1
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Yassaghi G, Kukačka Z, Fiala J, Kavan D, Halada P, Volný M, Novák P. Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation, and Electron-Capture Dissociation. Anal Chem 2022; 94:9993-10002. [PMID: 35797180 DOI: 10.1021/acs.analchem.1c05476] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fast photochemical oxidation of proteins (FPOP) footprinting is a structural mass spectrometry method that maps proteins by fast and irreversible chemical reactions. The position of oxidative modification reflects solvent accessibility and site reactivity and thus provides information about protein conformation, structural dynamics, and interactions. Bottom-up mass spectrometry is an established standard method to analyze FPOP samples. In the bottom-up approach, all forms of the protein are digested together by a protease of choice, which results in a mixture of peptides from various subpopulations of proteins with varying degrees of photochemical oxidation. Here, we investigate the possibility to analyze a specifically selected population of only singly oxidized proteins. This requires utilization of more specific top-down mass spectrometry approaches. The key element of any top-down experiment is the selection of a suitable method of ion isolation, excitation, and fragmentation. Here, we employ and compare collision-induced dissociation, electron-transfer dissociation, and electron-capture dissociation combined with multi-continuous accumulation of selected ions. A singly oxidized subpopulation of FPOP-labeled ubiquitin was used to optimize the method. The top-down approach in FPOP is limited to smaller proteins, but its usefulness was demonstrated by using it to visualize structural changes induced by co-factor removal from the holo/apo myoglobin system. The top-down data were compared with the literature and with the bottom-up data set obtained on the same samples. The top-down results were found to be in good agreement, which indicates that monitoring a singly oxidized FPOP ion population by the top-down approach is a functional workflow for oxidative protein footprinting.
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Affiliation(s)
- Ghazaleh Yassaghi
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Jan Fiala
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 2 128 00, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 2 128 00, Czech Republic
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Michael Volný
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Petr Novák
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
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2
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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: 5] [Impact Index Per Article: 2.5] [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.
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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
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3
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Fojtík L, Fiala J, Pompach P, Chmelík J, Matoušek V, Beier P, Kukačka Z, Novák P. Fast Fluoroalkylation of Proteins Uncovers the Structure and Dynamics of Biological Macromolecules. J Am Chem Soc 2021; 143:20670-20679. [PMID: 34846870 DOI: 10.1021/jacs.1c07771] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Covalent labeling of proteins in combination with mass spectrometry has been established as a complementary technique to classical structural methods, such as X-ray, NMR, or cryogenic electron microscopy (Cryo-EM), used for protein structure determination. Although the current covalent labeling techniques enable the protein solvent accessible areas with sufficient spatial resolution to be monitored, there is still high demand for alternative, less complicated, and inexpensive approaches. Here, we introduce a new covalent labeling method based on fast fluoroalkylation of proteins (FFAP). FFAP uses fluoroalkyl radicals formed by reductive decomposition of Togni reagents with ascorbic acid to label proteins on a time scale of seconds. The feasibility of FFAP to effectively label proteins was demonstrated by monitoring the differential amino acids modification of native horse heart apomyoglobin/holomyoglobin and the human haptoglobin-hemoglobin complex. The obtained data confirmed the Togni reagent-mediated FFAP is an advantageous alternative method for covalent labeling in applications such as protein footprinting and epitope mapping of proteins (and their complexes) in general. Data are accessible via the ProteomeXchange server with the data set identifier PXD027310.
