201
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Cruz AR, Boer MAD, Strasser J, Zwarthoff SA, Beurskens FJ, de Haas CJC, Aerts PC, Wang G, de Jong RN, Bagnoli F, van Strijp JAG, van Kessel KPM, Schuurman J, Preiner J, Heck AJR, Rooijakkers SHM. Staphylococcal protein A inhibits complement activation by interfering with IgG hexamer formation. Proc Natl Acad Sci U S A 2021; 118:e2016772118. [PMID: 33563762 PMCID: PMC7896290 DOI: 10.1073/pnas.2016772118] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Immunoglobulin (Ig) G molecules are essential players in the human immune response against bacterial infections. An important effector of IgG-dependent immunity is the induction of complement activation, a reaction that triggers a variety of responses that help kill bacteria. Antibody-dependent complement activation is promoted by the organization of target-bound IgGs into hexamers that are held together via noncovalent Fc-Fc interactions. Here we show that staphylococcal protein A (SpA), an important virulence factor and vaccine candidate of Staphylococcus aureus, effectively blocks IgG hexamerization and subsequent complement activation. Using native mass spectrometry and high-speed atomic force microscopy, we demonstrate that SpA blocks IgG hexamerization through competitive binding to the Fc-Fc interaction interface on IgG monomers. In concordance, we show that SpA interferes with the formation of (IgG)6:C1q complexes and prevents downstream complement activation on the surface of S. aureus. Finally, we demonstrate that IgG3 antibodies against S. aureus can potently induce complement activation and opsonophagocytic killing even in the presence of SpA. Together, our findings identify SpA as an immune evasion protein that specifically blocks IgG hexamerization.
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Affiliation(s)
- Ana Rita Cruz
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Maurits A den Boer
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Jürgen Strasser
- Nano Structuring and Bio-Analytics Group, TIMed Center, University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Seline A Zwarthoff
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | | | - Carla J C de Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Piet C Aerts
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Guanbo Wang
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
- School of Chemistry and Materials Science, Nanjing Normal University, 210023 Nanjing, China
| | | | | | - Jos A G van Strijp
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Kok P M van Kessel
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | | | - Johannes Preiner
- Nano Structuring and Bio-Analytics Group, TIMed Center, University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Albert J R Heck
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Suzan H M Rooijakkers
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands;
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202
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Targeting protein self-association in drug design. Drug Discov Today 2021; 26:1148-1163. [PMID: 33548462 DOI: 10.1016/j.drudis.2021.01.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/24/2020] [Accepted: 01/26/2021] [Indexed: 01/05/2023]
Abstract
Protein self-association is a universal phenomenon essential for stability and molecular recognition. Disrupting constitutive homomers constitutes an original and emerging strategy in drug design. Inhibition of homomeric proteins can be achieved through direct complex disruption, subunit intercalation, or by promoting inactive oligomeric states. Targeting self-interaction grants several advantages over active site inhibition because of the stimulation of protein degradation, the enhancement of selectivity, substoichiometric inhibition, and by-pass of compensatory mechanisms. This new landscape in protein inhibition is driven by the development of biophysical and biochemical tools suited for the study of homomeric proteins, such as differential scanning fluorimetry (DSF), native mass spectrometry (MS), Förster resonance energy transfer (FRET) spectroscopy, 2D nuclear magnetic resonance (NMR), and X-ray crystallography. In this review, we discuss the different aspects of this new paradigm in drug design.
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203
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Olinares PDB, Kang JY, Llewellyn E, Chiu C, Chen J, Malone B, Saecker RM, Campbell EA, Darst SA, Chait BT. Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM. Structure 2021; 29:186-195.e6. [PMID: 33217329 PMCID: PMC7867593 DOI: 10.1016/j.str.2020.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/26/2020] [Accepted: 11/02/2020] [Indexed: 01/19/2023]
Abstract
Recent advances in single-particle cryogenic electron microscopy (cryo-EM) have enabled the structural determination of numerous protein assemblies at high resolution, yielding unprecedented insights into their function. However, despite its extraordinary capabilities, cryo-EM remains time-consuming and resource-intensive. It is therefore beneficial to have a means for rapidly assessing and optimizing the quality of samples prior to lengthy cryo-EM analyses. To do this, we have developed a native mass spectrometry (nMS) platform that provides rapid feedback on sample quality and highly streamlined biochemical screening. Because nMS enables accurate mass analysis of protein complexes, it is well suited to routine evaluation of the composition, integrity, and homogeneity of samples prior to their plunge-freezing on EM grids. We demonstrate the utility of our nMS-based platform for facilitating cryo-EM studies using structural characterizations of exemplar bacterial transcription complexes as well as the replication-transcription assembly from the SARS-CoV-2 virus that is responsible for the COVID-19 pandemic.
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Affiliation(s)
- Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
| | - Jin Young Kang
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Eliza Llewellyn
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Courtney Chiu
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Brandon Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Ruth M Saecker
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
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204
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Martin LM, Konermann L. Sulfolane-Induced Supercharging of Electrosprayed Salt Clusters: An Experimental/Computational Perspective. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:486-496. [PMID: 33334096 DOI: 10.1021/jasms.0c00377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
It is well-known that supercharging agents (SCAs) such as sulfolane enhance the electrospray ionization (ESI) charge states of proteins, although the mechanistic origins of this effect remain contentious. Only very few studies have explored SCA effects on analytes other than proteins or peptides. This work examines how sulfolane affects electrosprayed NaI salt clusters. Such alkali metal halide clusters have played a key role for earlier ESI mechanistic studies, making them interesting targets for supercharging investigations. ESI of aqueous NaI solutions predominantly generated singly charged [NanI(n-1)]+ clusters. The addition of sulfolane resulted in abundant doubly charged [NanI(n-2)Sulfolanes]2+ species. These experimental data for the first time demonstrate that electrosprayed salt clusters can undergo supercharging. Molecular dynamics (MD) simulations of aqueous ESI nanodroplets containing Na+/I- with and without sulfolane were conducted to obtain atomistic insights into the supercharging mechanism. The simulations produced [NanIi]z+ and [NanIiSulfolanes]z+ clusters similar to those observed experimentally. The MD trajectories demonstrated that these clusters were released into the gas phase upon droplet evaporation to dryness, in line with the charged residue model. Sulfolane was found to evaporate much more slowly than water. This slow evaporation, in conjunction with the large dipole moment of sulfolane, resulted in electrostatic stabilization of the shrinking ESI droplets and the final clusters. Hence, charge-dipole stabilization causes the sulfolane-containing droplets and clusters to retain more charge, thereby providing the mechanistic foundation of salt cluster supercharging.
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Affiliation(s)
- Leanne M Martin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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205
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Norris CE, Keener JE, Perera SMDC, Weerasinghe N, Fried SDE, Resager WC, Rohrbough JG, Brown MF, Marty MT. Native Mass Spectrometry Reveals the Simultaneous Binding of Lipids and Zinc to Rhodopsin. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 460:116477. [PMID: 33281496 PMCID: PMC7709953 DOI: 10.1016/j.ijms.2020.116477] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Rhodopsin, a prototypical G-protein-coupled receptor, is responsible for scoptic vision at low-light levels. Although rhodopsin's photoactivation cascade is well understood, it remains unclear how lipid and zinc binding to the receptor are coupled. Using native mass spectrometry, we developed a novel data analysis strategy to deconvolve zinc and lipid bound to the proteoforms of rhodopsin and investigated the allosteric interaction between lipids and zinc binding. We discovered that phosphatidylcholine bound to rhodopsin with a greater affinity than phosphatidylserine or phosphatidylethanolamine, and that binding of all lipids was influenced by zinc but with different effects. In contrast, zinc binding was relatively unperturbed by lipids. Overall, these data reveal that lipid binding can be strongly and differentially influenced by metal ions.
