1
|
Jethva PN, Gross ML. Hydrogen Deuterium Exchange and other Mass Spectrometry-based Approaches for Epitope Mapping. FRONTIERS IN ANALYTICAL SCIENCE 2023; 3:1118749. [PMID: 37746528 PMCID: PMC10512744 DOI: 10.3389/frans.2023.1118749] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Antigen-antibody interactions are a fundamental subset of protein-protein interactions responsible for the "survival of the fittest". Determining the interacting interface of the antigen, called an epitope, and that on the antibody, called a paratope, is crucial to antibody development. Because each antigen presents multiple epitopes (unique footprints), sophisticated approaches are required to determine the target region for a given antibody. Although X-ray crystallography, Cryo-EM, and nuclear magnetic resonance can provide atomic details of an epitope, they are often laborious, poor in throughput, and insensitive. Mass spectrometry-based approaches offer rapid turnaround, intermediate structural resolution, and virtually no size limit for the antigen, making them a vital approach for epitope mapping. In this review, we describe in detail the principles of hydrogen deuterium exchange mass spectrometry in application to epitope mapping. We also show that a combination of MS-based approaches can assist or complement epitope mapping and push the limit of structural resolution to the residue level. We describe in detail the MS methods used in epitope mapping, provide our perspective about the approaches, and focus on elucidating the role that HDX-MS is playing now and in the future by organizing a discussion centered around several improvements in prototype instrument/applications used for epitope mapping. At the end, we provide a tabular summary of the current literature on HDX-MS-based epitope mapping.
Collapse
Affiliation(s)
- Prashant N. Jethva
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
| |
Collapse
|
2
|
Hogan JM, Lee PS, Wong SC, West SM, Morishige WH, Bee C, Tapia GC, Rajpal A, Strop P, Dollinger G. Residue-Level Characterization of Antibody Binding Epitopes Using Carbene Chemical Footprinting. Anal Chem 2023; 95:3922-3931. [PMID: 36791402 DOI: 10.1021/acs.analchem.2c03091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Characterization of antibody binding epitopes is an important factor in therapeutic drug discovery, as the binding site determines and drives antibody pharmacology and pharmacokinetics. Here, we present a novel application of carbene chemical footprinting with mass spectrometry for identification of antibody binding epitopes at the single-residue level. Two different photoactivated diazirine reagents provide complementary labeling information allowing structural refinement of the antibody binding interface. We applied this technique to map the epitopes of multiple MICA and CTLA-4 antibodies and validated the findings with X-ray crystallography and yeast surface display epitope mapping. The characterized epitopes were used to understand biolayer interferometry-derived competitive binding results at the structural level. We show that carbene footprinting provides fast and high-resolution epitope information critical in the antibody selection process and enables mechanistic understanding of function to accelerate the drug discovery process.
Collapse
Affiliation(s)
- Jason M Hogan
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Peter S Lee
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Susan C Wong
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Sean M West
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Winse H Morishige
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Christine Bee
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Gamze Camdere Tapia
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Arvind Rajpal
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Pavel Strop
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Gavin Dollinger
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| |
Collapse
|
3
|
Tremblay CY, Kirsch ZJ, Vachet RW. Complementary Structural Information for Antibody-Antigen Complexes from Hydrogen-Deuterium Exchange and Covalent Labeling Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1303-1314. [PMID: 35708229 PMCID: PMC9631465 DOI: 10.1021/jasms.2c00108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Characterizing antibody-antigen interactions is necessary for properly developing therapeutic antibodies, understanding their mechanisms of action, and patenting new drug molecules. Here, we demonstrate that hydrogen-deuterium exchange (HDX) mass spectrometry (MS) measurements together with diethylpyrocarbonate (DEPC) covalent labeling (CL) MS measurements provide higher order structural information about antibody-antigen interactions that is not available from either technique alone. Using the well-characterized model system of tumor necrosis factor α (TNFα) in complex with three different monoclonal antibodies (mAbs), we show that two techniques offer a more complete overall picture of TNFα's structural changes upon binding different mAbs, sometimes providing synergistic information about binding sites and changes in protein dynamics upon binding. Labeling decreases in CL generally occur near the TNFα epitope, whereas decreases in HDX can span the entire protein due to substantial stabilization that occurs when mAbs bind TNFα. Considering both data sets together clarifies the TNFα regions that undergo a decrease in solvent exposure due to mAb binding and that undergo a change in dynamics due to mAb binding. Moreover, the single-residue level resolution of DEPC-CL/MS can clarify HDX/MS data for long peptides. We feel that the two techniques should be used together when studying the mAb-antigen interactions because of the complementary information they provide.
