1
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Thibert S, Reid DJ, Wilson JW, Varikoti R, Maltseva N, Schultz KJ, Kruel A, Babnigg G, Joachimiak A, Kumar N, Zhou M. Native Mass Spectrometry Dissects the Structural Dynamics of an Allosteric Heterodimer of SARS-CoV-2 Nonstructural Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:912-921. [PMID: 38535992 PMCID: PMC11066969 DOI: 10.1021/jasms.3c00453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 05/02/2024]
Abstract
Structure-based drug design, which relies on precise understanding of the target protein and its interaction with the drug candidate, is dramatically expedited by advances in computational methods for candidate prediction. Yet, the accuracy needs to be improved with more structural data from high throughput experiments, which are challenging to generate, especially for dynamic and weak associations. Herein, we applied native mass spectrometry (native MS) to rapidly characterize ligand binding of an allosteric heterodimeric complex of SARS-CoV-2 nonstructural proteins (nsp) nsp10 and nsp16 (nsp10/16), a complex essential for virus survival in the host and thus a desirable drug target. Native MS showed that the dimer is in equilibrium with monomeric states in solution. Consistent with the literature, well characterized small cosubstrate, RNA substrate, and product bind with high specificity and affinity to the dimer but not the free monomers. Unsuccessfully designed ligands bind indiscriminately to all forms. Using neutral gas collision, the nsp16 monomer with bound cosubstrate can be released from the holo dimer complex, confirming the binding to nsp16 as revealed by the crystal structure. However, we observed an unusual migration of the endogenous zinc ions bound to nsp10 to nsp16 after collisional dissociation. The metal migration can be suppressed by using surface collision with reduced precursor charge states, which presumably resulted in minimal gas-phase structural rearrangement and highlighted the importance of complementary techniques. With minimal sample input (∼μg), native MS can rapidly detect ligand binding affinities and locations in dynamic multisubunit protein complexes, demonstrating the potential of an "all-in-one" native MS assay for rapid structural profiling of protein-to-AI-based compound systems to expedite drug discovery.
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Affiliation(s)
- Stephanie
M. Thibert
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Deseree J. Reid
- Chemical
and Biological Signature Sciences, Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jesse W. Wilson
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Rohith Varikoti
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Natalia Maltseva
- Center
for Structural Biology of Infectious Diseases, Consortium for Advanced
Science and Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Structural
Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Katherine J. Schultz
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Agustin Kruel
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Gyorgy Babnigg
- Center
for Structural Biology of Infectious Diseases, Consortium for Advanced
Science and Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Biosciences
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Andrzej Joachimiak
- Center
for Structural Biology of Infectious Diseases, Consortium for Advanced
Science and Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Structural
Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Neeraj Kumar
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Mowei Zhou
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
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2
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Townsend JA, Marty MT. What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry. Methods 2023; 218:1-13. [PMID: 37482149 PMCID: PMC10529358 DOI: 10.1016/j.ymeth.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.
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Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA.