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Affiliation(s)
- Carolanne E. Norris
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | | | - Nipuna Weerasinghe
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Steven D. E. Fried
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - William C. Resager
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - James G. Rohrbough
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
- Department of Physics, University of Arizona, Tucson, AZ 85721
- Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
- Bio5 Institute, University of Arizona, Tucson, AZ 85721
- Corresponding Author Dr. Michael T. Marty, 1306 E. University Blvd., Tucson, AZ 85721,
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206
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Affiliation(s)
- James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
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207
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Affiliation(s)
- Tobias
P. Wörner
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Tatiana M. Shamorkina
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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208
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Yin V, Konermann L. Probing the Effects of Heterogeneous Oxidative Modifications on the Stability of Cytochrome c in Solution and in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:73-83. [PMID: 32401029 DOI: 10.1021/jasms.0c00089] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Covalent modifications by reactive oxygen species can modulate the function and stability of proteins. Thermal unfolding experiments in solution are a standard tool for probing oxidation-induced stability changes. Complementary to such solution investigations, the stability of electrosprayed protein ions can be assessed in the gas phase by collision-induced unfolding (CIU) and ion-mobility spectrometry. A question that remains to be explored is whether oxidation-induced stability alterations in solution are mirrored by the CIU behavior of gaseous protein ions. Here, we address this question using chloramine-T-oxidized cytochrome c (CT-cyt c) as a model system. CT-cyt c comprises various proteoforms that have undergone MetO formation (+16 Da) and Lys carbonylation (LysCH2-NH2 → LysCHO, -1 Da). We found that CT-cyt c in solution was destabilized, with a ∼5 °C reduced melting temperature compared to unmodified controls. Surprisingly, CIU experiments revealed the opposite trend, i.e., a stabilization of CT-cyt c in the gas phase. To pinpoint the source of this effect, we performed proteoform-resolved CIU on CT-cyt c fractions that had been separated by cation exchange chromatography. In this way, it was possible to identify MetO formation at residue 80 as the key modification responsible for stabilization in the gas phase. Possibly, this effect is caused by newly formed contacts of the sulfoxide with aromatic residues in the protein core. Overall, our results demonstrate that oxidative modifications can affect protein stability in solution and in the gas phase very differently.
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Affiliation(s)
- Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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209
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Sever AIM, Yin V, Konermann L. Interrogating the Quaternary Structure of Noncanonical Hemoglobin Complexes by Electrospray Mass Spectrometry and Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:270-280. [PMID: 33124417 DOI: 10.1021/jasms.0c00320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Various activation methods are available for the fragmentation of gaseous protein complexes produced by electrospray ionization (ESI). Such experiments can potentially yield insights into quaternary structure. Collision-induced dissociation (CID) is the most widely used fragmentation technique. Unfortunately, CID of protein complexes is dominated by the ejection of highly charged monomers, a process that does not yield any structural insights. Using hemoglobin (Hb) as a model system, this work examines under what conditions CID generates structurally informative subcomplexes. Native ESI mainly produced tetrameric Hb ions. In addition, "noncanonical" hexameric and octameric complexes were observed. CID of all these species [(αβ)2, (αβ)3, and (αβ)4] predominantly generated highly charged monomers. In addition, we observed hexamer → tetramer + dimer dissociation, implying that hexamers have a tetramer··dimer architecture. Similarly, the observation of octamer → two tetramer dissociation revealed that octamers have a tetramer··tetramer composition. Gas-phase candidate structures of Hb assemblies were produced by molecular dynamics (MD) simulations. Ion mobility spectrometry was used to identify the most likely candidates. Our data reveal that the capability of CID to produce structurally informative subcomplexes depends on the fate of protein-protein interfaces after transfer into the gas phase. Collapse of low affinity interfaces conjoins the corresponding subunits and favors CID via monomer ejection. Structurally informative subcomplexes are formed only if low affinity interfaces do not undergo a major collapse. However, even in these favorable cases CID is still dominated by monomer ejection, requiring careful analysis of the experimental data for the identification of structurally informative subcomplexes.
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Affiliation(s)
- Alexander I M Sever
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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210
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Lermyte F, Theisen A, O'Connor PB. Solution Condition-Dependent Formation of Gas-Phase Protomers of Alpha-Synuclein in Electrospray Ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:364-372. [PMID: 33237779 DOI: 10.1021/jasms.0c00373] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
One of the main characteristics of biomolecular ions in mass spectrometry is their net charge, and a range of approaches exist to either increase or decrease this quantity in the gas phase. In the context of small molecules, it is well known that, in addition to the charge state, the charge site also has a profound effect on an ion's gas-phase behavior; however, this effect has been far less explored for peptides and intact proteins. Methods exist to determine charge sites of protein ions, and others have observed that the interplay of electrostatic repulsion and inherent basicity leads to different sites gaining or losing a charge depending on the total net charge. Here, we report two distinct protonation site isomers ("protomers") of α-synuclein occurring at the same charge state. The protomers showed important differences in their gas-phase fragmentation behavior and were furthermore distinguishable by ion mobility spectrometry. One protomer was produced under standard electrospray conditions, while the other was observed after addition of 10% dimethyl sulfoxide to the protein solution. Charge sites for both protomers were determined using ultraviolet photodissociation.
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Affiliation(s)
- Frederik Lermyte
- Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
- School of Engineering, University of Warwick, Coventry CV4 7AL, U.K
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Alina Theisen
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
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211
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Camperi J, Goyon A, Guillarme D, Zhang K, Stella C. Multi-dimensional LC-MS: the next generation characterization of antibody-based therapeutics by unified online bottom-up, middle-up and intact approaches. Analyst 2021; 146:747-769. [DOI: 10.1039/d0an01963a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review presents an overview of current analytical trends in antibody characterization by multidimensional LC-MS approaches.
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Affiliation(s)
- Julien Camperi
- Department of Protein Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
| | - Alexandre Goyon
- Department of Small Molecule Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
| | - Davy Guillarme
- School of Pharmaceutical Sciences
- University of Geneva
- 1206 Geneva
- Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO)
| | - Kelly Zhang
- Department of Small Molecule Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
| | - Cinzia Stella
- Department of Protein Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
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212
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Narimatsu Y, Büll C, Chen YH, Wandall HH, Yang Z, Clausen H. Genetic glycoengineering in mammalian cells. J Biol Chem 2021; 296:100448. [PMID: 33617880 PMCID: PMC8042171 DOI: 10.1016/j.jbc.2021.100448] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Advances in nuclease-based gene-editing technologies have enabled precise, stable, and systematic genetic engineering of glycosylation capacities in mammalian cells, opening up a plethora of opportunities for studying the glycome and exploiting glycans in biomedicine. Glycoengineering using chemical, enzymatic, and genetic approaches has a long history, and precise gene editing provides a nearly unlimited playground for stable engineering of glycosylation in mammalian cells to explore and dissect the glycome and its many biological functions. Genetic engineering of glycosylation in cells also brings studies of the glycome to the single cell level and opens up wider use and integration of data in traditional omics workflows in cell biology. The last few years have seen new applications of glycoengineering in mammalian cells with perspectives for wider use in basic and applied glycosciences, and these have already led to discoveries of functions of glycans and improved designs of glycoprotein therapeutics. Here, we review the current state of the art of genetic glycoengineering in mammalian cells and highlight emerging opportunities.
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Affiliation(s)
- Yoshiki Narimatsu
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark.
| | - Christian Büll
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark.
| | | | - Hans H Wandall
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Zhang Yang
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark
| | - Henrik Clausen
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark.