Collapse
|
4
|
Tremblay CY, Kirsch ZJ, Vachet RW. Epitope Mapping with Diethylpyrocarbonate Covalent Labeling-Mass Spectrometry. Anal Chem 2022; 94:1052-1059. [PMID: 34932327 PMCID: PMC8785103 DOI: 10.1021/acs.analchem.1c04038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antigen-antibody epitope mapping is essential for understanding binding mechanisms and developing new protein therapeutics. In this study, we investigate diethylpyrocarbonate (DEPC) covalent labeling-mass spectrometry as a means of analyzing antigen-antibody interactions using the well-characterized model system of TNFα in complex with three different antibodies. Results show that residues buried in the epitope undergo substantial decreases in labeling, as expected. Interestingly, serine, threonine, and tyrosine residues at the edges of the epitope undergo unexpected increases in labeling. The increased labeling of these weakly nucleophilic residues is caused by the formation of hydrophobic pockets upon antibody binding that presumably increase local DEPC concentrations. Residues that are distant from the epitope generally do not undergo changes in labeling extent; however, some that do change experience variations in their local microenvironment due to side-chain reorganization or stabilization of the TNFα trimer that occurs upon binding. Overall, DEPC labeling of antigen-antibody complexes is found to depend on both changes in solvent exposure and changes to the residue microenvironment.
Collapse
|
5
|
Lin Y, Gross ML. Mass Spectrometry-Based Structural Proteomics for Metal Ion/Protein Binding Studies. Biomolecules 2022; 12:135. [PMID: 35053283 PMCID: PMC8773722 DOI: 10.3390/biom12010135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 01/01/2023] Open
Abstract
Metal ions are critical for the biological and physiological functions of many proteins. Mass spectrometry (MS)-based structural proteomics is an ever-growing field that has been adopted to study protein and metal ion interactions. Native MS offers information on metal binding and its stoichiometry. Footprinting approaches coupled with MS, including hydrogen/deuterium exchange (HDX), "fast photochemical oxidation of proteins" (FPOP) and targeted amino-acid labeling, identify binding sites and regions undergoing conformational changes. MS-based titration methods, including "protein-ligand interactions by mass spectrometry, titration and HD exchange" (PLIMSTEX) and "ligand titration, fast photochemical oxidation of proteins and mass spectrometry" (LITPOMS), afford binding stoichiometry, binding affinity, and binding order. These MS-based structural proteomics approaches, their applications to answer questions regarding metal ion protein interactions, their limitations, and recent and potential improvements are discussed here. This review serves as a demonstration of the capabilities of these tools and as an introduction to wider applications to solve other questions.
Collapse
Affiliation(s)
- Yanchun Lin
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| |
Collapse
|
6
|
Huang RYC, Wang Y, Jhatakia AD, Deng AX, Bee C, Deshpande S, Rangan VS, Bezman N, Gudmundsson O, Chen G. Higher-Order Structure Characterization of NKG2A/CD94 Protein Complex and Anti-NKG2A Antibody Binding Epitopes by Mass Spectrometry-Based Protein Footprinting Strategies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1567-1574. [PMID: 33415981 DOI: 10.1021/jasms.0c00399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
NK group 2 member A (NKG2A), an immune checkpoint inhibitor, is an emerging therapeutic target in immuno-oncology. NKG2A forms a heterodimer with CD94 on the cell surface of NK and a subset of T cells and recognizes the nonclassical human leukocyte antigen (HLA-E) in humans. Therapeutic blocking antibodies that block the ligation between HLA-E and NKG2A/CD94 have been shown to enhance antitumor immunity in mice and humans. In this study, we illustrate the practical utilities of mass spectrometry (MS)-based protein footprinting in areas from reagent characterization to antibody epitope mapping. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) in the higher-order structure characterization of NKG2A in complex with CD94 provides novel insights into the conformational dynamics of NKG2A/CD94 heterodimer. To fully understand antibody/target interactions, we employed complementary protein footprinting methods, including HDX-MS and fast photochemical oxidation of proteins (FPOP)-MS, to determine the binding epitopes of therapeutic monoclonal antibodies targeting NKG2A. Such a combination approach provides molecular insights into the binding mechanisms of antibodies to NKG2A with high specificity, demonstrating the blockade of NKG2A/HLA-E interaction.
