1
|
Oney-Hawthorne SD, Barondeau DP. Fe-S cluster biosynthesis and maturation: Mass spectrometry-based methods advancing the field. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119784. [PMID: 38908802 DOI: 10.1016/j.bbamcr.2024.119784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
Iron‑sulfur (FeS) clusters are inorganic protein cofactors that perform essential functions in many physiological processes. Spectroscopic techniques have historically been used to elucidate details of FeS cluster type, their assembly and transfer, and changes in redox and ligand binding properties. Structural probes of protein topology, complex formation, and conformational dynamics are also necessary to fully understand these FeS protein systems. Recent developments in mass spectrometry (MS) instrumentation and methods provide new tools to investigate FeS cluster and structural properties. With the unique advantage of sampling all species in a mixture, MS-based methods can be utilized as a powerful complementary approach to probe native dynamic heterogeneity, interrogate protein folding and unfolding equilibria, and provide extensive insight into protein binding partners within an entire proteome. Here, we highlight key advances in FeS protein studies made possible by MS methodology and contribute an outlook for its role in the field.
Collapse
Affiliation(s)
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA.
| |
Collapse
|
2
|
Oates RN, Lieu LB, Srzentić K, Damoc E, Fornelli L. Characterization of a Monoclonal Antibody by Native and Denaturing Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2197-2208. [PMID: 39105725 DOI: 10.1021/jasms.4c00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Established in recent years as an important approach to unraveling the heterogeneity of intact monoclonal antibodies, native mass spectrometry has been rarely utilized for sequencing these complex biomolecules via tandem mass spectrometry. Typically, top-down mass spectrometry has been performed starting from highly charged precursor ions obtained via electrospray ionization under denaturing conditions (i.e., in the presence of organic solvents and acidic pH). Here we systematically benchmark four distinct ion dissociation methods─namely, higher-energy collisional dissociation, electron transfer dissociation, electron transfer dissociation/higher-energy collisional dissociation, and 213 nm ultraviolet photodissociation─in their capability to characterize a therapeutic monoclonal antibody, trastuzumab, starting from denatured and native-like precursor ions. Interestingly, native top-down mass spectrometry results in higher sequence coverage than the experiments carried out under denaturing conditions, with the exception of ultraviolet photodissociation. Globally, electron transfer dissociation followed by collision-based activation of product ions generates the largest number of backbone cleavages in disulfide protected regions, including the complementarity determining regions, regardless of electrospray ionization conditions. Overall, these findings suggest that native mass spectrometry can certainly be used for the gas-phase sequencing of whole monoclonal antibodies, although the dissociation of denatured precursor ions still returns a few backbone cleavages not identified in native experiments. Finally, a comparison of the fragmentation maps obtained under denaturing and native conditions strongly points toward disulfide bonds as the primary reason behind the largely overlapping dissociation patterns.
Collapse
Affiliation(s)
- Ryan N Oates
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Linda B Lieu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | | | - Eugen Damoc
- Thermo Fisher Scientific, Bremen, DE-HB 28199, Germany
| | - Luca Fornelli
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma 73019, United States
| |
Collapse
|
3
|
Adhikari J, Heffernan J, Edeling M, Fernandez E, Jethva PN, Diamond MS, Fremont DH, Gross ML. Epitope Mapping of Japanese Encephalitis Virus Neutralizing Antibodies by Native Mass Spectrometry and Hydrogen/Deuterium Exchange. Biomolecules 2024; 14:374. [PMID: 38540792 PMCID: PMC10967844 DOI: 10.3390/biom14030374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 06/27/2024] Open
Abstract
Japanese encephalitis virus (JEV) remains a global public health concern due to its epidemiological distribution and the existence of multiple strains. Neutralizing antibodies against this infection have shown efficacy in in vivo studies. Thus, elucidation of the epitopes of neutralizing antibodies can aid in the design and development of effective vaccines against different strains of JEV. Here, we describe a combination of native mass spectrometry (native-MS) and hydrogen/deuterium exchange mass spectrometry (HDX-MS) to complete screening of eight mouse monoclonal antibodies (MAbs) against JEV E-DIII to identify epitope regions. Native-MS was used as a first pass to identify the antibodies that formed a complex with the target antigen, and it revealed that seven of the eight monoclonal antibodies underwent binding. Native mass spectra of a MAb (JEV-27) known to be non-binding showed broad native-MS peaks and poor signal, suggesting the protein is a mixture or that there are impurities in the sample. We followed native-MS with HDX-MS to locate the binding sites for several of the complex-forming antibodies. This combination of two mass spectrometry-based approaches should be generally applicable and particularly suitable for screening of antigen-antibody and other protein-protein interactions when other traditional approaches give unclear results or are difficult, unavailable, or need to be validated.