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213
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Abstract
Iron-sulfur clusters constitute a large and widely distributed group of protein cofactors that play key roles in a wide range of metabolic processes. The inherent reactivity of iron-sulfur clusters toward small molecules, for example, O2, NO, or free Fe, makes them ideal for sensing changes in the cellular environment. Nondenaturing, or native, MS is unique in its ability to preserve the noncovalent interactions of many (if not all) species, including stable intermediates, while providing accurate mass measurements in both thermodynamic and kinetic experimental regimes. Here, we provide practical guidance for the study of iron-sulfur proteins by native MS, illustrated by examples where it has been used to unambiguously determine the type of cluster coordinated to the protein framework. We also describe the use of time-resolved native MS to follow the kinetics of cluster conversion, allowing the elucidation of the precise series of molecular events for all species involved. Finally, we provide advice on a unique approach to a typical thermodynamic titration, uncovering early, quasi-stable, intermediates in the reaction of a cluster with nitric oxide, resulting in cluster nitrosylation.
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Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, UK
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, UK.
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214
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Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2021; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
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215
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Bellamy‐Carter J, O'Grady L, Passmore M, Jenner M, Oldham NJ. Decoding Protein Gas‐Phase Stability with Alanine Scanning and Collision‐Induced Unfolding Ion Mobility Mass Spectrometry. ACTA ACUST UNITED AC 2020. [DOI: 10.1002/anse.202000019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Louisa O'Grady
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
| | - Munro Passmore
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
| | - Matthew Jenner
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Warwick Integrative Synthetic Biology Centre University of Warwick Coventry CV4 7AL UK
| | - Neil J. Oldham
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
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216
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Abdillahi AM, Lee KW, McLuckey SA. Mass Analysis of Macro-molecular Analytes via Multiply-Charged Ion Attachment. Anal Chem 2020; 92:16301-16306. [PMID: 33275425 DOI: 10.1021/acs.analchem.0c04335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A novel gas-phase charge and mass manipulation approach is demonstrated to facilitate the mass measurement of high mass complexes within the context of native mass spectrometry. Electrospray ionization applied to solutions generated under native or near-native conditions has been demonstrated to be capable of preserving biologically relevant complexes into the gas phase as multiply charged ions suitable for mass spectrometric analysis. However, charge state distributions tend to be narrow and extensive salt adduction, heterogeneity, and so on tend to lead to significantly broadened peaks. These issues can compromise mass measurement of high mass bio-complexes, particularly when charge states are not clearly resolved. In this work, we show that the attachment of high mass ions of known mass and charge to populations of ions of interest can lead to well-separated signals that can yield confident charge state and mass assignments from otherwise poorly resolved signals.
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Affiliation(s)
- Abdirahman M Abdillahi
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Kenneth W Lee
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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217
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Daems E, Dewaele D, Barylyuk K, De Wael K, Sobott F. Aptamer-ligand recognition studied by native ion mobility-mass spectrometry. Talanta 2020; 224:121917. [PMID: 33379118 DOI: 10.1016/j.talanta.2020.121917] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/31/2022]
Abstract
The range of applications for aptamers, small oligonucleotide-based receptors binding to their targets with high specificity and affinity, has been steadily expanding. Our understanding of the mechanisms governing aptamer-ligand recognition and binding is however lagging, stymieing the progress in the rational design of new aptamers and optimization of the known ones. Here we demonstrate the capabilities and limitations of native ion mobility-mass spectrometry for the analysis of their higher-order structure and non-covalent interactions. A set of related cocaine-binding aptamers, displaying a range of folding properties and ligand binding affinities, was used as a case study in both positive and negative electrospray ionization modes. Using carefully controlled experimental conditions, we probed their conformational behavior and interactions with the high-affinity ligand quinine as a surrogate for cocaine. The ratios of bound and unbound aptamers in the mass spectra were used to rank them according to their apparent quinine-binding affinity, qualitatively matching the published ranking order. The arrival time differences between the free aptamer and aptamer-quinine complexes were consistent with a small ligand-induced conformational change, and found to inversely correlate with the affinity of binding. This mass spectrometry-based approach provides a fast and convenient way to study the molecular basis of aptamer-ligand recognition.
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Affiliation(s)
- Elise Daems
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; AXES Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Debbie Dewaele
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Konstantin Barylyuk
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Karolien De Wael
- AXES Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Frank Sobott
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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218
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Hale OJ, Cooper HJ. Native Mass Spectrometry Imaging and In Situ Top-Down Identification of Intact Proteins Directly from Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2531-2537. [PMID: 32822168 DOI: 10.1021/jasms.0c00226] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mass spectrometry imaging (MSI) provides information on the spatial distribution of molecules within a biological substrate without the requirement for labeling. Its broad specificity, i.e., the capability to spatially profile any analyte ion detected, constitutes a major advantage over other imaging techniques. A separate branch of mass spectrometry, native mass spectrometry, provides information relating to protein structure through retention of solution-phase interactions in the gas phase. Integration of MSI and native mass spectrometry ("native MSI") affords opportunities for simultaneous acquisition of spatial and structural information on proteins directly from their physiological environment. Here, we demonstrate significant improvements in native MSI and associated protein identification of intact proteins and protein assemblies in thin sections of rat kidney by use of liquid extraction surface analysis on a state-of-the-art Orbitrap mass spectrometer optimized for intact protein analysis. Proteins of up to 47 kDa, including a trimeric protein complex, were imaged and identified.
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Affiliation(s)
- Oliver J Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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219
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Mallis CS, Zheng X, Qiu X, McCabe JW, Shirzadeh M, Lyu J, Laganowsky A, Russell DH. Development of Native MS Capabilities on an Extended Mass Range Q-TOF MS. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2020; 458:116451. [PMID: 33162786 PMCID: PMC7641504 DOI: 10.1016/j.ijms.2020.116451] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Native mass spectrometry (nMS) is increasingly used for studies of large biomolecules (>100 kDa), especially proteins and protein complexes. The growth in this area can be attributed to advances in native electrospray ionization as well as instrumentation that is capable of accessing high mass-to-charge (m/z) regimes without significant losses in sensitivity and resolution. Here, we describe modifications to the ESI source of an Agilent 6545XT Q-TOF MS that is tailored for analysis of large biomolecules. The modified ESI source was evaluated using both soluble and membrane protein complexes ranging from ~127 to ~232 kDa and the ~801 kDa protein chaperone GroEL. The increased mass resolution of the instrument affords the ability to resolve small molecule adducts and analyze collision-induced dissociation products of the native complexes.
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Affiliation(s)
| | - Xueyun Zheng
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Xi Qiu
- Agilent Technologies, Inc., Wilmington, DE 19808
| | - Jacob W. McCabe
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Correspondence to David H. Russell;
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220
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Lermyte F. Roles, Characteristics, and Analysis of Intrinsically Disordered Proteins: A Minireview. Life (Basel) 2020; 10:E320. [PMID: 33266184 PMCID: PMC7761095 DOI: 10.3390/life10120320] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
In recent years, there has been a growing understanding that a significant fraction of the eukaryotic proteome is intrinsically disordered, and that these conformationally dynamic proteins play a myriad of vital biological roles in both normal and pathological states. In this review, selected examples of intrinsically disordered proteins are highlighted, with particular attention for a few which are relevant in neurological disorders and in viral infection. Next, the underlying causes for the intrinsic disorder are discussed, along with computational methods used to predict whether a given amino acid sequence is likely to adopt a folded or unfolded state in the solution. Finally, biophysical methods for the analysis of intrinsically disordered proteins will be discussed, as well as the unique challenges they pose in this context due to their highly dynamic nature.