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Affiliation(s)
- Lukáš Fojtík
- Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Jan Fiala
- Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Petr Pompach
- Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic.,Institute of Biotechnology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Josef Chmelík
- Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | | | - Petr Beier
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 16610 Prague, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Novák
- Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
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4
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McKenzie-Coe A, Shortt R, Jones LM. THE MAKING OF A FOOTPRINT IN PROTEIN FOOTPRINTING: A REVIEW IN HONOR OF MICHAEL L. GROSS. MASS SPECTROMETRY REVIEWS 2021; 40:177-200. [PMID: 32400038 PMCID: PMC7849054 DOI: 10.1002/mas.21632] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/17/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Within the past decade protein footprinting in conjunction with mass spectrometry has become a powerful and versatile means to unravel the higher order structure of proteins. Footprinting-based approaches has demonstrated the capacity to inform on interaction sites and dynamic regions that participate in conformational changes. These findings when set in a biological perspective inform on protein folding/unfolding, protein-protein interactions, and protein-ligand interactions. In this review, we will look at the contribution of Dr. Michael L. Gross to protein footprinting approaches such as hydrogen deuterium exchange mass spectrometry and hydroxyl radical protein footprinting. This review details the development of novel footprinting methods as well as their applications to study higher order protein structure. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Alan McKenzie-Coe
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland, 21201
| | - Raquel Shortt
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland, 21201
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland, 21201
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5
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Chen Y, Doud E, Stone T, Xin L, Hong W, Li Y. Rapid global characterization of immunoglobulin G1 following oxidative stress. MAbs 2019; 11:1089-1100. [PMID: 31156028 PMCID: PMC6748588 DOI: 10.1080/19420862.2019.1625676] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Although peroxide and leachable metal-induced chemical modifications are among the most important quality attributes in bioprocess development, there is no mainstream characterization method covering all common modifications theoretically possible on therapeutic proteins that also gives consistent results quickly. Here, we describe a method for rapid and consistent global characterization of leachable metals- or peroxide-stressed immunoglobulin (Ig) G1 monoclonal antibodies (mAbs). Using two independent protease digestions, data-independent acquisition and data-dependent acquisition liquid chromatography high-resolution mass spectrometry, we monitored 55 potential chemical modifications on trastuzumab, a humanized IgG1 mAb. Processing templates including all observed peptides were developed on Skyline to consistently monitor all modifications throughout the stress conditions for both enzymatic digestions. The Global Characterization Data Processing Site, a universal automated data processing application, was created to batch process data, plot modification trends for peptides, generate sortable and downloadable modification tables, and produce Jmol code for three-dimensional structural models of the analyzed protein. In total, 53 sites on the mAb were found to be modified. Oxidation rates generally increased with the peroxide concentration, while leachable metals alone resulted in lower rates of modifications but more oxidative degradants. Multiple chemical modifications were found on IgG1 surfaces known to interact with FcɣRIII, complement protein C1q, and FcRn, potentially affecting activity. The combination of Skyline templates and the Global Characterization Data Processing Site results in a universally applicable assay allowing users to batch process numerous modifications. Applying this new method to stability studies will promote a broader and deeper understanding of stress modifications on therapeutic proteins.
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Affiliation(s)
- Yao Chen
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Emma Doud
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Todd Stone
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Lun Xin
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Wei Hong
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Yunsong Li
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
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6
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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.
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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
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7
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Liu P, Haruta M, Minkoff BB, Sussman MR. Probing a Plant Plasma Membrane Receptor Kinase’s Three-Dimensional Structure Using Mass Spectrometry-Based Protein Footprinting. Biochemistry 2018; 57:5159-5168. [DOI: 10.1021/acs.biochem.8b00471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Pei Liu
- Department of Biochemistry, Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Miyoshi Haruta
- Department of Biochemistry, Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Benjamin B. Minkoff
- Department of Biochemistry, Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Michael R. Sussman
- Department of Biochemistry, Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, United States
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8
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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.
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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
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9
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Wang L, Chance MR. Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment. Mol Cell Proteomics 2017; 16:706-716. [PMID: 28275051 DOI: 10.1074/mcp.o116.064386] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/06/2017] [Indexed: 12/17/2022] Open
Abstract
Protein footprinting mediated by mass spectrometry has evolved over the last 30 years from proof of concept to commonplace biophysics tool, with unique capabilities for assessing structure and dynamics of purified proteins in physiological states in solution. This review outlines the history and current capabilities of two major methods of protein footprinting: reversible hydrogen-deuterium exchange (HDX) and hydroxyl radical footprinting (HRF), an irreversible covalent labeling approach. Technological advances in both approaches now permit high-resolution assessments of protein structure including secondary and tertiary structure stability mediated by backbone interactions (measured via HDX) and solvent accessibility of side chains (measured via HRF). Applications across many academic fields and in biotechnology drug development are illustrated including: detection of protein interfaces, identification of ligand/drug binding sites, and monitoring dynamics of protein conformational changes along with future prospects for advancement of protein footprinting in structural biology and biophysics research.
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Affiliation(s)
- Liwen Wang
- From the ‡Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Mark R Chance
- From the ‡Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio
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10
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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.