Collapse
Affiliation(s)
- Jagat Adhikari
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.A.); (P.N.J.)
| | - James Heffernan
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA; (J.H.); (M.E.); (E.F.); (M.S.D.); (D.H.F.)
| | - Melissa Edeling
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA; (J.H.); (M.E.); (E.F.); (M.S.D.); (D.H.F.)
| | - Estefania Fernandez
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA; (J.H.); (M.E.); (E.F.); (M.S.D.); (D.H.F.)
| | - Prashant N. Jethva
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.A.); (P.N.J.)
| | - Michael S. Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA; (J.H.); (M.E.); (E.F.); (M.S.D.); (D.H.F.)
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63130, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63130, USA
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA
| | - Daved H. Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA; (J.H.); (M.E.); (E.F.); (M.S.D.); (D.H.F.)
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.A.); (P.N.J.)
| |
Collapse
|
4
|
McGee JP, Melani RD, Des Soye B, Croote D, Winton V, Quake SR, Kafader JO, Kelleher NL. Immunocomplexed Antigen Capture and Identification by Native Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2093-2097. [PMID: 37683262 PMCID: PMC10557138 DOI: 10.1021/jasms.3c00235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/26/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
Antibody-antigen interactions are central to the immune response. Variation of protein antigens such as isoforms and post-translational modifications can alter their antibody binding sites. To directly connect the recognition of protein antigens with their molecular composition, we probed antibody-antigen complexes by using native tandem mass spectrometry. Specifically, we characterized the prominent peanut allergen Ara h 2 and a convergent IgE variable region discovered in patients who are allergic to peanuts. In addition to measuring the antigen-induced dimerization of IgE antibodies, we demonstrated how immunocomplexes can be isolated in the gas phase and activated to eject, identify, and characterize proteoforms of their bound antigens. Using tandem experiments, we isolated the ejected antigens and then fragmented them to identify their chemical composition. These results establish native top-down mass spectrometry as a viable platform for precise and thorough characterization of immunocomplexes to relate structure to function and enable the discovery of antigen proteoforms and their binding sites.
Collapse
Affiliation(s)
- John P. McGee
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Ben Des Soye
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Derek Croote
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Valerie Winton
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Stephen R. Quake
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
| | - Jared O. Kafader
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
5
|
Brandner S, Habeck T, Lermyte F. New Insights into the Intrinsic Electron-Based Dissociation Behavior of Cytochrome c Oligomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1908-1916. [PMID: 37227392 DOI: 10.1021/jasms.3c00106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Between 2003 and 2017, four reports were published that demonstrated the intrinsic ability of the native iron-containing proteins cytochrome c and ferritin to undergo radical-based backbone fragmentation in the gas phase without the introduction of exogenous electrons. For cytochrome c in particular, this effect has so far only been reported to occur in the ion source, preventing the in-depth study of reactions occurring after gas-phase isolation of specific precursors. Here, we report the first observation of this intrinsic native electron capture dissociation behavior after quadrupole isolation of specific charge states of the cytochrome c dimer and trimer, providing direct experimental support for key aspects of the mechanism proposed 20 years ago. Furthermore, we provide evidence that, in contrast to some earlier proposals, these oligomeric states are formed in bulk solution rather than during the electrospray ionization process and that the observed fragmentation site preferences can be rationalized through the structure and interactions within these native oligomers rather than the monomer. We also show that the observed fragmentation pattern─and indeed, whether or not fragmentation occurs─is highly sensitive to the provenance and history of the protein samples, to the extent that samples can show distinct fragmentation behavior despite behaving identically in ion mobility experiments. This rather underexplored method therefore represents an exquisitely sensitive conformational probe and will hopefully receive more attention from the biomolecular mass spectrometry community in the future.