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Affiliation(s)
- Frederik Lermyte
- Department of Chemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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221
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O'Brien RE, Santos IC, Wrapp D, Bravo JPK, Schwartz EA, Brodbelt JS, Taylor DW. Structural basis for assembly of non-canonical small subunits into type I-C Cascade. Nat Commun 2020; 11:5931. [PMID: 33230133 PMCID: PMC7684278 DOI: 10.1038/s41467-020-19785-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/30/2020] [Indexed: 01/07/2023] Open
Abstract
Bacteria and archaea employ CRISPR (clustered, regularly, interspaced, short palindromic repeats)-Cas (CRISPR-associated) systems as a type of adaptive immunity to target and degrade foreign nucleic acids. While a myriad of CRISPR-Cas systems have been identified to date, type I-C is one of the most commonly found subtypes in nature. Interestingly, the type I-C system employs a minimal Cascade effector complex, which encodes only three unique subunits in its operon. Here, we present a 3.1 Å resolution cryo-EM structure of the Desulfovibrio vulgaris type I-C Cascade, revealing the molecular mechanisms that underlie RNA-directed complex assembly. We demonstrate how this minimal Cascade utilizes previously overlooked, non-canonical small subunits to stabilize R-loop formation. Furthermore, we describe putative PAM and Cas3 binding sites. These findings provide the structural basis for harnessing the type I-C Cascade as a genome-engineering tool.
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Affiliation(s)
- Roisin E O'Brien
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Evan A Schwartz
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - David W Taylor
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- Livestrong Cancer Institutes, Dell Medical School, Austin, TX, 78712, USA.
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222
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Wang G, Chaihu L, Tian M, Shao X, Dai R, de Jong RN, Ugurlar D, Gros P, Heck AJR. Releasing Nonperipheral Subunits from Protein Complexes in the Gas Phase. Anal Chem 2020; 92:15799-15805. [DOI: 10.1021/acs.analchem.0c02845] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Guanbo Wang
- School of Chemistry and Materials Science, Nanjing Normal University, 210023 Nanjing, China
| | - Lingxiao Chaihu
- School of Chemistry and Materials Science, Nanjing Normal University, 210023 Nanjing, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, 518132 Shenzhen, China
| | - Meng Tian
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Xinyang Shao
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
| | - Rongrong Dai
- School of Chemistry and Materials Science, Nanjing Normal University, 210023 Nanjing, China
| | | | - Deniz Ugurlar
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Piet Gros
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
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223
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Mehaffey MR, Xia Q, Brodbelt JS. Uniting Native Capillary Electrophoresis and Multistage Ultraviolet Photodissociation Mass Spectrometry for Online Separation and Characterization of Escherichia coli Ribosomal Proteins and Protein Complexes. Anal Chem 2020; 92:15202-15211. [PMID: 33156608 PMCID: PMC7788560 DOI: 10.1021/acs.analchem.0c03784] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
With an overarching goal of characterizing the structure of every protein within a cell, identifying its interacting partners, and quantifying the dynamics of the states in which it exists, key developments are still necessary to achieve comprehensive native proteomics by mass spectrometry (MS). In practice, much work remains to optimize reliable online separation methods that are compatible with native MS and improve tandem MS (MS/MS) approaches with respect to when and how energy is deposited into proteins of interest. Herein, we utilize native capillary zone electrophoresis coupled with MS to characterize the proteoforms in the Escherichia coli 70S ribosome. The capabilities of 193 nm ultraviolet photodissociation (UVPD) to yield informative backbone sequence ions are compared to those of higher-energy collisional dissociation (HCD). To further improve sequence coverage values, a multistage MS/MS approach is implemented involving front-end collisional activation to disassemble protein complexes into constituent subunits that are subsequently individually isolated and activated by HCD or UVPD. In total, 48 of the 55 known E. coli ribosomal proteins are identified as 84 unique proteoforms, including 22 protein-metal complexes and 10 protein-protein complexes. Additionally, mapping metal-bound holo fragment ions resulting from UVPD of protein-metal complexes offers insight into the metal-binding sites.
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Affiliation(s)
- M Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Qiangwei Xia
- CMP Scientific Corporation, Brooklyn, New York, New York 11226, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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224
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Fleeman RM, Macias LA, Brodbelt JS, Davies BW. Defining principles that influence antimicrobial peptide activity against capsulated Klebsiella pneumoniae. Proc Natl Acad Sci U S A 2020; 117:27620-27626. [PMID: 33087568 PMCID: PMC7959497 DOI: 10.1073/pnas.2007036117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The extracellular polysaccharide capsule of Klebsiella pneumoniae resists penetration by antimicrobials and protects the bacteria from the innate immune system. Host antimicrobial peptides are inactivated by the capsule as it impedes their penetration to the bacterial membrane. While the capsule sequesters most peptides, a few antimicrobial peptides have been identified that retain activity against encapsulated K. pneumoniae, suggesting that this bacterial defense can be overcome. However, it is unclear what factors allow peptides to avoid capsule inhibition. To address this, we created a peptide analog with strong antimicrobial activity toward several K. pneumoniae strains from a previously inactive peptide. We characterized the effects of these two peptides on K. pneumoniae, along with their physical interactions with K. pneumoniae capsule. Both peptides disrupted bacterial cell membranes, but only the active peptide displayed this activity against capsulated K. pneumoniae Unexpectedly, the active peptide showed no decrease in capsule binding, but did lose secondary structure in a capsule-dependent fashion compared with the inactive parent peptide. We found that these characteristics are associated with capsule-peptide aggregation, leading to disruption of the K. pneumoniae capsule. Our findings reveal a potential mechanism for disrupting the protective barrier that K. pneumoniae uses to avoid the immune system and last-resort antibiotics.
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Affiliation(s)
- Renee M Fleeman
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Luis A Macias
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - Bryan W Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712;
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712
- John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, TX 78712
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225
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Pino LK, Rose J, O'Broin A, Shah S, Schilling B. Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications. Biochem Soc Trans 2020; 48:1953-1966. [PMID: 33079175 PMCID: PMC7609030 DOI: 10.1042/bst20191091] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022]
Abstract
Research into the basic biology of human health and disease, as well as translational human research and clinical applications, all benefit from the growing accessibility and versatility of mass spectrometry (MS)-based proteomics. Although once limited in throughput and sensitivity, proteomic studies have quickly grown in scope and scale over the last decade due to significant advances in instrumentation, computational approaches, and bio-sample preparation. Here, we review these latest developments in MS and highlight how these techniques are used to study the mechanisms, diagnosis, and treatment of human diseases. We first describe recent groundbreaking technological advancements for MS-based proteomics, including novel data acquisition techniques and protein quantification approaches. Next, we describe innovations that enable the unprecedented depth of coverage in protein signaling and spatiotemporal protein distributions, including studies of post-translational modifications, protein turnover, and single-cell proteomics. Finally, we explore new workflows to investigate protein complexes and structures, and we present new approaches for protein-protein interaction studies and intact protein or top-down MS. While these approaches are only recently incipient, we anticipate that their use in biomedical MS proteomics research will offer actionable discoveries for the improvement of human health.