Collapse
Affiliation(s)
- Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey United States
| | - Yun Wang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey United States
| | - Amy D Jhatakia
- Discovery Biology, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Andy X Deng
- Discovery Biotherapeutics, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Christine Bee
- Discovery Biotherapeutics, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Shrikant Deshpande
- Discovery Biotherapeutics, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Vangipuram S Rangan
- Discovery Biotherapeutics, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Natalie Bezman
- Discovery Biology, Research and Early Development, Bristol Myers Squibb Company, Redwood City, California United States
| | - Olafur Gudmundsson
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey United States
| |
Collapse
|
7
|
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
|
8
|
Huang RYC, Wang F, Wheeler M, Wang Y, Langish R, Chau B, Dong J, Morishige W, Bezman N, Strop P, Rajpal A, Gudmundsson O, Chen G. Integrated Approach for Characterizing Bispecific Antibody/Antigens Complexes and Mapping Binding Epitopes with SEC/MALS, Native Mass Spectrometry, and Protein Footprinting. Anal Chem 2020; 92:10709-10716. [PMID: 32639723 DOI: 10.1021/acs.analchem.0c01876] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Bispecific antibodies (BsAbs), with a unique mechanism of recognizing two different epitopes or antigens, have shown potential in various therapeutic areas. Molecular characterization of BsAbs' epitopes not only allows for detailed understanding of their mechanism of actions but also guides the design and selection of drug candidate molecules. In this study, we illustrate the practical utility of an integrated approach, including size exclusion chromatography with multiangle light scattering and native mass spectrometry (MS) for the biophysical characterization of complex formation of a BsAb with two target antigens, cluster of differentiation 3 (CD3) and B-cell maturation antigen (BCMA). MS-based protein footprinting strategies, including hydrogen/deuterium exchange MS, fast photochemical oxidation of proteins, and carboxyl group footprinting with glycine ethyl ester, were further applied to determine BsAb's binding epitopes. This combination approach provides molecular details on the binding mechanisms of BsAb to the two distinct antigens with rapid output and high resolution.
Collapse
Affiliation(s)
- Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Feng Wang
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Matthew Wheeler
- Discovery Biology, Research and Early Development, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Yun Wang
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Robert Langish
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Bryant Chau
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Jia Dong
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Winse Morishige
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Natalie Bezman
- Discovery Biology, Research and Early Development, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Pavel Strop
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Arvind Rajpal
- Protein Engineering, Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Olafur Gudmundsson
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Nonclinical Research and Development, Bristol Myers Squibb Company, Princeton, New Jersey 08540, United States
| |
Collapse
|
9
|
Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
Collapse
Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
| |
Collapse
|
10
|
Zhao B, Zhuang J, Xu M, Liu T, Limpikirati P, Thayumanavan S, Vachet RW. Covalent Labeling with an α,β-Unsaturated Carbonyl Scaffold for Studying Protein Structure and Interactions by Mass Spectrometry. Anal Chem 2020; 92:6637-6644. [PMID: 32250591 PMCID: PMC7207043 DOI: 10.1021/acs.analchem.0c00463] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new covalent labeling (CL) reagent based on an α,β-unsaturated carbonyl scaffold has been developed for studying protein structure and protein-protein interactions when coupled with mass spectrometry. We show that this new reagent scaffold can react with up to 13 different types of residues on protein surfaces, thereby providing excellent structural resolution. To illustrate the value of this reagent scaffold, it is used to identify the residues involved in the protein-protein interface that is formed upon Zn(II) binding to the protein β-2-microglobulin. The modular design of the α,β-unsaturated carbonyl scaffold allows facile variation of the functional groups, enabling labeling kinetics and selectivity to be tuned. Moreover, by introducing isotopically enriched functional groups into the reagent structure, labeling sites can be more easily identified by MS and MS/MS. Overall, this reagent scaffold should be a valuable CL reagent for protein higher order structure characterization by MS.
