mass spectrometry is an integral part of the analytical toolbox across the industry, which is critical not only for quality control efforts, but also for discovery and development.
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Affiliation(s)
- Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA.
| | - Cedric E Bobst
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Jake Pawlowski
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Guanbo Wang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu Province, PR China
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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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Cooper-Knock J, Moll T, Ramesh T, Castelli L, Beer A, Robins H, Fox I, Niedermoser I, Van Damme P, Moisse M, Robberecht W, Hardiman O, Panades MP, Assialioui A, Mora JS, Basak AN, Morrison KE, Shaw CE, Al-Chalabi A, Landers JE, Wyles M, Heath PR, Higginbottom A, Walsh T, Kazoka M, McDermott CJ, Hautbergue GM, Kirby J, Shaw PJ. Mutations in the Glycosyltransferase Domain of GLT8D1 Are Associated with Familial Amyotrophic Lateral Sclerosis. Cell Rep 2019; 26:2298-2306.e5. [PMID: 30811981 PMCID: PMC7003067 DOI: 10.1016/j.celrep.2019.02.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/03/2019] [Accepted: 01/30/2019] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disorder without effective neuroprotective therapy. Known genetic variants impair pathways, including RNA processing, axonal transport, and protein homeostasis. We report ALS-causing mutations within the gene encoding the glycosyltransferase GLT8D1. Exome sequencing in an autosomal-dominant ALS pedigree identified p.R92C mutations in GLT8D1, which co-segregate with disease. Sequencing of local and international cohorts demonstrated significant ALS association in the same exon, including additional rare deleterious mutations in conserved amino acids. Mutations are associated with the substrate binding site, and both R92C and G78W changes impair GLT8D1 enzyme activity. Mutated GLT8D1 exhibits in vitro cytotoxicity and induces motor deficits in zebrafish consistent with ALS. Relative toxicity of mutations in model systems mirrors clinical severity. In conclusion, we have linked ALS pathophysiology to inherited mutations that diminish the activity of a glycosyltransferase enzyme.
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Affiliation(s)
- Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK.
| | - Tobias Moll
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Tennore Ramesh
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Lydia Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Alexander Beer
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Henry Robins
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Ian Fox
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Isabell Niedermoser
- Department of Molecular Evolution and Development Department, University of Vienna, Vienna 1090, Austria
| | - Philip Van Damme
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium; University Hospitals Leuven, Department of Neurology, Leuven, Belgium
| | - Matthieu Moisse
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Wim Robberecht
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium; University Hospitals Leuven, Department of Neurology, Leuven, Belgium
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | | | | | | | - A Nazli Basak
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul 34342, Turkey
| | - Karen E Morrison
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Christopher E Shaw
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - Ammar Al-Chalabi
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - John E Landers
- University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Matthew Wyles
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Paul R Heath
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Adrian Higginbottom
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Theresa Walsh
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Mbombe Kazoka
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Christopher J McDermott
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK.
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Kang J, Brooks KV. Optimization of biolayer interferometer-based binding assay of the interaction between the Candida albicans protein Pra1 and complement protein C3. Mol Immunol 2018; 101:635-637. [DOI: 10.1016/j.molimm.2018.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/05/2018] [Indexed: 11/30/2022]
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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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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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Mortensen DN, Williams ER. Electrothermal supercharging of proteins in native MS: effects of protein isoelectric point, buffer, and nanoESI-emitter tip size. Analyst 2016; 141:5598-606. [PMID: 27441318 PMCID: PMC5239670 DOI: 10.1039/c6an01380e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The extent of charging resulting from electrothermal supercharging for protein ions formed from various buffered aqueous solutions using nanoESI emitters with tip diameters between ∼1.5 μm and ∼310 nm is compared. Charging increases with decreasing tip size for proteins that are positively charged in solution but not for proteins that are negatively charged in solution. These results suggest that Coulombic attraction between positively charged protein molecules and the negatively charged glass surfaces in the tips of the emitters causes destabilization and even unfolding of proteins prior to nanoESI. Coulombic attraction to the negatively charged glass surfaces does not occur for negatively charged proteins and the extent of charging with electrothermal supercharging decreases with decreasing tip size. Smaller droplets are formed with smaller tips, and these droplets have shorter lifetimes for protein unfolding with electrothermal supercharging to occur prior to gaseous ion formation. Results from this study demonstrate simple principles to consider in order to optimize the extent of charging obtained with electrothermal supercharging, which should be useful for obtaining more structural information in tandem mass spectrometry.