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Affiliation(s)
- Lindsay K. Pino
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, CA, U.S.A
| | - Amy O'Broin
- Buck Institute for Research on Aging, Novato, CA, U.S.A
| | - Samah Shah
- Buck Institute for Research on Aging, Novato, CA, U.S.A
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226
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Zhou M, Lantz C, Brown KA, Ge Y, Paša-Tolić L, Loo JA, Lermyte F. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem Sci 2020; 11:12918-12936. [PMID: 34094482 PMCID: PMC8163214 DOI: 10.1039/d0sc04392c] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
In biology, it can be argued that if the genome contains the script for a cell's life cycle, then the proteome constitutes an ensemble cast of actors that brings these instructions to life. Their interactions with each other, co-factors, ligands, substrates, and so on, are key to understanding nearly any biological process. Mass spectrometry is well established as the method of choice to determine protein primary structure and location of post-translational modifications. In recent years, top-down fragmentation of intact proteins has been increasingly combined with ionisation of noncovalent assemblies under non-denaturing conditions, i.e., native mass spectrometry. Sequence, post-translational modifications, ligand/metal binding, protein folding, and complex stoichiometry can thus all be probed directly. Here, we review recent developments in this new and exciting field of research. While this work is written primarily from a mass spectrometry perspective, it is targeted to all bioanalytical scientists who are interested in applying these methods to their own biochemistry and chemical biology research.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Frederik Lermyte
- Department of Chemistry, Institute of Chemistry and Biochemistry, Technical University of Darmstadt 64287 Darmstadt Germany
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège 4000 Liège Belgium
- School of Engineering, University of Warwick Coventry CV4 7AL UK
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227
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Brown KA, Melby JA, Roberts DS, Ge Y. Top-down proteomics: challenges, innovations, and applications in basic and clinical research. Expert Rev Proteomics 2020; 17:719-733. [PMID: 33232185 PMCID: PMC7864889 DOI: 10.1080/14789450.2020.1855982] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022]
Abstract
Introduction- A better understanding of the underlying molecular mechanism of diseases is critical for developing more effective diagnostic tools and therapeutics toward precision medicine. However, many challenges remain to unravel the complex nature of diseases. Areas covered- Changes in protein isoform expression and post-translation modifications (PTMs) have gained recognition for their role in underlying disease mechanisms. Top-down mass spectrometry (MS)-based proteomics is increasingly recognized as an important method for the comprehensive characterization of proteoforms that arise from alternative splicing events and/or PTMs for basic and clinical research. Here, we review the challenges, technological innovations, and recent studies that utilize top-down proteomics to elucidate changes in the proteome with an emphasis on its use to study heart diseases. Expert opinion- Proteoform-resolved information can substantially contribute to the understanding of the molecular mechanisms underlying various diseases and for the identification of novel proteoform targets for better therapeutic development . Despite the challenges of sequencing intact proteins, top-down proteomics has enabled a wealth of information regarding protein isoform switching and changes in PTMs. Continuous developments in sample preparation, intact protein separation, and instrumentation for top-down MS have broadened its capabilities to characterize proteoforms from a range of samples on an increasingly global scale.
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin, United States
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228
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Du Y, Zhao F, Xing J, Cui M, Liu Z. Investigation of interactions between cytochrome c and ginsenosides by native mass spectrometry and molecular docking simulations. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8853. [PMID: 32511843 DOI: 10.1002/rcm.8853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/22/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Ginsenosides are considered to be the main functional components in ginseng and possess various important pharmacological activities. The study of the interactions between ginsenosides and proteins is indispensable for understanding the pharmacological activities of ginsenosides. In this work, the interactions of ginsenosides with cytochrome c (cyt c) were investigated by native mass spectrometry and molecular docking simulations. METHODS The interactions of four ginsenosides (Rb1 , Rb3 , Rf, Rg1 ) and cyt c in NH4 OAc solution were investigated by electrospray ionization linear ion trap mass spectrometry (ESI-LTQ-MS). Molecular docking simulations of cyt c complexes were carried out by AutoDock. RESULTS The native mass spectrometry results showed that the four ginsenosides were directly bound to cyt c, with stoichiometric ratios of 1:1 and 2:1 in NH4 OAc. The order of relative binding abilities of ginsenosides to cyt c obtained by ESI-MS was Rb1 > Rb3 > Rf > Rg1 , which was consistent with the docking results. Moreover, molecular docking simulations also indicated potential binding sites of cyt c and ginsenosides. Hydrogen-bond interaction played a very important role in cyt c binding with ginsenosides. CONCLUSIONS It has been demonstrated that native MS is a useful tool to investigate the interactions of ginsenosides with cyt c. Molecular docking is a good complement to ESI analysis, and can provide information on potential binding sites of cyt c-ginsenoside complexess. This strategy will be helpful to further understand the interactions of proteins and small molecules.
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Affiliation(s)
- Yang Du
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230029, China
| | - Fengjiao Zhao
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230029, China
| | - Junpeng Xing
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Meng Cui
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230029, China
| | - Zhiqiang Liu
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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229
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Prabhu GRD, Ponnusamy VK, Witek HA, Urban PL. Sample Flow Rate Scan in Electrospray Ionization Mass Spectrometry Reveals Alterations in Protein Charge State Distribution. Anal Chem 2020; 92:13042-13049. [PMID: 32893617 DOI: 10.1021/acs.analchem.0c01945] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sample flow rate is one of the parameters that influence the sensitivity of electrospray ionization (ESI) mass spectrometry. By varying the sample flow rate, initial droplets of different sizes can be generated. Protein molecules in small droplets may form gas-phase ions earlier than the ones in large droplets. Here, we have systematically studied the influence of sample flow rate on the ESI charge state distributions (CSDs) of model proteins. A dedicated programmable sample flow rate scanner was used to infuse protein samples at different flow rates into a mass spectrometer. The synergistic influence of sample flow rate and various electrolytes (ammonium acetate, ammonium bicarbonate, ammonium formate, and piperidine) was studied. Significant alterations to the CSDs with increasing flow rate were observed. For example, in the presence of ammonium acetate, at low flow rates, lower charge states of proteins showed high intensities, while at high flow rates, ions related to higher charge states of proteins dominated the spectra. On the other hand, in the presence of piperidine, a significant reduction in the ion currents of all charge states was observed during the flow rate scan. Our observations suggest that at low flow rates the protein molecules follow a charged residue model of ionization mechanism, and at high flow rates-due to structural changes in protein molecules in large ESI droplets-the charged residue and chain ejection models can possibly coexist. We propose the use of sample flow rate scan as a way to reveal the influence of flow rate on the CSDs of the studied proteins.
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Affiliation(s)
- Gurpur Rakesh D Prabhu
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan.,Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Vinoth Kumar Ponnusamy
- Department of Medicinal and Applied Chemistry & Research Center for Environmental Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung 807, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, 100 Shih-Chuan 1st Road, Kaohsiung 807, Taiwan
| | - Henryk A Witek
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan.,Center for Emergent Functional Matter Science, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
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230
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Abstract
Analysis of intact proteins by native mass spectrometry has emerged as a powerful tool for obtaining insight into subunit diversity, post-translational modifications, stoichiometry, structural arrangement, stability, and overall architecture. Typically, such an analysis is performed following protein purification procedures, which are time consuming, costly, and labor intensive. As this technology continues to move forward, advances in sample handling and instrumentation have enabled the investigation of intact proteins in situ and in crude samples, offering rapid analysis and improved conservation of the biological context. This emerging field, which involves various ion source platforms such as matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) for both spatial imaging and solution-based analysis, is expected to impact many scientific fields, including biotechnology, pharmaceuticals, and clinical sciences. In this Perspective, we discuss the information that can be retrieved by such experiments as well as the current advantages and technical challenges associated with the different sampling strategies. Furthermore, we present future directions of these MS-based methods, including current limitations and efforts that should be made to make these approaches more accessible. Considering the vast progress we have witnessed in recent years, we anticipate that the advent of further innovations enabling minimal handling of MS samples will make this field more robust, user friendly, and widespread.