Collapse
Affiliation(s)
- Bo Zhao
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Jiaming Zhuang
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Miaowei Xu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Tianying Liu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | - S. Thayumanavan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Center for Bioactive Delivery – Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Center for Bioactive Delivery – Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
| |
Collapse
|
11
|
Gupta S. Using X-ray Footprinting and Mass Spectrometry to Study the Structure and Function of Membrane Proteins. Protein Pept Lett 2019; 26:44-54. [PMID: 30484402 DOI: 10.2174/0929866526666181128142401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/22/2018] [Accepted: 11/06/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Membrane proteins are crucial for cellular sensory cascades and metabolite transport, and hence are key pharmacological targets. Structural studies by traditional highresolution techniques are limited by the requirements for high purity and stability when handled in high concentration and nonnative buffers. Hence, there is a growing requirement for the use of alternate methods in a complementary but orthogonal approach to study the dynamic and functional aspects of membrane proteins in physiologically relevant conditions. In recent years, significant progress has been made in the field of X-ray radiolytic labeling in combination with mass spectroscopy, commonly known as X-ray Footprinting and Mass Spectrometry (XFMS), which provide residue-specific information on the solvent accessibility of proteins. In combination with both lowresolution biophysical methods and high-resolution structural data, XFMS is capable of providing valuable insights into structure and dynamics of membrane proteins, which have been difficult to obtain by standalone high-resolution structural techniques. The XFMS method has also demonstrated a unique capability for identification of structural waters and their dynamics in protein cavities at both a high degree of spatial and temporal resolution, and thus capable of identifying conformational hot-spots in transmembrane proteins. CONCLUSION We provide a perspective on the place of XFMS amongst other structural biology methods and showcase some of the latest developments in its usage for studying conformational changes in membrane proteins.
Collapse
Affiliation(s)
- Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| |
Collapse
|
12
|
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
|
13
|
Limpikirati P, Hale JE, Hazelbaker M, Huang Y, Jia Z, Yazdani M, Graban EM, Vaughan RC, Vachet RW. Covalent labeling and mass spectrometry reveal subtle higher order structural changes for antibody therapeutics. MAbs 2019; 11:463-476. [PMID: 30636503 DOI: 10.1080/19420862.2019.1565748] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Monoclonal antibodies are among the fastest growing therapeutics in the pharmaceutical industry. Detecting higher-order structure changes of antibodies upon storage or mishandling, however, is a challenging problem. In this study, we describe the use of diethylpyrocarbonate (DEPC)-based covalent labeling (CL) - mass spectrometry (MS) to detect conformational changes caused by heat stress, using rituximab as a model system. The structural resolution obtained from DEPC CL-MS is high enough to probe subtle conformation changes that are not detectable by common biophysical techniques. Results demonstrate that DEPC CL-MS can detect and identify sites of conformational changes at the temperatures below the antibody melting temperature (e.g., 55 ᴼC). The observed labeling changes at lower temperatures are validated by activity assays that indicate changes in the Fab region. At higher temperatures (e.g., 65 ᴼC), conformational changes and aggregation sites are identified from changes in CL levels, and these results are confirmed by complementary biophysical and activity measurements. Given the sensitivity and simplicity of DEPC CL-MS, this method should be amenable to the structural investigations of other antibody therapeutics.
Collapse
Affiliation(s)
| | | | - Mark Hazelbaker
- c Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN , USA
| | - Yongbo Huang
- c Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN , USA
| | - Zhiguang Jia
- a Department of Chemistry , University of Massachusetts Amherst , Amherst , MA , USA
| | - Mahdieh Yazdani
- a Department of Chemistry , University of Massachusetts Amherst , Amherst , MA , USA
| | | | - Robert C Vaughan
- c Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN , USA
| | - Richard W Vachet
- a Department of Chemistry , University of Massachusetts Amherst , Amherst , MA , USA
| |
Collapse
|
14
|
Guo C, Cheng M, Gross ML. Protein-Metal-Ion Interactions Studied by Mass Spectrometry-Based Footprinting with Isotope-Encoded Benzhydrazide. Anal Chem 2018; 91:1416-1423. [PMID: 30495934 DOI: 10.1021/acs.analchem.8b04088] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Metal ions, usually bound by various amino-acid side chains in proteins, play multiple roles in protein folding, conformational change, cellular communication, and catalysis. Ca(II) and Mg(II), abundant among biologically relevant cations, execute their cellular functions associated with the conformational change of bound proteins. They bind with proteins where carboxylic acid residues are dominant ligands. To develop mass spectrometry for mapping protein-binding sites, we implemented a new carboxyl group footprinter, benzhydrazide, and refined it with isotope encoding. The method uses carbodiimide chemistry to footprint carboxylic residues, whereby 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide activates a carboxyl group followed by nucleophilic attack by benzhydrazide forming a stable labeled product. We tested the effectiveness of isotope-encoded benzhydrazide by studying Ca2+ and Mg2+ binding of calmodulin, an EF-hand protein. The footprinting results indicate that the four active sites for metal-ion binding (EF hands I, II, III, and IV) and the linker region (peptide 78-86) undergo conformational changes upon Ca(II) and Mg(II) binding, respectively. The outcome is consistent with previously reported results and 3-D structures, thereby validating a new reagent that is more reactive and discriminating for specific amino-acid protein footprinting. This reagent should be important for locating metal-binding sites of other metalloproteins.