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11
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Leitner A. Cross-linking and other structural proteomics techniques: how chemistry is enabling mass spectrometry applications in structural biology. Chem Sci 2016; 7:4792-4803. [PMID: 30155128 PMCID: PMC6016523 DOI: 10.1039/c5sc04196a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 04/25/2016] [Indexed: 01/05/2023] Open
Abstract
The biological function of proteins is heavily influenced by their structures and their organization into assemblies such as protein complexes and regulatory networks. Mass spectrometry (MS) has been a key enabling technology for high-throughput and comprehensive protein identification and quantification on a proteome-wide scale. Besides these essential contributions, MS can also be used to study higher-order structures of biomacromolecules in a variety of ways. In one approach, intact proteins or protein complexes may be directly probed in the mass spectrometer. Alternatively, various forms of solution-phase chemistry are used to introduce modifications in intact proteins and localizing these modifications by MS analysis at the peptide level is used to derive structural information. Here, I will put a spotlight on the central role of chemistry in such mass spectrometry-based methods that bridge proteomics and structural biology, with a particular emphasis on chemical cross-linking of protein complexes.
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Affiliation(s)
- Alexander Leitner
- Department of Biology , Institute of Molecular Systems Biology , ETH Zurich , Auguste-Piccard-Hof 1 , 8093 Zurich , Switzerland .
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12
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Kaur P, Tomechko SE, Kiselar J, Shi W, Deperalta G, Wecksler AT, Gokulrangan G, Ling V, Chance MR. Characterizing monoclonal antibody structure by carboxyl group footprinting. MAbs 2016; 7:540-52. [PMID: 25933350 DOI: 10.1080/19420862.2015.1023683] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Structural characterization of proteins and their antigen complexes is essential to the development of new biologic-based medicines. Amino acid-specific covalent labeling (CL) is well suited to probe such structures, especially for cases that are difficult to examine by alternative means due to size, complexity, or instability. We present here a detailed account of carboxyl group labeling (with glycine ethyl ester (GEE) tagging) applied to a glycosylated monoclonal antibody therapeutic (mAb). The experiments were optimized to preserve the structural integrity of the mAb, and experimental conditions were varied and replicated to establish the reproducibility of the technique. Homology-based models were generated and used to compare the solvent accessibility of the labeled residues, which include aspartic acid (D), glutamic acid (E), and the C-terminus (i.e., the target probes), with the experimental data in order to understand the accuracy of the approach. Data from the mAb were compared to reactivity measures of several model peptides to explain observed variations in reactivity. Attenuation of reactivity in otherwise solvent accessible probes is documented as arising from the effects of positive charge or bond formation between adjacent amine and carboxyl groups, the latter accompanied by observed water loss. A comparison of results with previously published data by Deperalta et al using hydroxyl radical footprinting showed that 55% (32/58) of target residues were GEE labeled in this study whereas the previous study reported 21% of the targets were labeled. Although the number of target residues in GEE labeling is fewer, the two approaches provide complementary information. The results highlight advantages of this approach, such as the ease of use at the bench top, the linearity of the dose response plots at high levels of labeling, reproducibility of replicate experiments (<2% variation in modification extent), the similar reactivity of the three target probes, and significant correlation of reactivity and solvent accessible surface area.