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Affiliation(s)
- Daniel N Mortensen
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA.
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Pedro L, Van Voorhis WC, Quinn RJ. Optimization of Electrospray Ionization by Statistical Design of Experiments and Response Surface Methodology: Protein-Ligand Equilibrium Dissociation Constant Determinations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1520-30. [PMID: 27225419 PMCID: PMC4972871 DOI: 10.1007/s13361-016-1417-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 04/29/2016] [Accepted: 05/04/2016] [Indexed: 05/28/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) binding studies between proteins and ligands under native conditions require that instrumental ESI source conditions are optimized if relative solution-phase equilibrium concentrations between the protein-ligand complex and free protein are to be retained. Instrumental ESI source conditions that simultaneously maximize the relative ionization efficiency of the protein-ligand complex over free protein and minimize the protein-ligand complex dissociation during the ESI process and the transfer from atmospheric pressure to vacuum are generally specific for each protein-ligand system and should be established when an accurate equilibrium dissociation constant (KD) is to be determined via titration. In this paper, a straightforward and systematic approach for ESI source optimization is presented. The method uses statistical design of experiments (DOE) in conjunction with response surface methodology (RSM) and is demonstrated for the complexes between Plasmodium vivax guanylate kinase (PvGK) and two ligands: 5'-guanosine monophosphate (GMP) and 5'-guanosine diphosphate (GDP). It was verified that even though the ligands are structurally similar, the most appropriate ESI conditions for KD determination by titration are different for each. Graphical Abstract ᅟ.
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Affiliation(s)
- Liliana Pedro
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | | | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
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Native Mass Spectrometry in Fragment-Based Drug Discovery. Molecules 2016; 21:molecules21080984. [PMID: 27483215 PMCID: PMC6274484 DOI: 10.3390/molecules21080984] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/14/2016] [Accepted: 07/23/2016] [Indexed: 11/17/2022] Open
Abstract
The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.
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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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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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15
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Cassou CA, Williams ER. Anions in electrothermal supercharging of proteins with electrospray ionization follow a reverse Hofmeister series. Anal Chem 2014; 86:1640-7. [PMID: 24410546 PMCID: PMC3983018 DOI: 10.1021/ac403398j] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
The
effects of different anions on the extent of electrothermal
supercharging of proteins from aqueous ammonium and sodium salt solutions
were investigated. Sulfate and hydrogen phosphate are the most effective
anions at producing high charge state protein ions from buffered aqueous
solution, whereas iodide and perchlorate are ineffective with electrothermal
supercharging. The propensity for these anions to produce high charge
state protein ions follows the following trend: sulfate > hydrogen
phosphate > thiocyanate > bicarbonate > chloride > formate
≈
bromide > acetate > iodide > perchlorate. This trend correlates
with
the reverse Hofmeister series over a wide range of salt concentrations
(1 mM to 2 M) and with several physical properties, including solvent
surface tension, anion viscosity B-coefficient, and anion surface/bulk
partitioning coefficient, all of which are related to the Hofmeister
series. The effectiveness of electrothermal supercharging does not
depend on bubble formation, either from thermal degradation of the
buffer or from coalescence of dissolved gas. These results provide
evidence that the effect of different ions in the formation of high
charge state ions by electrothermal supercharging is largely a result
of Hofmeister effects on protein stability leading to protein unfolding
in the heated ESI droplet.