Collapse
Affiliation(s)
- Sarah Brandner
- Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, 64287 Darmstadt, Germany
| | - Tanja Habeck
- Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, 64287 Darmstadt, Germany
| | - Frederik Lermyte
- Department of Chemistry, Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, 64287 Darmstadt, Germany
| |
Collapse
|
6
|
Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
Collapse
Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
7
|
Jooß K, McGee JP, Kelleher NL. Native Mass Spectrometry at the Convergence of Structural Biology and Compositional Proteomics. Acc Chem Res 2022; 55:1928-1937. [PMID: 35749283 DOI: 10.1021/acs.accounts.2c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ConspectusBiology is driven by a vast set of molecular interactions that evolved over billions of years. Just as covalent modifications like acetylations and phosphorylations can change a protein's function, so too can noncovalent interactions with metals, small molecules, and other proteins. However, much of the language of protein-level biology is left either undiscovered or inferred, as traditional methods used in the field of proteomics use conditions that dissociate noncovalent interactions and denature proteins.Just in the past few years, mass spectrometry (MS) has evolved the capacity to preserve and subsequently characterize the complete composition of endogenous protein complexes. Using this "native" type of mass spectrometry, a complex can be activated to liberate some or all of its subunits, typically via collisions with neutral gas or solid surfaces and isolated before further characterization ("Native Top-Down MS," or nTDMS). The subunit mass, the parent ion mass, and the fragment ions of the activated subunits can be used to piece together the precise molecular composition of the parent complex. When performed en masse in discovery mode (i.e., "native proteomics"), the interactions of life─including protein modifications─will eventually be clarified and linked to dysfunction in human disease states.In this Account, we describe the current and future components of the native MS toolkit, covering the challenges the field faces to characterize ever larger bioassemblies. Each of the three pillars of native proteomics are addressed: (i) separations, (ii) top-down mass spectrometry, and (iii) integration with structural biology. Complexes such as endogenous nucleosomes can be targeted now using nTDMS, whereas virus particles, exosomes, and high-density lipoprotein particles will be tackled in the coming few years. The future work to adequately address the size and complexity of mega- to gigadalton complexes will include native separations, single ion mass spectrometry, and new data types. The use of nTDMS in discovery mode will incorporate native-compatible separation techniques to maximize the number of proteoforms in complexes identified. With a new wave of innovations, both targeted and discovery mode nTDMS will expand to include extremely scarce and exceedingly heterogeneous bioassemblies. Understanding the proteinaceous interactions of life and how they go wrong (e.g., misfolding, forming complexes in dysfunctional stoichiometries and configurations) will not only inform the development of life-restoring therapeutics but also deepen our understanding of life at the molecular level.
Collapse
Affiliation(s)
- Kevin Jooß
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - John P McGee
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States.,Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Gross ML, Rempel DL. A PERSPECTIVE ON PERSONAL CONTRIBUTIONS TO FT-ICR MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2022; 41:178-193. [PMID: 32960989 PMCID: PMC8888036 DOI: 10.1002/mas.21657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
This is a personal perspective on our contributions to FT-ICR, many of early ones in a collaboration with Charles Wilkins and Michael Gross starting in the mid-1970s and then continuing for many years in collaboration of Don Rempel and Michael Gross. The perspective is to honor Alan Marshall, who with Melvin Comisarow, first demonstrated FT-ICR MS in 1974 (Comisarow & Marshall, 1974 ). Our intention is to review the contributions made together with Wilkins, Rempel, and a group of graduate and postdoctoral students, starting at the University of Nebraska-Lincoln and continuing here at Washington University in St. Louis. Besides offering a chance to reminisce about the early and exciting days of FT-ICR MS when academic laboratories were building and modifying mass spectrometers and other instruments, a nearly lost art, I am reminded of my editorship of this journal occurring over part of that time.
Collapse
Affiliation(s)
- Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130
| | - Don L Rempel
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130
| |
Collapse
|
10
|
Campuzano IDG, Sandoval W. Denaturing and Native Mass Spectrometric Analytics for Biotherapeutic Drug Discovery Research: Historical, Current, and Future Personal Perspectives. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1861-1885. [PMID: 33886297 DOI: 10.1021/jasms.1c00036] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Mass spectrometry (MS) plays a key role throughout all stages of drug development and is now as ubiquitous as other analytical techniques such as surface plasmon resonance, nuclear magnetic resonance, and supercritical fluid chromatography, among others. Herein, we aim to discuss the history of MS, both electrospray and matrix-assisted laser desorption ionization, specifically for the analysis of antibodies, evolving through to denaturing and native-MS analysis of newer biologic moieties such as antibody-drug conjugates, multispecific antibodies, and interfering nucleic acid-based therapies. We discuss challenging therapeutic target characterization such as membrane protein receptors. Importantly, we compare and contrast the MS and hyphenated analytical chromatographic methods used to characterize these therapeutic modalities and targets within biopharmaceutical research and highlight the importance of appropriate MS deconvolution software and its essential contribution to project progression. Finally, we describe emerging applications and MS technologies that are still predominantly within either a development or academic stage of use but are poised to have significant impact on future drug development within the biopharmaceutic industry once matured. The views reflected herein are personal and are not meant to be an exhaustive list of all relevant MS performed within biopharmaceutical research but are what we feel have been historically, are currently, and will be in the future the most impactful for the drug development process.