Collapse
Affiliation(s)
- Chunyang Guo
- Department of Chemistry , Washington University , St. Louis , Missouri 63130 , United States
| | - Ming Cheng
- Department of Chemistry , Washington University , St. Louis , Missouri 63130 , United States
| | - Michael L Gross
- Department of Chemistry , Washington University , St. Louis , Missouri 63130 , United States
| |
Collapse
|
15
|
Tokmina-Lukaszewska M, Patterson A, Berry L, Scott L, Balasubramanian N, Bothner B. The Role of Mass Spectrometry in Structural Studies of Flavin-Based Electron Bifurcating Enzymes. Front Microbiol 2018; 9:1397. [PMID: 30026733 PMCID: PMC6041385 DOI: 10.3389/fmicb.2018.01397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/07/2018] [Indexed: 12/01/2022] Open
Abstract
For decades, biologists and biochemists have taken advantage of atomic resolution structural models of proteins from X-ray crystallography, nuclear magnetic resonance spectroscopy, and more recently cryo-electron microscopy. However, not all proteins relent to structural analyses using these approaches, and as the depth of knowledge increases, additional data elucidating a mechanistic understanding of protein function is desired. Flavin-based electron bifurcating enzymes, which are responsible for producing high energy compounds through the simultaneous endergonic and exergonic reduction of two intercellular electron carriers (i.e., NAD+ and ferredoxin) are one class of proteins that have challenged structural biologists and in which there is great interest to understand the mechanism behind electron gating. A limited number of X-ray crystallography projects have been successful; however, it is clear that to understand how these enzymes function, techniques that can reveal detailed in solution information about protein structure, dynamics, and interactions involved in the bifurcating reaction are needed. In this review, we cover a general set of mass spectrometry-based techniques that, combined with protein modeling, are capable of providing information on both protein structure and dynamics. Techniques discussed include surface labeling, covalent cross-linking, native mass spectrometry, and hydrogen/deuterium exchange. We cover how biophysical data can be used to validate computationally generated protein models and develop mechanistic explanations for regulation and performance of enzymes and protein complexes. Our focus will be on flavin-based electron bifurcating enzymes, but the broad applicability of the techniques will be showcased.
Collapse
Affiliation(s)
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Luke Berry
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Liam Scott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| |
Collapse
|
16
|
Kiselar J, Chance MR. High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery. Annu Rev Biophys 2018. [DOI: 10.1146/annurev-biophys-070317-033123] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hydroxyl radical footprinting (HRF) of proteins with mass spectrometry (MS) is a widespread approach for assessing protein structure. Hydroxyl radicals react with a wide variety of protein side chains, and the ease with which radicals can be generated (by radiolysis or photolysis) has made the approach popular with many laboratories. As some side chains are less reactive and thus cannot be probed, additional specific and nonspecific labeling reagents have been introduced to extend the approach. At the same time, advances in liquid chromatography and MS approaches permit an examination of the labeling of individual residues, transforming the approach to high resolution. Lastly, advances in understanding of the chemistry of the approach have led to the determination of absolute protein topologies from HRF data. Overall, the technology can provide precise and accurate measures of side-chain solvent accessibility in a wide range of interesting and useful contexts for the study of protein structure and dynamics in both academia and industry.