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Affiliation(s)
- Catherine A Cassou
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States
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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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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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19
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Kötzler MP, Blank S, Bantleon FI, Wienke M, Spillner E, Meyer B. Donor assists acceptor binding and catalysis of human α1,6-fucosyltransferase. ACS Chem Biol 2013; 8:1830-40. [PMID: 23730796 DOI: 10.1021/cb400140u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
α1,6-Core-fucosyltransferase (FUT8) is a vital enzyme in mammalian physiological and pathophysiological processes such as tumorigenesis and progress of, among others, non-small cell lung cancer and colon carcinoma. It was also shown that therapeutic antibodies have a dramatically higher efficacy if the α1,6-fucosyl residue is absent. However, specific and potent inhibitors for FUT8 and related enzymes are lacking. Hence, it is crucial to elucidate the structural basis of acceptor binding and the catalytic mechanism. We present here the first structural model of FUT8 in complex with its acceptor and donor molecules. An unusually large acceptor, i.e., a hexasaccharide from the core of N-glycans, is required as minimal structure. Acceptor substrate binding of FUT8 is being dissected experimentally by STD NMR and SPR and theoretically by molecular dynamics simulations. The acceptor binding site forms an unusually large and shallow binding site. Binding of the acceptor to the enzyme is much faster and stronger if the donor is present. This is due to strong hydrogen bonding between O6 of the proximal N-acetylglucosamine and an oxygen atom of the β-phosphate of GDP-fucose. Therefore, we propose an ordered Bi Bi mechanism for FUT8 where the donor molecule binds first. No specific amino acid is present that could act as base during catalysis. Our results indicate a donor-assisted mechanism, where an oxygen of the β-phosphate deprotonates the acceptor. Knowledge of the mechanism of FUT8 is now being used for rational design of targeted inhibitors to address metastasis and prognosis of carcinomas.
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Affiliation(s)
- Miriam P. Kötzler
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
| | - Simon Blank
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
| | - Frank I. Bantleon
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
| | - Martin Wienke
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
| | - Edzard Spillner
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
| | - Bernd Meyer
- Institute
of Organic Chemistry and ‡Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146,
Germany
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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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Wang B, Huang F, Nguyen T, Xu Y, Lin Q. Microcantilever-Based Label-Free Characterization of Temperature-Dependent Biomolecular Affinity Binding. SENSORS AND ACTUATORS. B, CHEMICAL 2013; 176:653-659. [PMID: 24723743 PMCID: PMC3979549 DOI: 10.1016/j.snb.2012.02.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This paper presents label-free characterization of temperature-dependent biomolecular affinity binding on solid surfaces using a microcantilever-based device. The device consists of a Parylene cantilever one side of which is coated with a gold film and functionalized with molecules as an affinity receptor to a target analyte. The cantilever is located in a poly(dimethylsiloxane) (PDMS) microfluidic chamber that is integrated with a transparent indium tin oxide (ITO) resistive temperature sensor on the underlying substrate. The ITO sensor allows for real-time measurements of the chamber temperature, as well as unobstructed optical access for reflection-based optical detection of the cantilever deflection. To test the temperature-dependent binding between the target and receptor, the temperature of the chamber is maintained at a constant setpoint, while a solution of unlabeled analyte molecules is continuously infused through the chamber. The measured cantilever deflection is used to determine the target-receptor binding characteristics. We demonstrate label-free characterization of temperature-dependent binding kinetics of the platelet-derived growth factor (PDGF) protein with an aptamer receptor. Affinity binding properties including the association and dissociation rate constants as well as equilibrium dissociation constant are obtained, and shown to exhibit significant dependencies on temperature.