Collapse
MESH Headings
- Antibodies, Monoclonal/analysis
- Automation, Laboratory
- Biopharmaceutics/methods
- Chromatography, Liquid
- Drug Discovery/methods
- Drug Industry/history
- History, 20th Century
- History, 21st Century
- Humans
- Immunoconjugates/analysis
- Immunoconjugates/chemistry
- Protein Denaturation
- Protein Processing, Post-Translational
- Proteins/analysis
- Spectrometry, Mass, Electrospray Ionization/history
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/history
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Collapse
Affiliation(s)
- Iain D G Campuzano
- Discovery Attribute Sciences, Amgen Research, 1 Amgen Center Drive, Thousand Oaks, California 92130, United States
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| |
Collapse
|
11
|
Wagner ND, Huang Y, Liu T, Gross ML. Post-HDX Deglycosylation of Fc Gamma Receptor IIIa Glycoprotein Enables HDX Characterization of Its Binding Interface with IgG. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1638-1643. [PMID: 33625217 PMCID: PMC8906513 DOI: 10.1021/jasms.1c00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protein glycosylation is a common and highly heterogeneous post-translational modification that challenges biophysical characterization technologies. The heterogeneity of glycoproteins makes their structural analysis difficult; in particular, hydrogen-deuterium exchange mass spectrometry (HDX-MS) often suffers from poor sequence coverage near the glycosylation site. A pertinent example is the Fc gamma receptor RIIIa (FcγRIIIa, CD16a), a glycoprotein expressed on the surface of natural killer cells (NK) that binds the Fc domain of IgG antibodies as a trigger for antibody-dependent cell-mediated cytotoxicity (ADCC). Here, we describe an adaptation of a previously reported method using PNGase A for post-HDX deglycosylation to characterize the binding between the highly glycosylated CD16a and IgG1. Upon optimization of the method to improve sequence coverage while minimizing back-exchange, we achieved coverage of four of the five glycosylation sites of CD16a. Despite some back-exchange, trends in HDX are consistent with previously reported CD16a/IgG-Fc complex structures; furthermore, binding of peptides covering the glycosylated asparagine-164 can be interrogated when using this protocol, previously not seen using standard HDX-MS.
Collapse
Affiliation(s)
- Nicole D. Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130 United States
| | - Yining Huang
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285 United States
- Corresponding Authors: ,
| | - Tun Liu
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285 United States
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130 United States
- Corresponding Authors: ,
| |
Collapse
|
12
|
Adhikari J, Zhao H, Fernandez E, Huang Y, Diamond MS, Fremont DH, Gross ML. Hydrogen-deuterium exchange mass spectrometry identifies spatially distinct antibody epitopes on domain III of the Zika virus envelope protein. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4685. [PMID: 36101787 PMCID: PMC9467453 DOI: 10.1002/jms.4685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/10/2020] [Indexed: 06/15/2023]
Abstract
Zika Virus (ZIKV) has become a global public health concern because it causes fetal microcephaly and other neurological complications in humans. Currently, there are no approved treatments or vaccines for ZIKV infection. We describe here the detailed epitopes for six monoclonal antibodies (mAbs) that bind to domain III of the envelope protein of ZIKV, some of which have therapeutic potential. We show that by using hydrogen-deuterium exchange mass spectrometry (HDX-MS), we can identify three spatially distinct epitopes for the six mAbs investigated. The HDX-MS approach identified epitopes for three mAbs that agreed well with recently reported X-ray crystallography data. The HDX-MS determined epitopes for the other three anti-ZIKV mAbs for which there were no crystal structures, and the epitopes were confirmed by structure-guided mutagenesis and biolayer interferometry (BLI) competition binding assay. Our results have implications for the design of vaccine and antibody therapeutics against ZIKV and demonstrate the use of HDX-MS as a rapid and valid approach for epitope mapping.