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3
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Konermann L, Liu Z, Haidar Y, Willans MJ, Bainbridge NA. On the Chemistry of Aqueous Ammonium Acetate Droplets during Native Electrospray Ionization Mass Spectrometry. Anal Chem 2023; 95:13957-13966. [PMID: 37669319 DOI: 10.1021/acs.analchem.3c02546] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Ammonium acetate (NH4Ac) is a widely used solvent additive in native electrospray ionization (ESI) mass spectrometry. NH4Ac can undergo proton transfer to form ammonia and acetic acid (NH4+ + Ac- → NH3 + HAc). The volatility of these products ensures that electrosprayed ions are free of undesired adducts. NH4Ac dissolution in water yields pH 7, providing "physiological" conditions. However, NH4Ac is not a buffer at pH 7 because NH4+ and Ac- are not a conjugate acid/base pair (Konermann, L. J. Am. Soc. Mass Spectrom. 2017, 28, 1827-1835.). In native ESI, it is desirable that analytes experience physiological conditions not only in bulk solution but also while they reside in ESI droplets. Little is known about the internal milieu of NH4Ac-containing ESI droplets. The current work explored the acid/base chemistry of such droplets, starting from a pH 7 analyte solution. We used a two-pronged approach involving evaporation experiments on bulk solutions under ESI-mimicking conditions, as well as molecular dynamics simulations using a newly developed algorithm that allows for proton transfer. Our results reveal that during droplet formation at the tip of the Taylor cone, electrolytically generated protons get neutralized by Ac-, making NH4+ the net charge carriers in the weakly acidic nascent droplets. During the subsequent evaporation, the droplets lose water as well as NH3 and HAc that were generated by proton transfer. NH3 departs more quickly because of its greater volatility, causing the accumulation of HAc. Together with residual Ac-, these HAc molecules form an acetate buffer that stabilizes the average droplet pH at 5.4 ± 0.1, as governed by the Henderson-Hasselbalch equation. The remarkable success of native ESI investigations in the literature implies that this pH drop by ∼1.6 units relative to the initially neutral analyte solution can be tolerated by most biomolecular analytes on the short time scale of the ESI process.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Zeyuan Liu
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Yousef Haidar
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Mathew J Willans
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Nicholas A Bainbridge
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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4
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Lin CL, Sojitra M, Carpenter EJ, Hayhoe ES, Sarkar S, Volker EA, Wang C, Bui DT, Yang L, Klassen JS, Wu P, Macauley MS, Lowary TL, Derda R. Chemoenzymatic synthesis of genetically-encoded multivalent liquid N-glycan arrays. Nat Commun 2023; 14:5237. [PMID: 37640713 PMCID: PMC10462762 DOI: 10.1038/s41467-023-40900-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Cellular glycosylation is characterized by chemical complexity and heterogeneity, which is challenging to reproduce synthetically. Here we show chemoenzymatic synthesis on phage to produce a genetically-encoded liquid glycan array (LiGA) of complex type N-glycans. Implementing the approach involved by ligating an azide-containing sialylglycosyl-asparagine to phage functionalized with 50-1000 copies of dibenzocyclooctyne. The resulting intermediate can be trimmed by glycosidases and extended by glycosyltransferases yielding a phage library with different N-glycans. Post-reaction analysis by MALDI-TOF MS allows rigorous characterization of N-glycan structure and mean density, which are both encoded in the phage DNA. Use of this LiGA with fifteen glycan-binding proteins, including CD22 or DC-SIGN on cells, reveals optimal structure/density combinations for recognition. Injection of the LiGA into mice identifies glycoconjugates with structures and avidity necessary for enrichment in specific organs. This work provides a quantitative evaluation of the interaction of complex N-glycans with GBPs in vitro and in vivo.