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Key Words
- 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide
- ACN, acetonitrile
- CD, circular dichroism
- CL, covalent labeling
- DR, dose response
- EDC, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide
- EIC, extracted ion chromatogram
- GEE, glycine ethyl ester
- HC, heavy chain
- HDX, hydrogen-deuterium exchange
- HRF, hydroxyl radical footprinting
- IT, ion trap
- IgG, immunoglobulin gamma
- LC, light chain
- Lys-C, lysyl endopeptidase
- MS, mass spectrometry
- RC, rate constant
- SASA, solvent accessible surface area
- SEC, size-exclusion chromatography
- acetonitrile
- circular dichroism
- covalent labeling
- dose response
- extracted ion chromatogram
- glycine ethyl ester
- heavy chain
- hydrogen-deuterium exchange
- hydroxyl radical footprinting
- immunoglobulin gamma
- ion trap
- light chain
- lysyl endopeptidase
- mAb, monoclonal antibody
- mass spectrometry
- monoclonal antibody
- rate constant
- size-exclusion chromatography
- solvent accessible surface area
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Affiliation(s)
- Parminder Kaur
- a Center for Proteomics and Bioinformatics; School of Medicine; Case Western Reserve University ; Cleveland , OH , USA
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13
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Zhang H, Liu H, Blankenship RE, Gross ML. Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:178-81. [PMID: 26384685 PMCID: PMC4688080 DOI: 10.1007/s13361-015-1260-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 05/03/2023]
Abstract
We report an isotope-encoding method coupled with carboxyl-group footprinting to monitor protein conformational changes. The carboxyl groups of aspartic/glutamic acids and of the C-terminus of proteins can serve as reporters for protein conformational changes when labeled with glycine ethyl ester (GEE) mediated by carbodiimide. In the new development, isotope-encoded "heavy" and "light" GEE are used to label separately the two states of the orange carotenoid protein (OCP) from cyanobacteria. Two samples are mixed (1:1 ratio) and analyzed by a single LC-MS/MS experiment. The differences in labeling extent between the two states are represented by the ratio of the "heavy" and "light" peptides, providing information about protein conformational changes. Combining isotope-encoded MS quantitative analysis and carboxyl-group footprinting reduces the time of MS analysis and improves the sensitivity of GEE and other footprinting.
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Affiliation(s)
- Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Haijun Liu
- Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St. Louis, MO, 63130, USA
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St. Louis, MO, 63130, USA
- Department of Biology, 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.
- Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St. Louis, MO, 63130, USA.
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15
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Kaur P, Tomechko S, Kiselar J, Shi W, Deperalta G, Wecksler AT, Gokulrangan G, Ling V, Chance MR. Characterizing monoclonal antibody structure by carbodiimide/GEE footprinting. MAbs 2015; 6:1486-99. [PMID: 25484052 DOI: 10.4161/19420862.2014.975096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Amino acid-specific covalent labeling is well suited to probe protein structure and macromolecular interactions, especially for macromolecules and their complexes that are difficult to examine by alternative means, due to size, complexity, or instability. Here we present a detailed account of carbodiimide-based covalent labeling (with GEE tagging) applied to a glycosylated monoclonal antibody therapeutic, which represents an important class of biologic drugs. Characterization of such proteins and their antigen complexes is essential to development of new biologic-based medicines. In this study, the experiments were optimized to preserve the structural integrity of the protein, and experimental conditions were varied and replicated to establish the reproducibility and precision of the technique. Homology-based models were generated and used to compare the solvent accessibility of the labeled residues, which include D, E, and the C-terminus, against the experimental surface accessibility data in order to understand the accuracy of the approach in providing an unbiased assessment of structure. Data from the protein were also compared to reactivity measures of several model peptides to explain sequence or structure-based variations in reactivity. The results highlight several advantages of this approach. These include: the ease of use at the bench top, the linearity of the dose response plots at high levels of labeling (indicating that the label does not significantly perturb the structure of the protein), the high reproducibility of replicate experiments (<2 % variation in modification extent), the similar reactivity of the 3 target probe residues (as suggested by analysis of model peptides), and the overall positive and significant correlation of reactivity and solvent accessible surface area (the latter values predicted by the homology modeling). Attenuation of reactivity, in otherwise solvent accessible probes, is documented as arising from the effects of positive charge or bond formation between adjacent amine and carboxyl groups, the latter accompanied by observed water loss. The results are also compared with data from hydroxyl radical-mediated oxidative footprinting on the same protein, showing that complementary information is gained from the 2 approaches, although the number of target residues in carbodiimide/GEE labeling is fewer. Overall, this approach is an accurate and precise method for assessing protein structure of biologic drugs.