Collapse
Affiliation(s)
- Jagat Adhikari
- Department of Chemistry, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Haiyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Estefania Fernandez
- Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Yining Huang
- Department of Chemistry, Washington University in St. Louis, Saint Louis, Missouri, USA
- Present address: Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, Saint Louis, Missouri, USA
| |
Collapse
|
13
|
Mehaffey MR, Lee J, Jung J, Lanzillotti MB, Escobar EE, Morgenstern KR, Georgiou G, Brodbelt JS. Mapping a Conformational Epitope of Hemagglutinin A Using Native Mass Spectrometry and Ultraviolet Photodissociation. Anal Chem 2020; 92:11869-11878. [PMID: 32867493 PMCID: PMC7808878 DOI: 10.1021/acs.analchem.0c02237] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As the importance of effective vaccines and the role of protein therapeutics in the drug industry continue to expand, alternative strategies to characterize protein complexes are needed. Mass spectrometry (MS) in conjunction with enzymatic digestion or chemical probes has been widely used for mapping binding epitopes at the molecular level. However, advances in instrumentation and application of activation methods capable of accessing higher energy dissociation pathways have recently allowed direct analysis of protein complexes. Here we demonstrate a workflow utilizing native MS and ultraviolet photodissociation (UVPD) to map the antigenic determinants of a model antibody-antigen complex involving hemagglutinin (HA), the primary immunogenic antigen of the influenza virus, and the D1 H1-17/H3-14 antibody which has been shown to confer potent protection to lethal infection in mice despite lacking neutralization activity. Comparison of sequence coverages upon UV photoactivation of HA and of the HA·antibody complex indicates the elimination of some sequence ions that originate from backbone cleavages exclusively along the putative epitope regions of HA in the presence of the antibody. Mapping the number of sequence ions covering the HA antigen versus the HA·antibody complex highlights regions with suppressed backbone cleavage and allows elucidation of unknown epitopes. Moreover, examining the observed fragment ion types generated by UVPD demonstrates a loss in diversity exclusively along the antigenic determinants upon MS/MS of the antibody-antigen complex. UVPD-MS shows promise as a method to rapidly map epitope regions along antibody-antigen complexes as novel antibodies are discovered or developed.
Collapse
Affiliation(s)
| | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
| | | | | | | | | | | | | |
Collapse
|
14
|
Williams JP, Morrison LJ, Brown JM, Beckman JS, Voinov VG, Lermyte F. Top-Down Characterization of Denatured Proteins and Native Protein Complexes Using Electron Capture Dissociation Implemented within a Modified Ion Mobility-Mass Spectrometer. Anal Chem 2020; 92:3674-3681. [PMID: 31999103 DOI: 10.1021/acs.analchem.9b04763] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Electron-based fragmentation methods have revolutionized biomolecular mass spectrometry, in particular native and top-down protein analysis. Here, we report the use of a new electromagnetostatic cell to perform electron capture dissociation (ECD) within a quadrupole/ion mobility/time-of-flight mass spectrometer. This cell was installed between the ion mobility and time-of-flight regions of the instrument, and fragmentation was fast enough to be compatible with mobility separation. The instrument was already fitted with electron transfer dissociation (ETD) between the quadrupole and mobility regions prior to modification. We show excellent fragmentation efficiency for denatured peptides and proteins without the need to trap ions in the gas phase. Additionally, we demonstrate native top-down backbone fragmentation of noncovalent protein complexes, leading to comparable sequence coverage to what was achieved using the instrument's existing ETD capabilities. Limited collisional ion activation of the hemoglobin tetramer before ECD was reflected in the observed fragmentation pattern, and complementary ion mobility measurements prior to ECD provided orthogonal evidence of monomer unfolding within this complex. The approach demonstrated here provides a powerful platform for both top-down proteomics and mass spectrometry-based structural biology studies.
Collapse
Affiliation(s)
- Jonathan P Williams
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Lindsay J Morrison
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Joseph S Beckman
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Valery G Voinov
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States.,Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Frederik Lermyte
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom.,Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
15
|
Lermyte F, Tsybin YO, O'Connor PB, Loo JA. Top or Middle? Up or Down? Toward a Standard Lexicon for Protein Top-Down and Allied Mass Spectrometry Approaches. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1149-1157. [PMID: 31073892 PMCID: PMC6591204 DOI: 10.1007/s13361-019-02201-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 05/18/2023]
Abstract
In recent years, there has been increasing interest in top-down mass spectrometry (TDMS) approaches for protein analysis, driven both by technological advancements and efforts such as those by the multinational Consortium for Top-Down Proteomics (CTDP). Today, diverse sample preparation and ionization methods are employed to facilitate TDMS analysis of denatured and native proteins and their complexes. The goals of these studies vary, ranging from protein and proteoform identification, to determination of the binding site of a (non)covalently-bound ligand, and in some cases even with the aim to study the higher order structure of proteins and complexes. Currently, however, no widely accepted terminology exists to precisely and unambiguously distinguish between the different types of TDMS experiments that can be performed. Instead, ad hoc developed terminology is often used, which potentially complicates communication of top-down and allied methods and their results. In this communication, we consider the different types of top-down (or top-down-related) MS experiments that have been performed and reported, and define distinct categories based on the protocol used and type(s) of information that can be obtained. We also consider the different possible conventions for distinguishing between middle- and top-down MS, based on both sample preparation and precursor ion mass. We believe that the proposed framework presented here will prove helpful for researchers to communicate about TDMS and will be an important step toward harmonizing and standardizing this growing field. Graphical Abstract.