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Affiliation(s)
- Chih-Lan Lin
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Mirat Sojitra
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Eric J Carpenter
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ellen S Hayhoe
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Susmita Sarkar
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Elizabeth A Volker
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Chao Wang
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Duong T Bui
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Loretta Yang
- Lectenz Bio, 111 Riverbend Rd, Athens, GA, 30602, USA
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Peng Wu
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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5
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Bui D, Favell J, Kitova EN, Li Z, McCord KA, Schmidt EN, Mozaneh F, Elaish M, El-Hawiet A, St-Pierre Y, Hobman TC, Macauley MS, Mahal LK, Flynn MR, Klassen JS. Absolute Affinities from Quantitative Shotgun Glycomics Using Concentration-Independent (COIN) Native Mass Spectrometry. ACS CENTRAL SCIENCE 2023; 9:1374-1387. [PMID: 37521792 PMCID: PMC10303200 DOI: 10.1021/acscentsci.3c00294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Indexed: 08/01/2023]
Abstract
Native mass spectrometry (nMS) screening of natural glycan libraries against glycan-binding proteins (GBPs) is a powerful tool for ligand discovery. However, as the glycan concentrations are unknown, affinities cannot be measured directly from natural libraries. Here, we introduce Concentration-Independent (COIN)-nMS, which enables quantitative screening of natural glycan libraries by exploiting slow mixing of solutions inside a nanoflow electrospray ionization emitter. The affinities (Kd) of detected GBP-glycan interactions are determined, simultaneously, from nMS analysis of their time-dependent relative abundance changes. We establish the reliability of COIN-nMS using interactions between purified glycans and GBPs with known Kd values. We also demonstrate the implementation of COIN-nMS using the catch-and-release (CaR)-nMS assay for glycosylated GBPs. The COIN-CaR-nMS results obtained for plant, fungal, viral, and human lectins with natural libraries containing hundreds of N-glycans and glycopeptides highlight the assay's versatility for discovering new ligands, precisely measuring their affinities, and uncovering "fine" specificities. Notably, the COIN-CaR-nMS results clarify the sialoglycan binding properties of the SARS-CoV-2 receptor binding domain and establish the recognition of monosialylated hybrid and biantennary N-glycans. Moreover, pharmacological depletion of host complex N-glycans reduces both pseudotyped virions and SARS-CoV-2 cell entry, suggesting that complex N-glycans may serve as attachment factors.
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Affiliation(s)
- Duong
T. Bui
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - James Favell
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Elena N. Kitova
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Zhixiong Li
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Kelli A. McCord
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Edward N. Schmidt
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Fahima Mozaneh
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Mohamed Elaish
- Department
of Cell Biology, University of Alberta, Edmonton T6G 2H7, AB, Canada
- Poultry
Diseases Department, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Amr El-Hawiet
- Department
of Pharmacognosy, Faculty of Pharmacy, Alexandria
University, Alexandria 21561, Egypt
| | - Yves St-Pierre
- Institut
National de la Recherche Scientifique (INRS), INRS-Centre Armand-Frappier
Santé Biotechnologie, Laval H7 V 1B7, QC, Canada
| | - Tom C. Hobman
- Department
of Cell Biology, University of Alberta, Edmonton T6G 2H7, AB, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton T6G 2E1, AB, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton T6G 2E1, Alberta, Canada
| | - Matthew S. Macauley
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton T6G 2E1, AB, Canada
| | - Lara K. Mahal
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Morris R. Flynn
- Department
of Mechanical Engineering, Faculty of Engineering, University of Alberta, Edmonton T6G 1H9, Alberta, Canada
| | - John S. Klassen
- Department
of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
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6
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Walker T, Sun HM, Gunnels T, Wysocki V, Laganowsky A, Rye H, Russell D. Dissecting the Thermodynamics of ATP Binding to GroEL One Nucleotide at a Time. ACS CENTRAL SCIENCE 2023; 9:466-475. [PMID: 36968544 PMCID: PMC10037461 DOI: 10.1021/acscentsci.2c01065] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Indexed: 06/18/2023]
Abstract
Variable-temperature electrospray ionization (vT-ESI) native mass spectrometry (nMS) is used to determine the thermodynamics for stepwise binding of up to 14 ATP molecules to the 801 kDa GroEL tetradecamer chaperonin complex. Detailed analysis reveals strong enthalpy-entropy compensation (EEC) for the ATP binding events leading to formation of GroEL-ATP7 and GroEL-ATP14 complexes. The observed variations in EEC and stepwise free energy changes of specific ATP binding are consistent with the well-established nested cooperativity model describing GroEL-ATP interactions, viz., intraring positive cooperativity and inter-ring negative cooperativity (Dyachenko A.; Proc. Natl. Acad. Sci. U.S.A.2013, 110, 7235-7239). Entropy-driven ATP binding is to be expected for ligand-induced conformational changes of the GroEL tetradecamer, though the magnitude of the entropy change suggests that reorganization of GroEL-hydrating water molecules and/or expulsion of water from the GroEL cavity may also play key roles. The capability for determining complete thermodynamic signatures (ΔG, ΔH, and -TΔS) for individual ligand binding reactions for the large, nearly megadalton GroEL complex expands our fundamental view of chaperonin functional chemistry. Moreover, this work and related studies of protein-ligand interactions illustrate important new capabilities of vT-ESI-nMS for thermodynamic studies of protein interactions with ligands and other molecules such as proteins and drugs.