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Key Words
- ACN, acetonitrile
- CD, circular dichroism
- CL, covalent labeling
- DR, dose response
- EDC, 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide
- EIC, extracts the ion chromatogram
- FPOP, fast photochemical oxidation of proteins
- GEE
- GEE, glycine ethyl ester
- HC, heavy chain
- HDX, hydrogen-deuterium exchange
- HRF, hydroxyl radical footprinting
- IT, ion trap
- IgG, immunoglobulin gamma
- LC, light chain
- LysC, Lysyl endopeptidase
- MS, mass spectrometry
- NMR, nuclear magnetic resonance
- RC, rate constant
- SASA, solvent accessible surface area
- SEC, size-exclusion chromatography
- VEGF, vascular endothelial growth factor
- covalent labeling
- footprinting
- mAb, monoclonal antibody
- protein structure
- structural proteomics
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Affiliation(s)
- Parminder Kaur
- a Center for Proteomics and Bioinformatics ; Case Western Reserve University ; Cleveland , OH USA
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16
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Liu H, Zhang H, King JD, Wolf NR, Prado M, Gross ML, Blankenship RE. Mass spectrometry footprinting reveals the structural rearrangements of cyanobacterial orange carotenoid protein upon light activation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1837:1955-1963. [PMID: 25256653 DOI: 10.1016/j.bbabio.2014.09.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/09/2014] [Accepted: 09/12/2014] [Indexed: 11/25/2022]
Abstract
The orange carotenoid protein (OCP), a member of the family of blue light photoactive proteins, is required for efficient photoprotection in many cyanobacteria. Photoexcitation of the carotenoid in the OCP results in structural changes within the chromophore and the protein to give an active red form of OCP that is required for phycobilisome binding and consequent fluorescence quenching. We characterized the light-dependent structural changes by mass spectrometry-based carboxyl footprinting and found that an α helix in the N-terminal extension of OCP plays a key role in this photoactivation process. Although this helix is located on and associates with the outside of the β-sheet core in the C-terminal domain of OCP in the dark, photoinduced changes in the domain structure disrupt this interaction. We propose that this mechanism couples light-dependent carotenoid conformational changes to global protein conformational dynamics in favor of functional phycobilisome binding, and is an essential part of the OCP photocycle.
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Affiliation(s)
- Haijun Liu
- Department of Biology, Washington University in St. Louis, MO 63130, USA; Department of Chemistry, Washington University in St. Louis, MO 63130, USA; Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, MO 63130, USA.
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, MO 63130, USA; Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, MO 63130, USA
| | - Jeremy D King
- Department of Biology, Washington University in St. Louis, MO 63130, USA; Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, MO 63130, USA
| | - Nathan R Wolf
- Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, MO 63130, USA
| | - Mindy Prado
- Department of Biology, Washington University in St. Louis, MO 63130, USA; Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, MO 63130, USA; Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, MO 63130, USA
| | - Robert E Blankenship
- Department of Biology, Washington University in St. Louis, MO 63130, USA; Department of Chemistry, Washington University in St. Louis, MO 63130, USA; Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, MO 63130, USA
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17
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Yan Y, Chen G, Wei H, Huang RYC, Mo J, Rempel DL, Tymiak AA, Gross ML. Fast photochemical oxidation of proteins (FPOP) maps the epitope of EGFR binding to adnectin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2084-92. [PMID: 25267085 PMCID: PMC4224620 DOI: 10.1007/s13361-014-0993-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/15/2014] [Accepted: 08/21/2014] [Indexed: 05/11/2023]
Abstract
Epitope mapping is an important tool for the development of monoclonal antibodies, mAbs, as therapeutic drugs. Recently, a class of therapeutic mAb alternatives, adnectins, has been developed as targeted biologics. They are derived from the 10th type III domain of human fibronectin ((10)Fn3). A common approach to map the epitope binding of these therapeutic proteins to their binding partners is X-ray crystallography. Although the crystal structure is known for Adnectin 1 binding to human epidermal growth factor receptor (EGFR), we seek to determine complementary binding in solution and to test the efficacy of footprinting for this purpose. As a relatively new tool in structural biology and complementary to X-ray crystallography, protein footprinting coupled with mass spectrometry is promising for protein-protein interaction studies. We report here the use of fast photochemical oxidation of proteins (FPOP) coupled with MS to map the epitope of EGFR-Adnectin 1 at both the peptide and amino-acid residue levels. The data correlate well with the previously determined epitopes from the crystal structure and are consistent with HDX MS data, which are presented in an accompanying paper. The FPOP-determined binding interface involves various amino-acid and peptide regions near the N terminus of EGFR. The outcome adds credibility to oxidative labeling by FPOP for epitope mapping and motivates more applications in the therapeutic protein area as a stand-alone method or in conjunction with X-ray crystallography, NMR, site-directed mutagenesis, and other orthogonal methods.