Collapse
Affiliation(s)
- Frederik Lermyte
- School of Engineering, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park, 1015, Lausanne, Switzerland
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, David Geffen School of Medicine, and UCLA/DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, USA
| |
Collapse
|
16
|
Chen G, Karauzum H, Long H, Carranza D, Holtsberg FW, Howell KA, Abaandou L, Zhang B, Jarvik N, Ye W, Liao GC, Gross ML, Leung DW, Amarasinghe GK, Aman MJ, Sidhu SS. Potent Neutralization of Staphylococcal Enterotoxin B In Vivo by Antibodies that Block Binding to the T-Cell Receptor. J Mol Biol 2019; 431:4354-4367. [PMID: 30928493 DOI: 10.1016/j.jmb.2019.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 11/15/2022]
Abstract
To develop an antibody (Ab) therapeutic against staphylococcal enterotoxin B (SEB), a potential incapacitating bioterrorism agent and a major cause of food poisoning, we developed a "class T" anti-SEB neutralizing Ab (GC132) targeting an epitope on SEB distinct from that of previously developed "class M" Abs. A systematic engineering approach was applied to affinity-mature Ab GC132 to yield an optimized therapeutic candidate (GC132a) with sub-nanomolar binding affinity. Mapping of the binding interface by hydrogen-deuterium exchange coupled to mass spectrometry revealed that the class T epitope on SEB overlapped with the T-cell receptor binding site, whereas other evidence suggested that the class M epitope overlapped with the binding site for the major histocompatibility complex. In the IgG format, GC132a showed ∼50-fold more potent toxin-neutralizing efficacy than the best class M Ab in vitro, and fully protected mice from lethal challenge in a toxic shock post-exposure model. We also engineered bispecific Abs (bsAbs) that bound tetravalently by utilizing two class M binding sites and two class T binding sites. The bsAbs displayed enhanced toxin neutralization efficacy compared with the respective monospecific Ab subunits as well as a mixture of the two, indicating that enhanced efficacy was due to heterotypic tetravalent binding to two non-overlapping epitopes on SEB. Together, these results suggest that class T anti-SEB Ab GC132a is an excellent candidate for clinical development and for bsAb engineering.
Collapse
Affiliation(s)
- Gang Chen
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | | | - Hua Long
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Danielle Carranza
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | | | - Katie A Howell
- Integrated Biotherapeutics, Inc., Rockville, MD 20850, USA
| | - Laura Abaandou
- Integrated Biotherapeutics, Inc., Rockville, MD 20850, USA
| | - Bojie Zhang
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
| | - Nick Jarvik
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Wei Ye
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Grant C Liao
- Integrated Biotherapeutics, Inc., Rockville, MD 20850, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - M Javad Aman
- Integrated Biotherapeutics, Inc., Rockville, MD 20850, USA.
| | - Sachdev S Sidhu
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
| |
Collapse
|
17
|
Garcia NK, Deperalta G, Wecksler AT. Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry. Protein Pept Lett 2019; 26:35-43. [PMID: 30484396 DOI: 10.2174/0929866526666181128141953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/01/2018] [Accepted: 10/29/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. CONCLUSION Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.
Collapse
Affiliation(s)
- Natalie K Garcia
- Department of Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA 94080, United States
| | - Galahad Deperalta
- Department of Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA 94080, United States
| | - Aaron T Wecksler
- Department of Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA 94080, United States
| |
Collapse
|
18
|
Łącki MK, Lermyte F, Miasojedow B, Startek MP, Sobott F, Valkenborg D, Gambin A. masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry. Anal Chem 2019; 91:1801-1807. [DOI: 10.1021/acs.analchem.8b01479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mateusz K. Łącki
- University Medical Center, Johannes Gutenberg University, Mainz D-55131, Germany
| | - Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp 2000, Belgium
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Błażej Miasojedow
- Department of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw 02-097, Poland
| | - Michał P. Startek
- Department of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw 02-097, Poland
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp 2000, Belgium
- Flemish Institute for Technological Research (VITO), Mol 2400, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt 3500, Belgium
| | - Anna Gambin
- Department of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw 02-097, Poland
| |
Collapse
|
19
|
Lermyte F, Valkenborg D, Loo JA, Sobott F. Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure. MASS SPECTROMETRY REVIEWS 2018; 37:750-771. [PMID: 29425406 PMCID: PMC6131092 DOI: 10.1002/mas.21560] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 05/11/2023]
Abstract
In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation. Although we focus on the two most widely used methods-ECD and ETD-we also discuss the use of other ion/electron, ion/ion, and ion/neutral fragmentation methods, useful for interrogation of a range of classes of biomolecules in positive- and negative-ion mode, and speculate about how this exciting field might evolve in the coming years.