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Affiliation(s)
- Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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231
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Bohl J, Sicard C, Rezaei H, Van der Rest G, Halgand F. Evidence of conformational landscape alteration and macromolecular complex formation in the early stages of in vitro human prion protein oxidation. Arch Biochem Biophys 2020; 690:108432. [PMID: 32663474 DOI: 10.1016/j.abb.2020.108432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 10/23/2022]
Abstract
Oxidative stress is proposed to be one of the major causes of neurodegenerative diseases. Cellular prion protein (PrP) oxidation has been widely studied using chemical reagents such as hydrogen peroxide. However, the experimental conditions used do not faithfully reflect the physiological environment of the cell. With the goal to explore the conformational landscape of PrP under oxidative stress, we conducted a set of experiments combining the careful control of the nature and the amount of ROS produced by a60Co γ-irradiation source. Characterization of the resulting protein species was achieved using a set of analytical techniques. Under our experimental condition hydroxyl radical are the main reactive species produced. The most important findings are i) the formation of molecular assemblies under oxidative stress, ii) the detection of a majority of unmodified monomer mixed with oxidized monomers in these molecular assemblies at low hydroxyl radical concentration, iii) the absence of significant oxidation on the monomer fraction after irradiation. Molecular assemblies are produced in small amounts and were shown to be an octamer. These results suggest either i) an active recruitment of intact monomers by molecular assemblies' oxidized monomers then inducing a structural change of their intact counterparts or ii) an intrinsic capability of intact monomer conformers to spontaneously associate to form stable molecular assemblies when oxidized monomers are present. Finally, abundances of the intact monomer conformers after irradiation were modified. This suggests that monomers of the molecular assemblies exchange structural information with intact irradiated monomer. All these results shed a new light on structural exchange information between PrP monomers under oxidative stress.
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Affiliation(s)
- Jan Bohl
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France
| | - Cécile Sicard
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France
| | - Human Rezaei
- Institut National de la Recherche Agronomique, UR892, Virologie Immunologie Moléculaires, Domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Guillaume Van der Rest
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France
| | - Frédéric Halgand
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France.
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232
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Zoppi C, Nocentini A, Supuran CT, Pratesi A, Messori L. Native mass spectrometry of human carbonic anhydrase I and its inhibitor complexes. J Biol Inorg Chem 2020; 25:979-993. [PMID: 32926233 PMCID: PMC7584553 DOI: 10.1007/s00775-020-01818-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/30/2020] [Indexed: 02/03/2023]
Abstract
Abstract Native mass spectrometry is a potent technique to study and characterize biomacromolecules in their native state. Here, we have applied this method to explore the solution chemistry of human carbonic anhydrase I (hCA I) and its interactions with four different inhibitors, namely three sulfonamide inhibitors (AAZ, MZA, SLC-0111) and the dithiocarbamate derivative of morpholine (DTC). Through high-resolution ESI-Q-TOF measurements, the native state of hCA I and the binding of the above inhibitors were characterized in the molecular detail. Native mass spectrometry was also exploited to assess the direct competition in solution among the various inhibitors in relation to their affinity constants. Additional studies were conducted on the interaction of hCA I with the metallodrug auranofin, under various solution and instrumental conditions. Auranofin is a selective reagent for solvent-accessible free cysteine residues, and its reactivity was analyzed also in the presence of CA inhibitors. Overall, our investigation reveals that native mass spectrometry represents an excellent tool to characterize the solution behavior of carbonic anhydrase. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01818-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carlotta Zoppi
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Alessio Nocentini
- Department of Neurofarba, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Claudiu T Supuran
- Department of Neurofarba, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Alessandro Pratesi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy.
| | - Luigi Messori
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy.
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233
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Deslignière E, Ehkirch A, Botzanowski T, Beck A, Hernandez-Alba O, Cianférani S. Toward Automation of Collision-Induced Unfolding Experiments through Online Size Exclusion Chromatography Coupled to Native Mass Spectrometry. Anal Chem 2020; 92:12900-12908. [DOI: 10.1021/acs.analchem.0c01426] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Anthony Ehkirch
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Alain Beck
- IRPF—Centre d’Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
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234
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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.
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Affiliation(s)
| | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
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235
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Native high-resolution mass spectrometry analysis of noncovalent protein complexes up to 450 kDa. Bioanalysis 2020; 12:1353-1362. [PMID: 32830519 DOI: 10.4155/bio-2020-0145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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236
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McCabe JW, Mallis CS, Kocurek KI, Poltash ML, Shirzadeh M, Hebert MJ, Fan L, Walker TE, Zheng X, Jiang T, Dong S, Lin CW, Laganowsky A, Russell DH. First-Principles Collision Cross Section Measurements of Large Proteins and Protein Complexes. Anal Chem 2020; 92:11155-11163. [PMID: 32662991 PMCID: PMC7967297 DOI: 10.1021/acs.analchem.0c01285] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rotationally averaged collision cross section (CCS) values for a series of proteins and protein complexes ranging in size from 8.6 to 810 kDa are reported. The CCSs were obtained using a native electrospray ionization drift tube ion mobility-Orbitrap mass spectrometer specifically designed to enhance sensitivity while having high-resolution ion mobility and mass capabilities. Periodic focusing (PF)-drift tube (DT)-ion mobility (IM) provides first-principles determination of the CCS of large biomolecules that can then be used as CCS calibrants. The experimental, first-principles CCS values are compared to previously reported experimentally determined and computationally calculated CCS using projected superposition approximation (PSA), the Ion Mobility Projection Approximation Calculation Tool (IMPACT), and Collidoscope. Experimental CCS values are generally in agreement with previously reported CCSs, with values falling within ∼5.5%. In addition, an ion mobility resolution (CCS centroid divided by CCS fwhm) of ∼60 is obtained for pyruvate kinase (MW ∼ 233 kDa); however, ion mobility resolution for bovine serum albumin (MW ∼ 68 kDa) is less than ∼20, which arises from sample impurities and underscores the importance of sample quality. The high resolution afforded by the ion mobility-Orbitrap mass analyzer provides new opportunities to understand the intricate details of protein complexes such as the impact of post-translational modifications (PTMs), stoichiometry, and conformational changes induced by ligand binding.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Christopher S Mallis
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Klaudia I Kocurek
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael L Poltash
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Liqi Fan
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xueyun Zheng
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Ting Jiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Shiyu Dong
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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237
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Mehaffey MR, Ahn YC, Rivera DD, Thomas PW, Cheng Z, Crowder MW, Pratt RF, Fast W, Brodbelt JS. Elusive structural changes of New Delhi metallo-β-lactamase revealed by ultraviolet photodissociation mass spectrometry. Chem Sci 2020; 11:8999-9010. [PMID: 34123154 PMCID: PMC8163344 DOI: 10.1039/d0sc02503h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We use mass spectrometry (MS), under denaturing and non-denaturing solution conditions, along with ultraviolet photodissociation (UVPD) to characterize structural variations in New Delhi metallo-β-lactamase (NDM) upon perturbation by ligands or mutation. Mapping changes in the abundances and distributions of fragment ions enables sensitive detection of structural alterations throughout the protein. Binding of three covalent inhibitors was characterized: a pentafluorphenyl ester, an O-aryloxycarbonyl hydroxamate, and ebselen. The first two inhibitors modify Lys211 and maintain dizinc binding, although the pentafluorophenyl ester is not selective (Lys214 and Lys216 are also modified). Ebselen reacts with the sole Cys (Cys208) and ejects Zn2 from the active site. For each inhibitor, native UVPD-MS enabled simultaneous detection of the closing of a substrate-binding beta-hairpin loop, identification of covalently-modified residue(s), reporting of the metalation state of the enzyme, and in the case of ebselen, observation of the induction of partial disorder in the C-terminus of the protein. Owing to the ability of native UVPD-MS to track structural changes and metalation state with high sensitivity, we further used this method to evaluate the impact of mutations found in NDM clinical variants. Changes introduced by NDM-4 (M154L) and NDM-6 (A233V) are revealed to propagate through separate networks of interactions to direct zinc ligands, and the combination of these two mutations in NDM-15 (M154L, A233V) results in additive as well as additional structural changes. Insight from UVPD-MS helps to elucidate how distant mutations impact zinc affinity in the evolution of this antibiotic resistance determinant. UVPD-MS is a powerful tool capable of simultaneous reporting of ligand binding, conformational changes and metalation state of NDM, revealing structural aspects of ligand recognition and clinical variants that have proven difficult to probe. We use mass spectrometry (MS) along with ultraviolet photodissociation (UVPD) to characterize structural variations in New Delhi metallo-β-lactamase (NDM) upon perturbation by ligands or mutation.![]()