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Affiliation(s)
- Yuetian Yan
- Center for Biomedical and Bioorganic Mass Spectrometry, Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130-4899, USA
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18
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Cammarata M, Lin KY, Pruet J, Liu HW, Brodbelt J. Probing the Unfolding of Myoglobin and Domain C of PARP-1 with Covalent Labeling and Top-Down Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2014; 86:2534-42. [DOI: 10.1021/ac4036235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Michael Cammarata
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Ke-Yi Lin
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Jeff Pruet
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Hung-wen Liu
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Jennifer Brodbelt
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
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19
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Zhang H, Cui W, Gross ML. Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies. FEBS Lett 2013; 588:308-17. [PMID: 24291257 DOI: 10.1016/j.febslet.2013.11.027] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/16/2013] [Accepted: 11/18/2013] [Indexed: 10/26/2022]
Abstract
Monoclonal antibodies (mAbs) are powerful therapeutics, and their characterization has drawn considerable attention and urgency. Unlike small-molecule drugs (150-600 Da) that have rigid structures, mAbs (∼150 kDa) are engineered proteins that undergo complicated folding and can exist in a number of low-energy structures, posing a challenge for traditional methods in structural biology. Mass spectrometry (MS)-based biophysical characterization approaches can provide structural information, bringing high sensitivity, fast turnaround, and small sample consumption. This review outlines various MS-based strategies for protein biophysical characterization and then reviews how these strategies provide structural information of mAbs at the protein level (intact or top-down approaches), peptide, and residue level (bottom-up approaches), affording information on higher order structure, aggregation, and the nature of antibody complexes.
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Affiliation(s)
- Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Weidong Cui
- 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.
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20
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Collier TS, Diraviyam K, Monsey J, Shen W, Sept D, Bose R. Carboxyl group footprinting mass spectrometry and molecular dynamics identify key interactions in the HER2-HER3 receptor tyrosine kinase interface. J Biol Chem 2013; 288:25254-25264. [PMID: 23843458 DOI: 10.1074/jbc.m113.474882] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The HER2 receptor tyrosine kinase is a driver oncogene in many human cancers, including breast and gastric cancer. Under physiologic levels of expression, HER2 heterodimerizes with other members of the EGF receptor/HER/ErbB family, and the HER2-HER3 dimer forms one of the most potent oncogenic receptor pairs. Previous structural biology studies have individually crystallized the kinase domains of HER2 and HER3, but the HER2-HER3 kinase domain heterodimer structure has yet to be solved. Using a reconstituted membrane system to form HER2-HER3 kinase domain heterodimers and carboxyl group footprinting mass spectrometry, we observed that HER2 and HER3 kinase domains preferentially form asymmetric heterodimers with HER3 and HER2 monomers occupying the donor and acceptor kinase positions, respectively. Conformational changes in the HER2 activation loop, as measured by changes in carboxyl group labeling, required both dimerization and nucleotide binding but did not require activation loop phosphorylation at Tyr-877. Molecular dynamics simulations on HER2-HER3 kinase dimers identify specific inter- and intramolecular interactions and were in good agreement with MS measurements. Specifically, several intermolecular ionic interactions between HER2 Lys-716-HER3 Glu-909, HER2 Glu-717-HER3 Lys-907, and HER2 Asp-871-HER3 Arg-948 were identified by molecular dynamics. We also evaluated the effect of the cancer-associated mutations HER2 D769H/D769Y, HER3 E909G, and HER3 R948K (also numbered HER3 E928G and R967K) on kinase activity in the context of this new structural model. This study provides valuable insights into the EGF receptor/HER/ErbB kinase structure and interactions, which can guide the design of future therapies.
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Affiliation(s)
| | - Karthikeyan Diraviyam
- the Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109
| | - John Monsey
- From the Division of Oncology, Department of Medicine, and
| | - Wei Shen
- From the Division of Oncology, Department of Medicine, and
| | - David Sept
- the Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109
| | - Ron Bose
- From the Division of Oncology, Department of Medicine, and; the Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110 and.