Collapse
Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Agoralaan, Diepenbeek, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
20
|
Terral G, Champion T, Debaene F, Colas O, Bourguet M, Wagner-Rousset E, Corvaia N, Beck A, Cianferani S. Epitope characterization of anti-JAM-A antibodies using orthogonal mass spectrometry and surface plasmon resonance approaches. MAbs 2017; 9:1317-1326. [PMID: 28933642 DOI: 10.1080/19420862.2017.1380762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Junctional adhesion molecule-A (JAM-A) is an adherens and tight junction protein expressed by endothelial and epithelial cells and associated with cancer progression. We present here the extensive characterization of immune complexes involving JAM-A antigen and three monoclonal antibodies (mAbs), including hz6F4-2, a humanized version of anti-tumoral 6F4 mAb identified by a functional and proteomic approach in our laboratory. A specific workflow that combines orthogonal approaches has been designed to determine binding stoichiometries along with JAM-A epitope mapping determination at high resolution for these three mAbs. Native mass spectrometry experiments revealed different binding stoichiometries and affinities, with two molecules of JAM-A being able to bind to hz6F4-2 and F11 Fab, while only one JAM-A was bound to J10.4. Surface plasmon resonance indirect competitive binding assays suggested epitopes located in close proximity for hz6F4-2 and F11. Finally, hydrogen-deuterium exchange mass spectrometry was used to precisely identify epitopes for all mAbs. The results obtained by orthogonal biophysical approaches showed a clear correlation between the determined epitopes and JAM-A binding characteristics, allowing the basis for molecular recognition of JAM-A by hz6F4-2 to be definitively established for the first time. Taken together, our results highlight the power of MS-based structural approaches for epitope mapping and mAb conformational characterization.
Collapse
Affiliation(s)
- Guillaume Terral
- a Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178 , Strasbourg , France
| | - Thierry Champion
- b Centre d'Immunologie Pierre-Fabre (CIPF) , Saint-Julien-en-Genevois , France
| | - François Debaene
- a Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178 , Strasbourg , France
| | - Olivier Colas
- b Centre d'Immunologie Pierre-Fabre (CIPF) , Saint-Julien-en-Genevois , France
| | - Maxime Bourguet
- a Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178 , Strasbourg , France
| | - Elsa Wagner-Rousset
- b Centre d'Immunologie Pierre-Fabre (CIPF) , Saint-Julien-en-Genevois , France
| | - Nathalie Corvaia
- b Centre d'Immunologie Pierre-Fabre (CIPF) , Saint-Julien-en-Genevois , France
| | - Alain Beck
- b Centre d'Immunologie Pierre-Fabre (CIPF) , Saint-Julien-en-Genevois , France
| | - Sarah Cianferani
- a Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178 , Strasbourg , France
| |
Collapse
|
21
|
Wang B, Qin Q, Chang M, Li S, Shi X, Xu G. Molecular interaction study of flavonoids with human serum albumin using native mass spectrometry and molecular modeling. Anal Bioanal Chem 2017; 410:827-837. [PMID: 28840311 DOI: 10.1007/s00216-017-0564-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/30/2017] [Accepted: 08/02/2017] [Indexed: 11/29/2022]
Abstract
Noncovalent interactions between proteins and small-molecule ligands widely exist in biological bodies and play significant roles in many physiological and pathological processes. Native mass spectrometry (MS) has emerged as a new powerful tool to study noncovalent interactions by directly analyzing the ligand-protein complexes. In this work, an ultrahigh-resolution native MS method based on a 15-T SolariX XR Fourier transform ion cyclotron resonance mass spectrometer was firstly used to investigate the interaction between human serum albumin (HSA) and flavonoids. Various flavonoids with similar structure were selected to unravel the relationship between the structure of flavonoids and their binding affinity for HSA. It was found that the position of the hydroxyl groups and double bond of flavonoids could influence the noncovalent interaction. Through a competitive experiment between HSA binding site markers and apigenin, the subdomain IIA (site 1) of HSA was determined as the binding site for flavonoids. Moreover, a cooperative allosteric interaction between apigenin and ibuprofen was found from their different HSA binding sites, which was further verified by circular dichroism spectroscopy and molecular docking studies. These results show that native MS is a useful tool to investigate the molecular interaction between a protein and its ligands. Graphical abstract Unravel the relationship between the structure of flavonoids and their binding affinity to HSA by native MS.