Collapse
Affiliation(s)
- Janna Kiselar
- Center for Proteomics and Bioinformatics, and Department of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Mark R. Chance
- Center for Proteomics and Bioinformatics, and Department of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106, USA
| |
Collapse
|
17
|
Lin M, Krawitz D, Callahan MD, Deperalta G, Wecksler AT. Characterization of ELISA Antibody-Antigen Interaction using Footprinting-Mass Spectrometry and Negative Staining Transmission Electron Microscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:961-971. [PMID: 29512051 DOI: 10.1007/s13361-017-1883-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 06/08/2023]
Abstract
We describe epitope mapping data using multiple covalent labeling footprinting-mass spectrometry (MS) techniques coupled with negative stain transmission electron microscopy (TEM) data to analyze the antibody-antigen interactions in a sandwich enzyme-linked immunosorbant assay (ELISA). Our hydroxyl radical footprinting-MS data using fast photochemical oxidation of proteins (FPOP) indicates suppression of labeling across the antigen upon binding either of the monoclonal antibodies (mAbs) utilized in the ELISA. Combining these data with Western blot analysis enabled the identification of the putative epitopes that appeared to span regions containing N-linked glycans. An additional structural mapping technique, carboxyl group footprinting-mass spectrometry using glycine ethyl ester (GEE) labeling, was used to confirm the epitopes. Deglycosylation of the antigen resulted in loss of potency in the ELISA, supporting the FPOP and GEE labeling data by indicating N-linked glycans are necessary for antigen binding. Finally, mapping of the epitopes onto the antigen crystal structure revealed an approximate 90° relative spatial orientation, optimal for a noncompetitive binding ELISA. TEM data shows both linear and diamond antibody-antigen complexes with a similar binding orientation as predicted from the two footprinting-MS techniques. This study is the first of its kind to utilize multiple bottom-up footprinting-MS techniques and TEM visualization to characterize the monoclonal antibody-antigen binding interactions of critical reagents used in a quality control (QC) lot-release ELISA. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Margaret Lin
- Analytical Operations, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Denise Krawitz
- CMC Paradigms LLC, 49 Oak Springs Drive, San Anselmo, CA, 94960, USA
| | - Matthew D Callahan
- Protein Analytical Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Galahad Deperalta
- Protein Analytical Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Aaron T Wecksler
- Protein Analytical Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
| |
Collapse
|
18
|
Venkatramani C, Huang SR, Al-Sayah M, Patel I, Wigman L. High-resolution two-dimensional liquid chromatography analysis of key linker drug intermediate used in antibody drug conjugates. J Chromatogr A 2017; 1521:63-72. [DOI: 10.1016/j.chroma.2017.09.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 08/23/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
|
19
|
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
|
20
|
Li KS, Chen G, Mo J, Huang RYC, Deyanova EG, Beno BR, O’Neil SR, Tymiak AA, Gross ML. Orthogonal Mass Spectrometry-Based Footprinting for Epitope Mapping and Structural Characterization: The IL-6 Receptor upon Binding of Protein Therapeutics. Anal Chem 2017; 89:7742-7749. [PMID: 28621526 PMCID: PMC5549780 DOI: 10.1021/acs.analchem.7b01748] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Higher-order structure (HOS) is a crucial determinant for the biological functions and quality attributes of protein therapeutics. Mass spectrometry (MS)-based protein footprinting approaches play an important role in elucidating the relationship between protein biophysical properties and structure. Here, we describe the use of a combined method including hydrogen-deuterium exchange (HDX), fast photochemical oxidation of proteins (FPOP), and site-specific carboxyl group footprinting to investigate the HOS of protein and protein complexes. The work focuses on implementing complementary solution-phase footprinting approaches that differ in time scale, specificity for protein residue side chains vs backbone as well as selectivity for different residue types to map integratively the epitope of human interleukin-6 receptor (IL-6R) for two adnectins with distinct affinities (Kd, Adnectin1 ∼ 6.2 pM vs Kd, Adnectin2 ∼ 46 nM). Furthermore, the study evaluates the resultant conformation/dynamic change of IL-6R. The suggested epitope, which is conserved for adnectin1 and adnectin2 binding, is a flexible loop that connects two β-strands in the cytokine-binding domain (DII) of IL-6R. We also found that adnectin1, the more strongly binding ligand, induces structural perturbations on two unstructured loops that are distally located beyond the epitope. Those changes are either attenuated or not detected for the case of adnectin2 binding. In addition to providing credibility in epitope determination, utilization of those combined approaches reveals the structural effects that can differentiate protein therapeutics with apparently similar biophysical properties.