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21
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Liu H, Chen J, Huang RYC, Weisz D, Gross ML, Pakrasi HB. Mass spectrometry-based footprinting reveals structural dynamics of loop E of the chlorophyll-binding protein CP43 during photosystem II assembly in the cyanobacterium Synechocystis 6803. J Biol Chem 2013; 288:14212-14220. [PMID: 23546881 DOI: 10.1074/jbc.m113.467613] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The PSII repair cycle is required for sustainable photosynthesis in oxygenic photosynthetic organisms. In cyanobacteria and higher plants, proteolysis of the precursor D1 protein (pD1) to expose a C-terminal carboxylate group is an essential step leading to coordination of the Mn4CaO5 cluster, the site of water oxidation. Psb27 appears to associate with both pD1- and D1-containing PSII assembly intermediates by closely interacting with CP43. Here, we report that reduced binding affinity between CP43 and Psb27 is triggered by the removal of the C-terminal extension of the pD1 protein. A mass spectrometry-based footprinting strategy was adopted to probe solvent-exposed aspartic and glutamic acid residues on the CP43 protein. By comparing the extent of footprinting between HT3ΔctpAΔ27PSII and HT3ΔctpAPSII, two genetically modified PSII assembly complexes, we found that Psb27 binds to CP43 on the side of Loop E distal to the pseudo-symmetrical D1-D2 axis. By comparing a second pair of PSII assembly complexes, we discovered that Loop E of CP43 undergoes a significant conformational rearrangement due to the removal of the pD1 C-terminal extension, altering the Psb27-CP43 binding interface. The significance of this conformational rearrangement is discussed in the context of recruitment of the PSII lumenal extrinsic proteins and Mn4CaO5 cluster assembly. In addition to CP43's previously known function as one of the core PSII antenna proteins, this work demonstrates that Loop E of CP43 plays an important role in the functional assembly of the Water Oxidizing Center (WOC) during PSII biogenesis.
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Affiliation(s)
- Haijun Liu
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Jiawei Chen
- Department of Chemistry, Washington University, St. Louis, Missouri 63130
| | - Richard Y-C Huang
- Department of Chemistry, Washington University, St. Louis, Missouri 63130
| | - Daniel Weisz
- Department of Biology, Washington University, St. Louis, Missouri 63130; Department of Chemistry, Washington University, St. Louis, Missouri 63130
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, Missouri 63130
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, Missouri 63130.
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22
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Abstract
Integral membrane proteins reside within the bilayer membranes that surround cells and organelles, playing critical roles in movement of molecules across them and the transduction of energy and signals. While their extreme amphipathicity presents technical challenges, biological mass spectrometry has been applied to all aspects of membrane protein chemistry and biology, including analysis of primary, secondary, tertiary, and quaternary structures as well as the dynamics that accompany functional cycles and catalysis.
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Affiliation(s)
- Julian P Whitelegge
- The Pasarow Mass Spectrometry Laboratory, The NPI-Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, California 90095, United States.
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23
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Malecka KA, Szentpetery Z, Peterson JR. Synergistic activation of p21-activated kinase 1 by phosphatidylinositol 4,5-bisphosphate and Rho GTPases. J Biol Chem 2013; 288:8887-97. [PMID: 23393142 DOI: 10.1074/jbc.m112.428904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Autoinhibited p21-activated kinase 1 (Pak1) can be activated in vitro by the plasma membrane-bound Rho GTPases Rac1 and Cdc42 as well as by the lipid phosphatidylinositol (4,5)-bisphosphate (PIP2). Activator binding is mediated by a GTPase-binding motif and an adjacent phosphoinositide-binding motif. Whether these two classes of activators play alternative, additive, or synergistic roles in Pak1 activation is unknown, as is their contributions to Pak1 activation in vivo. To address these questions, we developed a system to mimic the membrane anchoring of Rho GTPases by creating liposomes containing both PIP2 and a Ni(2+)-NTA modified lipid capable of binding hexahistidine-tagged Cdc42. We find that among all biologically relevant phosphoinositides, only PIP2 is able to synergistically activate Pak1 in concert with Cdc42. Membrane binding of the kinase was highly sensitive to the spatial density of PIP2 and Pak1 demonstrated dramatically enhanced affinity for Cdc42 anchored in a PIP2 environment. To validate these findings in vivo, we utilized an inducible recruitment system to drive the ectopic synthesis of PIP2 on Golgi membranes, which normally have active Cdc42 but lack significant concentrations of PIP2. Pak1 was recruited to PIP2-containing membranes in a manner dependent on the ability of Pak1 to bind to both PIP2 and Cdc42. These findings provide a mechanistic explanation for the essential role of both phosphoinositides and GTPases in Pak1 recruitment and activation. In contrast, Ack, another Cdc42 effector kinase that lacks an analogous phosphoinositide-binding motif, fails to show the same enhancement of membrane binding and activation by PIP2, thus indicating that regulation by PIP2 and Cdc42 could provide a combinatorial code for activation of different GTPase effectors in different subcellular locations.