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Affiliation(s)
- M Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Yeong-Chan Ahn
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Dann D Rivera
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Pei W Thomas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University Oxford OH 45056 USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University Oxford OH 45056 USA
| | - R F Pratt
- Department of Chemistry, Wesleyan University Middletown CT 06459 USA
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
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238
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Macedo-da-Silva J, Marinho CRF, Palmisano G, Rosa-Fernandes L. Lights and Shadows of TORCH Infection Proteomics. Genes (Basel) 2020; 11:E894. [PMID: 32764347 PMCID: PMC7464470 DOI: 10.3390/genes11080894] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/25/2022] Open
Abstract
Congenital abnormalities cause serious fetal consequences. The term TORCH is used to designate the most common perinatal infections, where: (T) refers to toxoplasmosis, (O) means "others" and includes syphilis, varicella-zoster, parvovirus B19, zika virus (ZIKV), and malaria among others, (R) refers to rubella, (C) relates to cytomegalovirus infection, and (H) to herpes simplex virus infections. Among the main abnormalities identified in neonates exposed to congenital infections are central nervous system (CNS) damage, microcephaly, hearing loss, and ophthalmological impairment, all requiring regular follow-up to monitor its progression. Protein changes such as mutations, post-translational modifications, abundance, structure, and function may indicate a pathological condition before the onset of the first symptoms, allowing early diagnosis and understanding of a particular disease or infection. The term "proteomics" is defined as the science that studies the proteome, which consists of the total protein content of a cell, tissue or organism in a given space and time, including post-translational modifications (PTMs) and interactions between proteins. Currently, quantitative bottom-up proteomic strategies allow rapid and high throughput characterization of complex biological mixtures. Investigating proteome modulation during host-pathogen interaction helps in elucidating the mechanisms of infection and in predicting disease progression. This "molecular battle" between host and pathogen is a key to identify drug targets and diagnostic markers. Here, we conducted a survey on proteomic techniques applied to congenital diseases classified in the terminology "TORCH", including toxoplasmosis, ZIKV, malaria, syphilis, human immunodeficiency virus (HIV), herpes simplex virus (HSV) and human cytomegalovirus (HCVM). We have highlighted proteins and/or protein complexes actively involved in the infection. Most of the proteomic studies reported have been performed in cell line models, and the evaluation of tissues (brain, muscle, and placenta) and biofluids (plasma, serum and urine) in animal models is still underexplored. Moreover, there are a plethora of studies focusing on the pathogen or the host without considering the triad mother-fetus-pathogen as a dynamic and interconnected system.
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Affiliation(s)
- Janaina Macedo-da-Silva
- Glycoproteomics Laboratory, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
| | - Claudio Romero Farias Marinho
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
| | - Giuseppe Palmisano
- Glycoproteomics Laboratory, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
| | - Livia Rosa-Fernandes
- Glycoproteomics Laboratory, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
- Laboratory of Experimental Immunoparasitology, Department of Parasitology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
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239
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Beveridge R, Kessler D, Rumpel K, Ettmayer P, Meinhart A, Clausen T. Native Mass Spectrometry Can Effectively Predict PROTAC Efficacy. ACS CENTRAL SCIENCE 2020; 6:1223-1230. [PMID: 32724856 PMCID: PMC7379389 DOI: 10.1021/acscentsci.0c00049] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Indexed: 05/16/2023]
Abstract
Protein degraders, also known as proteolysis targeting chimeras (PROTACs), are bifunctional small molecules that promote cellular degradation of a protein of interest (POI). PROTACs act as molecular mediators, bringing an E3 ligase and a POI into proximity, thus promoting ubiquitination and degradation of the targeted POI. Despite their great promise as next-generation pharmaceutical drugs, the development of new PROTACs is challenged by the complexity of the system, which involves binary and ternary interactions between components. Here, we demonstrate the strength of native mass spectrometry (nMS), a label-free technique, to provide novel insight into PROTAC-mediated protein interactions. We show that nMS can monitor the formation of ternary E3-PROTAC-POI complexes and detect various intermediate species in a single experiment. A unique benefit of the method is its ability to reveal preferentially formed E3-PROTAC-POI combinations in competition experiments with multiple substrate proteins, thereby positioning it as an ideal high-throughput screening strategy during the development of new PROTACs.
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Affiliation(s)
- Rebecca Beveridge
- Research
Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Dirk Kessler
- Discovery
Research, Boehringer Ingelheim Regional
Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Klaus Rumpel
- Discovery
Research, Boehringer Ingelheim Regional
Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Peter Ettmayer
- Discovery
Research, Boehringer Ingelheim Regional
Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Anton Meinhart
- Research
Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Tim Clausen
- Research
Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
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240
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Garcia AM, Giorgiutti C, El Khoury Y, Bauer V, Spiegelhalter C, Leize-Wagner E, Hellwig P, Potier N, Torbeev V. Aggregation and Amyloidogenicity of the Nuclear Coactivator Binding Domain of CREB-Binding Protein. Chemistry 2020; 26:9889-9899. [PMID: 32364648 DOI: 10.1002/chem.202001847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/30/2020] [Indexed: 12/28/2022]
Abstract
The nuclear coactivator binding domain (NCBD) of transcriptional co-regulator CREB-binding protein (CBP) is an example of conformationally malleable proteins that can bind to structurally unrelated protein targets and adopt distinct folds in the respective protein complexes. Here, we show that the folding landscape of NCBD contains an alternative pathway that results in protein aggregation and self-assembly into amyloid fibers. The initial steps of such protein misfolding are driven by intermolecular interactions of its N-terminal α-helix bringing multiple NCBD molecules into contact. These oligomers then undergo slow but progressive interconversion into β-sheet-containing aggregates. To reveal the concealed aggregation potential of NCBD we used a chemically synthesized mirror-image d-NCBD form. The addition of d-NCBD promoted self-assembly into amyloid precipitates presumably due to formation of thermodynamically more stable racemic β-sheet structures. The unexpected aggregation of NCBD needs to be taken into consideration given the multitude of protein-protein interactions and resulting biological functions mediated by CBP.
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Affiliation(s)
- Ana Maria Garcia
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Christophe Giorgiutti
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Youssef El Khoury
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Valentin Bauer
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Coralie Spiegelhalter
- Imaging Center, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM-U964, University of Strasbourg, CNRS-UMR 7104, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Emmanuelle Leize-Wagner
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Petra Hellwig
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
- Institute for Advanced Study, USIAS University of Strasbourg, 5 allée du Général Rouvillois, 67083, Strasbourg, France
| | - Noelle Potier
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Vladimir Torbeev
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
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241
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Structural insights into Escherichia coli phosphopantothenoylcysteine synthetase by native ion mobility-mass spectrometry. Biochem J 2020; 476:3125-3139. [PMID: 31488574 DOI: 10.1042/bcj20190318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/22/2019] [Accepted: 09/05/2019] [Indexed: 12/19/2022]
Abstract
CoaBC, part of the vital coenzyme A biosynthetic pathway in bacteria, has recently been validated as a promising antimicrobial target. In this work, we employed native ion mobility-mass spectrometry to gain structural insights into the phosphopantothenoylcysteine synthetase domain of E. coli CoaBC. Moreover, native mass spectrometry was validated as a screening tool to identify novel inhibitors of this enzyme, highlighting the utility and versatility of this technique both for structural biology and for drug discovery.