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Affiliation(s)
- Thomas Walker
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - He Mirabel Sun
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tiffany Gunnels
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Vicki Wysocki
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Arthur Laganowsky
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hays Rye
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - David Russell
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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7
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Gheorghita AA, Li YE, Kitova EN, Bui DT, Pfoh R, Low KE, Whitfield GB, Walvoort MTC, Zhang Q, Codée JDC, Klassen JS, Howell PL. Structure of the AlgKX modification and secretion complex required for alginate production and biofilm attachment in Pseudomonas aeruginosa. Nat Commun 2022; 13:7631. [PMID: 36494359 PMCID: PMC9734138 DOI: 10.1038/s41467-022-35131-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Synthase-dependent secretion systems are a conserved mechanism for producing exopolysaccharides in Gram-negative bacteria. Although widely studied, it is not well understood how these systems are organized to coordinate polymer biosynthesis, modification, and export across both membranes and the peptidoglycan. To investigate how synthase-dependent secretion systems produce polymer at a molecular level, we determined the crystal structure of the AlgK-AlgX (AlgKX) complex involved in Pseudomonas aeruginosa alginate exopolysaccharide acetylation and export. We demonstrate that AlgKX directly binds alginate oligosaccharides and that formation of the complex is vital for polymer production and biofilm attachment. Finally, we propose a structural model for the AlgEKX outer membrane modification and secretion complex. Together, our study provides insight into how alginate biosynthesis proteins coordinate production of a key exopolysaccharide involved in establishing persistent Pseudomonas lung infections.
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Affiliation(s)
- Andreea A. Gheorghita
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada
| | - Yancheng E. Li
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada ,grid.20861.3d0000000107068890Present Address: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA USA
| | - Elena N. Kitova
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - Duong T. Bui
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - Roland Pfoh
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada
| | - Kristin E. Low
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.55614.330000 0001 1302 4958Present Address: Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Gregory B. Whitfield
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada ,grid.14848.310000 0001 2292 3357Present Address: Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC Canada
| | - Marthe T. C. Walvoort
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands ,grid.4830.f0000 0004 0407 1981Present Address: Department of Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
| | - Qingju Zhang
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands ,grid.411862.80000 0000 8732 9757Present Address: National Research Centre for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang, China
| | - Jeroen D. C. Codée
- grid.5132.50000 0001 2312 1970Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - John S. Klassen
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, Edmonton, AB Canada
| | - P. Lynne Howell
- grid.42327.300000 0004 0473 9646Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Biochemistry, University of Toronto, Toronto, ON Canada
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8
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Bui DT, Kitova EN, Mahal LK, Klassen JS. Mass spectrometry-based shotgun glycomics for discovery of natural ligands of glycan-binding proteins. Curr Opin Struct Biol 2022; 77:102448. [PMID: 36088799 DOI: 10.1016/j.sbi.2022.102448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/15/2022] [Accepted: 07/26/2022] [Indexed: 12/14/2022]
Abstract
The non-covalent associations of complex carbohydrates (glycans) with glycan-binding proteins mediate many important physiological and pathophysiological processes. Identifying these interactions is essential to understanding their diverse biological functions and enables the development of new disease treatments and diagnostics. Knowledge of the repertoire of glycans recognized by most glycan-binding proteins and their affinities is incomplete. Mass spectrometry-based screening of natural glycan libraries has emerged as a promising approach to defining the glycan interactome of glycan-binding proteins. Here, we review recent advances in mass spectrometry-based natural library screening that have led to the discovery of glycan ligands of endogenous and exogenous proteins and illuminated their binding specificities.