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Affiliation(s)
- Kimberly A Malecka
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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24
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Ahsan N, Huang Y, Tovar-Mendez A, Swatek KN, Zhang J, Miernyk JA, Xu D, Thelen JJ. A versatile mass spectrometry-based method to both identify kinase client-relationships and characterize signaling network topology. J Proteome Res 2013; 12:937-48. [PMID: 23270405 PMCID: PMC3888875 DOI: 10.1021/pr3009995] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While more than a thousand protein kinases (PK) have been identified in the Arabidopsis thaliana genome, relatively little progress has been made toward identifying their individual client proteins. Herein we describe the use of a mass spectrometry-based in vitro phosphorylation strategy, termed Kinase Client assay (KiC assay), to study a targeted-aspect of signaling. A synthetic peptide library comprising 377 in vivo phosphorylation sequences from developing seed was screened using 71 recombinant A. thaliana PK. Among the initial results, we identified 23 proteins as putative clients of 17 PK. In one instance protein phosphatase inhibitor-2 (AtPPI-2) was phosphorylated at multiple-sites by three distinct PK, casein kinase1-like 10, AME3, and a Ser PK-like protein. To confirm this result, full-length recombinant AtPPI-2 was reconstituted with each of these PK. The results confirmed multiple distinct phosphorylation sites within this protein. Biochemical analyses indicate that AtPPI-2 inhibits type 1 protein phosphatase (TOPP) activity, and that the phosphorylated forms of AtPPI-2 are more potent inhibitors. Structural modeling revealed that phosphorylation of AtPPI-2 induces conformational changes that modulate TOPP binding.
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Affiliation(s)
- Nagib Ahsan
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA
| | - Yadong Huang
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA
| | - Alejandro Tovar-Mendez
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA
| | - Kirby N. Swatek
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA
| | - Jingfen Zhang
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA
- Department of Computer Science and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Ján A. Miernyk
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
- Plant Genetics Research Unit, USDA, Agricultural Research Service, University of Missouri, Columbia, MO 65211 USA
| | - Dong Xu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA
- Department of Computer Science and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
| | - Jay J. Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211 USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211 USA
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25
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Allosteric post-translational modification codes. Trends Biochem Sci 2012; 37:447-55. [DOI: 10.1016/j.tibs.2012.07.001] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/25/2012] [Accepted: 07/11/2012] [Indexed: 12/24/2022]
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26
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Zhang H, Wen J, Huang RYC, Blankenship RE, Gross ML. Mass spectrometry-based carboxyl footprinting of proteins: method evaluation. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2012; 312:78-86. [PMID: 22408386 PMCID: PMC3293472 DOI: 10.1016/j.ijms.2011.07.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Protein structure determines function in biology, and a variety of approaches have been employed to obtain structural information about proteins. Mass spectrometry-based protein footprinting is one fast-growing approach. One labeling-based footprinting approach is the use of a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and glycine ethyl ester (GEE) to modify solvent-accessible carboxyl groups on glutamate (E) and aspartate (D). This paper describes method development of carboxyl-group modification in protein footprinting. The modification protocol was evaluated by using the protein calmodulin as a model. Because carboxyl-group modification is a slow reaction relative to protein folding and unfolding, there is an issue that modifications at certain sites may induce protein unfolding and lead to additional modification at sites that are not solvent-accessible in the wild-type protein. We investigated this possibility by using hydrogen deuterium amide exchange (H/DX). The study demonstrated that application of carboxyl group modification in probing conformational changes in calmodulin induced by Ca(2+) binding provides useful information that is not compromised by modification-induced protein unfolding.
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Affiliation(s)
- Hao Zhang
- Department of Chemistry, Washington University in St. Louis, MO 63130
| | - Jianzhong Wen
- Department of Chemistry, Washington University in St. Louis, MO 63130
- Department of Biology, Washington University in St. Louis, MO 63130
| | - Richard Y-C Huang
- Department of Chemistry, Washington University in St. Louis, MO 63130
| | - Robert E. Blankenship
- Department of Chemistry, Washington University in St. Louis, MO 63130
- Department of Biology, Washington University in St. Louis, MO 63130
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, MO 63130
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