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Affiliation(s)
- Bin Wang
- Department of Mechanical Engineering, Columbia University, New York, USA
| | - Fengliang Huang
- Department of Mechanical Engineering, Columbia University, New York, USA
- School of Electrical & Automation Engineering, Nanjing Normal University, Nanjing, China
| | - ThaiHuu Nguyen
- Department of Mechanical Engineering, Columbia University, New York, USA
| | - Yong Xu
- Department of Electrical and Computer Engineering, Wayne State University, Detroit, USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, USA
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22
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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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23
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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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24
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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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25
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Kötzler MP, Blank S, Behnken HN, Alpers D, Bantleon FI, Spillner E, Meyer B. Formation of the immunogenic α1,3-fucose epitope: elucidation of substrate specificity and of enzyme mechanism of core fucosyltransferase A. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 42:116-125. [PMID: 22182589 DOI: 10.1016/j.ibmb.2011.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 11/21/2011] [Accepted: 11/22/2011] [Indexed: 05/31/2023]
Abstract
Glycans of glycoproteins are often associated with IgE mediated allergic immune responses. Hymenoptera venoms, e.g., carry α1,3-fucosyl residues linked to the proximal GlcNAc of glycoproteins. This epitope, formed selectively by α1,3-fucosyltransferase (FucTA), is xenobiotic and as such highly immunogenic and it also shows cross-reactivity if present on different proteins. Production of post-translationally modified proteins in insect cells is however commonly used and, thus, resulting glycoproteins can carry this highly immunogenic epitope with potentially significant side effects on mammals. To analyze mechanism, specificity and reaction kinetics of the key enzyme, we chose FucTA from Apis mellifera (honeybee) and characterized it by saturation transfer difference (STD) NMR and surface plasmon resonance (SPR) experiments. Specifically, we show here that the donor substrate, GDP-Fucose, binds mostly via its guanine and less so via pyrophosphate and fucosyl fragments and has a K(D) = 37 μM. Affinity and kinetic studies with both the core α1,6-fucosylated and the unfucosylated octa- or heptasaccharides, respectively, as acceptor substrate revealed that honeybee FucTA prefers the latter structure with affinities of K(D) ∼ 10 mM. Establishment of progress curve analysis using an explicit solution of the integrated Michaelis-Menten equation allowed for determination of key constants of the transfer reaction of the glycosyl residue. The dominant minimum acceptor substrate is an unfucosylated heptasaccharide with K(m) = 420 μM and k(cat) = 6 min(-1). Time-resolved NMR spectra as well as STD NMR allow molecular insights into specificity, activity and interaction of the enzyme with substrates and acceptors.
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26
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Ganguly A, Rajdev P, Williams SM, Chatterji D. Nonspecific Interaction between DNA and Protein allows for Cooperativity: A Case Study with Mycobacterium DNA Binding Protein. J Phys Chem B 2011; 116:621-32. [DOI: 10.1021/jp209423n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Abantika Ganguly
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | | | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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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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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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29
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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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Rademacher C, Landström J, Sindhuwinata N, Palcic MM, Widmalm G, Peters T. NMR-based exploration of the acceptor binding site of human blood group B galactosyltransferase with molecular fragments. Glycoconj J 2010; 27:349-58. [DOI: 10.1007/s10719-010-9282-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 02/08/2010] [Accepted: 02/11/2010] [Indexed: 12/01/2022]
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Sun N, Soya N, Kitova EN, Klassen JS. Nonspecific interactions between proteins and charged biomolecules in electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:472-481. [PMID: 20089416 DOI: 10.1016/j.jasms.2009.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 12/08/2009] [Accepted: 12/10/2009] [Indexed: 05/28/2023]
Abstract
An investigation of the nonspecific association of small charged biomolecules and proteins in electrospray ionization mass spectrometry (ES-MS) is described. Aqueous solutions containing pairs of proteins and a small acidic or basic biomolecule that does not interact specifically with either of the proteins were analyzed by ES-MS and the distributions of the biomolecules bound nonspecifically to each pair of proteins compared. For the basic amino acid arginine and the peptide RGVFRR, nonequivalent distributions were measured in positive ion mode, but equivalent distributions were measured in negative ion mode. In the case of uridine 5'-diphosphate, nonequivalent distributions were measured in negative ion mode, but equivalent distributions observed in positive ion mode. The results of dissociation experiments performed on the gaseous ions of the nonspecific complexes suggest that the nonequivalent distributions result from differences in the extent to which the nonspecific complexes undergo in-source dissociation. To test this hypothesis, the distributions of nonspecifically bound basic molecules measured in the presence of imidazole, which protects complexes from in-source dissociation, were compared. In all cases, equivalent distributions were obtained. The results indicate that nonspecific binding of charged molecules to proteins during ES is a statistical process, independent of protein structure and size. However, the kinetic stabilities of the nonspecific interactions are sensitive to the nature of the protein ions. It is concluded that the reference protein method for correcting ES mass spectra for nonspecific ligand-protein binding can be applied to the analysis of ionic ligands, provided that in-source dissociation of the nonspecific interactions is minimized.