Collapse
Affiliation(s)
- Bohong Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengmeng Chang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyan Li
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| |
Collapse
|
22
|
Zhang Y, Wecksler AT, Molina P, Deperalta G, Gross ML. Mapping the Binding Interface of VEGF and a Monoclonal Antibody Fab-1 Fragment with Fast Photochemical Oxidation of Proteins (FPOP) and Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:850-858. [PMID: 28255747 PMCID: PMC5624547 DOI: 10.1007/s13361-017-1601-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 05/11/2023]
Abstract
We previously analyzed the Fab-1:VEGF (vascular endothelial growth factor) system described in this work, with both native top-down mass spectrometry and bottom-up mass spectrometry (carboxyl-group or GEE footprinting) techniques. This work continues bottom-up mass spectrometry analysis using a fast photochemical oxidation of proteins (FPOP) platform to map the solution binding interface of VEGF and a fragment antigen binding region of an antibody (Fab-1). In this study, we use FPOP to compare the changes in solvent accessibility by quantitating the extent of oxidative modification in the unbound versus bound states. Determining the changes in solvent accessibility enables the inference of the protein binding sites (epitope and paratopes) and a comparison to the previously published Fab-1:VEGF crystal structure, adding to the top-down and bottom-up data. Using this method, we investigated peptide-level and residue-level changes in solvent accessibility between the unbound proteins and bound complex. Mapping these data onto the Fab-1:VEGF crystal structure enabled successful characterization of both the binding region and regions of remote conformation changes. These data, coupled with our previous higher order structure (HOS) studies, demonstrate the value of a comprehensive toolbox of methods for identifying the putative epitopes and paratopes for biotherapeutic antibodies. Graphical abstract ᅟ.
Collapse
Affiliation(s)
- Ying Zhang
- Center for Biomedical and Bioorganic Mass Spectrometry, Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Analytical Research and Development, Pfizer Inc., Andover, MA, 01810, USA
| | - Aaron T Wecksler
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, 94080, USA.
| | - Patricia Molina
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Galahad Deperalta
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Michael L Gross
- Center for Biomedical and Bioorganic Mass Spectrometry, Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| |
Collapse
|
23
|
Zhang H, Harrington LB, Lu Y, Prado M, Saer R, Rempel D, Blankenship RE, Gross ML. Native Mass Spectrometry Characterizes the Photosynthetic Reaction Center Complex from the Purple Bacterium Rhodobacter sphaeroides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:87-95. [PMID: 27506206 PMCID: PMC5613939 DOI: 10.1007/s13361-016-1451-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/07/2016] [Accepted: 07/10/2016] [Indexed: 06/06/2023]
Abstract
Native mass spectrometry (MS) is an emerging approach to study protein complexes in their near-native states and to elucidate their stoichiometry and topology. Here, we report a native MS study of the membrane-embedded reaction center (RC) protein complex from the purple photosynthetic bacterium Rhodobacter sphaeroides. The membrane-embedded RC protein complex is stabilized by detergent micelles in aqueous solution, directly introduced into a mass spectrometer by nano-electrospray (nESI), and freed of detergents and dissociated in the gas phase by collisional activation. As the collision energy is increased, the chlorophyll pigments are gradually released from the RC complex, suggesting that native MS introduces a near-native structure that continues to bind pigments. Two bacteriochlorophyll a pigments remain tightly bound to the RC protein at the highest collision energy. The order of pigment release and their resistance to release by gas-phase activation indicates the strength of pigment interaction in the RC complex. This investigation sets the stage for future native MS studies of membrane-embedded photosynthetic pigment-protein and related complexes.Graphical Abstract.
Collapse
Affiliation(s)
- Hao Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Lucas B Harrington
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Yue Lu
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Mindy Prado
- Department of Biology, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Rafael Saer
- Department of Biology, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Don Rempel
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
- Department of Biology, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
- Photosynthetic Antenna Research Center, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
| |
Collapse
|