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Affiliation(s)
- Duong T Bui
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada. https://twitter.com/@Duong_T_Bui
| | - Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
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9
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Han L, Nguyen L, Schmidt EN, Esmaili M, Kitova EN, Overduin M, Macauley MS, Klassen JS. How Choice of Model Membrane Affects Protein–Glycosphingolipid Interactions: Insights from Native Mass Spectrometry. Anal Chem 2022; 94:16042-16049. [PMID: 36367338 DOI: 10.1021/acs.analchem.2c03067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Interactions between glycan-binding proteins (GBPs) and glycosphingolipids (GSLs) are involved in numerous physiological and pathophysiological processes. Many model membrane systems are available for studying GBP-GSL interactions, but a systematic investigation has not been carried out on how the nature of the model membrane affects binding. In this work, we use electrospray ionization mass spectrometry (ESI-MS), both direct and competitive assays, to measure the binding of cholera toxin B subunit homopentamer (CTB5) to GM1 ganglioside in liposomes, bilayer islands [styrene maleic acid lipid particles (SMALPs), nanodiscs (NDs), and picodiscs (PDs)], and micelles. We find that direct ESI-MS analysis of CTB5 binding to GM1 is unreliable due to non-uniform response factors, incomplete extraction of bound GM1 in the gas phase, and nonspecific CTB5-GM1 interactions. Conversely, indirect proxy ligand ESI-MS measurements show that the intrinsic (per binding site) association constants of CTB5 for PDs, NDs, and SMALPs are similar and comparable to the affinity of soluble GM1 pentasaccharide (GM1os). The observed affinity decreases with increasing GM1 content due to molecular crowding stemming from GM1 clustering. Unlike the smaller model membranes, the observed affinity of CTB5 toward GM1 liposomes is ∼10-fold weaker than GM1os and relatively insensitive to the GM1 content. GM1 glycomicelles exhibit the lowest affinity, ∼35-fold weaker than GM1os. Together, the results highlight experimental design considerations for quantitative GBP-GSL binding studies involving multisubunit GBPs and factors to consider when comparing results obtained with different membrane systems. Notably, they suggest that bilayer islands with a low percentage of GSL, wherein clustering is minimized, are ideal for assessing intrinsic strength of GBP-GSL interactions in a membrane environment, while binding to liposomes, which is sub-optimal due to extensive clustering, may be more representative of authentic cellular environments.
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Affiliation(s)
- Ling Han
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Linh Nguyen
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Edward N. Schmidt
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton T6G 2R3, Canada
| | - Elena N. Kitova
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton T6G 2R3, Canada
| | - Matthew S. Macauley
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton T6G 2E1, Alberta, Canada
| | - John S. Klassen
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
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10
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Marty MT. Fundamentals: How Do We Calculate Mass, Error, and Uncertainty in Native Mass Spectrometry? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1807-1812. [PMID: 36130030 DOI: 10.1021/jasms.2c00218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry (MS) is uniquely powerful for measuring the mass of intact proteins and other biomolecules. New applications have expanded intact protein analysis into biopharmaceuticals, native MS, and top-down proteomics, all of which have driven the need for more automated data-processing pipelines. However, key metrics in the field are often not precisely defined. For example, there are different views on how to calculate uncertainty from spectra. This Critical Insight will explore the different definitions of mass, error, and uncertainty. It will discuss situations where different definitions may be more suitable and provide recommendations for best practices. Targeting both beginners and experts, the goal of the discussion is to provide a common foundation of terminology, enhance statistical rigor, and improve automation of data analysis.
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Affiliation(s)
- Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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