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Affiliation(s)
- Nian Sun
- Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Deng L, Sun N, Kitova EN, Klassen JS. Direct Quantification of Protein−Metal Ion Affinities by Electrospray Ionization Mass Spectrometry. Anal Chem 2010; 82:2170-4. [DOI: 10.1021/ac902633d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lu Deng
- Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Nian Sun
- Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Elena N. Kitova
- Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - John S. Klassen
- Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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Sindhuwinata N, Munoz E, Munoz FJ, Palcic MM, Peters H, Peters T. Binding of an acceptor substrate analog enhances the enzymatic activity of human blood group B galactosyltransferase. Glycobiology 2010; 20:718-23. [PMID: 20154292 DOI: 10.1093/glycob/cwq019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The hydrolysis of the donor substrate uridine diphosphate galactose (UDP-Gal) by human blood group B galactosyltransferase (GTB) has been followed by nuclear magnetic resonance in the presence and in the absence of an acceptor substrate analog. It is observed that the presence of the acceptor substrate analog promotes hydrolysis of UDP-Gal. Subsequent analysis of the kinetics of the enzymatic hydrolysis suggests that this effect is due to an increased affinity of GTB for UDP-Gal in the presence of the acceptor analog. Isothermal titration calorimetry experiments substantiate this conclusion. As hydrolysis may be understood as a glycosyl transfer reaction where water serves as universal acceptor, we suggest that in general the binding of acceptor substrates to retaining glycosyltransferases modulates the rate of glycosyl transfer. In fact, this may point to a general mechanism used by retaining glycosyltransferases to discriminate acceptor substrates under physiological conditions.
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Affiliation(s)
- Nora Sindhuwinata
- Institute of Chemistry, University of Luebeck, Ratzeburger Allee 160, 23538 Luebeck Germany
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Soya N, Shoemaker GK, Palcic MM, Klassen JS. Comparative study of substrate and product binding to the human ABO(H) blood group glycosyltransferases. Glycobiology 2009; 19:1224-34. [DOI: 10.1093/glycob/cwp114] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Bagal D, Kitova EN, Liu L, El-Hawiet A, Schnier PD, Klassen JS. Gas Phase Stabilization of Noncovalent Protein Complexes Formed by Electrospray Ionization. Anal Chem 2009; 81:7801-6. [DOI: 10.1021/ac900611a] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dhanashri Bagal
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Elena N. Kitova
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Lan Liu
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Amr El-Hawiet
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Paul D. Schnier
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - John S. Klassen
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Alberta Ingenuity Center for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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Sun N, Sun J, Kitova EN, Klassen JS. Identifying nonspecific ligand binding in electrospray ionization mass spectrometry using the reporter molecule method. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1242-1250. [PMID: 19321359 DOI: 10.1016/j.jasms.2009.02.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 02/12/2009] [Accepted: 02/13/2009] [Indexed: 05/27/2023]
Abstract
The application of the reporter molecule (M(rep)) method for identifying nonspecific complexes in the ES-MS analysis of protein-ligand and DNA-ligand interactions in vitro is described. To test the reliability of the method, it was applied to the ES-MS analysis of protein-carbohydrate complexes originating from specific interactions in solution and from nonspecific interactions in the ES process. These control experiments confirm the basic assumptions underlying the M(rep) method, namely that nonspecific ligand binding is a random process, and that the ES droplet histories for specific and nonspecific complexes are distinct. The application of the M(rep) method to the ES-MS analysis of the sequential binding of the ethidium cation, a DNA intercalator, to single and double strand oligodeoxynucleotides is also described, and highlights the general utility of the method.
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Affiliation(s)
- Nian Sun
- Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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