Collapse
Affiliation(s)
- Ke Sherry Li
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb, Princeton, NJ 08540, USA
| | - Jingjie Mo
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb, Princeton, NJ 08540, USA
| | - Richard Y-C Huang
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb, Princeton, NJ 08540, USA
| | - Ekaterina G. Deyanova
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb, Princeton, NJ 08540, USA
| | - Brett R. Beno
- Molecular Discovery Technologies, Research and Development, Bristol-Myers Squibb, Wallingford, CT 06492, and Waltham, MA 02453, USA
| | - Steve R. O’Neil
- Molecular Discovery Technologies, Research and Development, Bristol-Myers Squibb, Wallingford, CT 06492, and Waltham, MA 02453, USA
| | - Adrienne A. Tymiak
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb, Princeton, NJ 08540, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| |
Collapse
|
21
|
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
|
22
|
Pan LY, Salas-Solano O, Valliere-Douglass JF. Localized conformational interrogation of antibody and antibody-drug conjugates by site-specific carboxyl group footprinting. MAbs 2016; 9:307-318. [PMID: 27929747 DOI: 10.1080/19420862.2016.1268306] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Establishing and maintaining conformational integrity of monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs) during development and manufacturing is critical for ensuring their clinical efficacy. As presented here, we applied site-specific carboxyl group footprinting (CGF) for localized conformational interrogation of mAbs. The approach relies on covalent labeling that introduces glycine ethyl ester tags onto solvent-accessible side chains of protein carboxylates. Peptide mapping is used to monitor the labeling kinetics of carboxyl residues and the labeling kinetics reflects the conformation or solvent-accessibility of side chains. Our results for two case studies are shown here. The first study was aimed at defining the conformational changes of mAbs induced by deglycosylation. We found that two residues in CH2 domain (D268 and E297) show significantly enhanced side chain accessibility upon deglycosylation. This site-specific result highlighted the advantage of monitoring the labeling kinetics at the amino acid level as opposed to the peptide level, which would result in averaging out of highly localized conformational differences. The second study was designed to assess conformational effects brought on by conjugation of mAbs with drug-linkers. All 59 monitored carboxyl residues displayed similar solvent-accessibility between the ADC and mAb under native conditions, which suggests the ADC and mAb share similar side chain conformation. The findings are well correlated and complementary with results from other assays. This work illustrated that site-specific CGF is capable of pinpointing local conformational changes in mAbs or ADCs that might arise during development and manufacturing. The methodology can be readily implemented within the industry to provide comprehensive conformational assessment of these molecules.
Collapse
|
23
|
Zhang Y, Cui W, Wecksler AT, Zhang H, Molina P, Deperalta G, Gross ML. Native MS and ECD Characterization of a Fab-Antigen Complex May Facilitate Crystallization for X-ray Diffraction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1139-42. [PMID: 27103115 PMCID: PMC4899112 DOI: 10.1007/s13361-016-1398-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 05/11/2023]
Abstract
Native mass spectrometry (MS) and top-down electron-capture dissociation (ECD) combine as a powerful approach for characterizing large proteins and protein assemblies. Here, we report their use to study an antibody Fab (Fab-1)-VEGF complex in its near-native state. Native ESI with analysis by FTICR mass spectrometry confirms that VEGF is a dimer in solution and that its complex with Fab-1 has a binding stoichiometry of 2:2. Applying combinations of collisionally activated dissociation (CAD), ECD, and infrared multiphoton dissociation (IRMPD) allows identification of flexible regions of the complex, potentially serving as a guide for crystallization and X-ray diffraction analysis. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
- Analytical Research and Development, Pfizer Inc., Chesterfield, MO, 63017, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Aaron T Wecksler
- Protein Analytical Chemistry, Genentech, a Member of the Roche Group, South San Francisco, CA, 94080, USA
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA
| | - Patricia Molina
- Protein Analytical Chemistry, Genentech, a Member of the Roche Group, South San Francisco, CA, 94080, USA
| | - Galahad Deperalta
- Protein Analytical Chemistry, Genentech, a Member of the Roche Group, South San Francisco, CA, 94080, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO, 63130, USA.
| |
Collapse
|