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242
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Tamara S, Franc V, Heck AJR. A wealth of genotype-specific proteoforms fine-tunes hemoglobin scavenging by haptoglobin. Proc Natl Acad Sci U S A 2020; 117:15554-15564. [PMID: 32561649 PMCID: PMC7355005 DOI: 10.1073/pnas.2002483117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The serum haptoglobin protein (Hp) scavenges toxic hemoglobin (Hb) leaked into the bloodstream from erythrocytes. In humans, there are two frequently occurring allelic forms of Hp, resulting in three genotypes: Homozygous Hp 1-1 and Hp 2-2, and heterozygous Hp 2-1. The Hp genetic polymorphism has an intriguing effect on the quaternary structure of Hp. The simplest form, Hp 1-1, forms dimers consisting of two α1β units, connected by disulfide bridges. Hp 2-1 forms mixtures of linear (α1)2(α2)n-2(β)n oligomers (n > 1) while Hp 2-2 occurs in cyclic (α2)n(β)n oligomers (n > 2). Different Hp genotypes bind Hb with different affinities, with Hp 2-2 being the weakest binder. This behavior has a significant influence on Hp's antioxidant capacity, with potentially distinctive personalized clinical consequences. Although Hp has been studied extensively in the past, the finest molecular details of the observed differences in interactions between Hp and Hb are not yet fully understood. Here, we determined the full proteoform profiles and proteoform assemblies of all three most common genetic Hp variants. We combined several state-of-the-art analytical methods, including various forms of chromatography, mass photometry, and different tiers of mass spectrometry, to reveal how the tens to hundreds distinct proteoforms and their assemblies influence Hp's capacity for Hb binding. We extend the current knowledge by showing that Hb binding does not just depend on the donor's genotype, but is also affected by variations in Hp oligomerization, glycosylation, and proteolytic processing of the Hp α-chain.
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Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands;
- Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
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243
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Miller CF, Burris BJ, Badu-Tawiah AK. Spray Mechanism of Contained-Electrospray Ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1499-1508. [PMID: 32407083 DOI: 10.1021/jasms.0c00044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Analytical characteristics of contained electrospray ionization (ESI) are summarized in terms of its potential to modify the analyte solution during the stages of droplet formation to provide opportunities to generate native versus denatured biomolecular gas-phase ions, without the need for bulk-phase analyte modifications. The real-time modification of the charged microdroplets occurs in a cavity that is included in the outlet of the contained-ESI ion source. Close examination of the inside of the cavity using a high-speed camera revealed the formation of discrete droplets as well as thin liquid films in the droplets wake. When operated at 20 psi N2 pressure, the droplets were observed to move at an average speed of 8 mm/s providing ∼1 s mixing time in a 10 mm cavity length. Evidence is provided for the presence of highly reactive charged droplets based on myoglobin charge state distribution, apo-myoglobin contents, and ion mobility drift time profiles under different spray conditions. Mechanistic insights for the capture of vapor-phase reagents and droplet dynamics as influenced by different operational modes are also described.
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Affiliation(s)
- Colbert F Miller
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Benjamin J Burris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Abraham K Badu-Tawiah
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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244
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Yan Y, Xing T, Wang S, Daly TJ, Li N. Online coupling of analytical hydrophobic interaction chromatography with native mass spectrometry for the characterization of monoclonal antibodies and related products. J Pharm Biomed Anal 2020; 186:113313. [DOI: 10.1016/j.jpba.2020.113313] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 11/25/2022]
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245
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Aliyari E, Konermann L. Formation of Gaseous Proteins via the Ion Evaporation Model (IEM) in Electrospray Mass Spectrometry. Anal Chem 2020; 92:10807-10814. [DOI: 10.1021/acs.analchem.0c02290] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Elnaz Aliyari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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246
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Kaur U, Johnson DT, Jones LM. Validation of the Applicability of In-Cell Fast Photochemical Oxidation of Proteins across Multiple Eukaryotic Cell Lines. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1372-1379. [PMID: 32142260 DOI: 10.1021/jasms.0c00014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fast photochemical oxidation of proteins (FPOP), a hydroxyl radical-based protein footprinting method, coupled to mass spectrometry has been extensively used to study protein structure and protein-protein interactions in vitro. This method utilizes hydroxyl radicals to oxidatively modify solvent-accessible amino acids and has recently been demonstrated to modify proteins within live cells (IC-FPOP) and Caenorhabditis elegans. Here, we have expanded the application of IC-FPOP into a variety of commonly used cell lines to verify the applicability of the method across various cellular systems. IC-FPOP was able to successfully modify proteins in five different cell lines (Vero, HEK 293T, CHO, MCF-10A, and MCF-7). To increase the number of oxidatively modified proteins identified, we have also employed the use of offline high pH reversed-phase liquid chromatography (RPLC) followed by concatenation and online low-pH RPLC. The coupling of IC-FPOP to 2D-LC MS/MS resulted in a 1.7-fold increase in total identifications of oxidatively modified proteins, which expanded the dynamic range of the method. This work demonstrates the efficacy of using IC-FPOP to study protein-protein interactions in cells.
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Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Danté T Johnson
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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247
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Recent advances in LC–MS based characterization of protein-based bio-therapeutics – mastering analytical challenges posed by the increasing format complexity. J Pharm Biomed Anal 2020; 186:113251. [DOI: 10.1016/j.jpba.2020.113251] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 12/25/2022]
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248
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Soltermann F, Foley EDB, Pagnoni V, Galpin M, Benesch JLP, Kukura P, Struwe WB. Quantifying Protein–Protein Interactions by Molecular Counting with Mass Photometry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Eric D. B. Foley
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Veronica Pagnoni
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Martin Galpin
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Justin L. P. Benesch
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Philipp Kukura
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
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249
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Soltermann F, Foley EDB, Pagnoni V, Galpin M, Benesch JLP, Kukura P, Struwe WB. Quantifying Protein-Protein Interactions by Molecular Counting with Mass Photometry. Angew Chem Int Ed Engl 2020; 59:10774-10779. [PMID: 32167227 PMCID: PMC7318626 DOI: 10.1002/anie.202001578] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/11/2020] [Indexed: 12/12/2022]
Abstract
Interactions between biomolecules control the processes of life in health and their malfunction in disease, making their characterization and quantification essential. Immobilization- and label-free analytical techniques are desirable because of their simplicity and minimal invasiveness, but they struggle with quantifying tight interactions. Here, we show that mass photometry can accurately count, distinguish by molecular mass, and thereby reveal the relative abundances of different unlabelled biomolecules and their complexes in mixtures at the single-molecule level. These measurements determine binding affinities over four orders of magnitude at equilibrium for both simple and complex stoichiometries within minutes, as well as the associated kinetics. These results introduce mass photometry as a rapid, simple and label-free method for studying sub-micromolar binding affinities, with potential for extension towards a universal approach for characterizing complex biomolecular interactions.
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Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Eric D. B. Foley
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Veronica Pagnoni
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Martin Galpin
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Justin L. P. Benesch
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Philipp Kukura
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
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250
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Donald LJ, Spearman M, Mishra N, Komatsu E, Butler M, Perreault H. Mass spectrometric analysis of core fucosylation and sequence variation in a human-camelid monoclonal antibody. Mol Omics 2020; 16:221-230. [PMID: 32163054 DOI: 10.1039/c9mo00168a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrospray mass spectrometry (ESI-MS) was used to measure the masses of an intact dimeric monoclonal antibody (Mab) and assess the fucosylation level. The Mab under study was EG2-hFc, a chimeric human-camelid antibody of about 80 kDa (A. Bell et al., Cancer Lett., 2010, 289(1), 81-90). It was obtained from cell culture with and without a fucosylation inhibitor, and treated with EndoS which cleaves between the two core N-acetyl glucosamine (GlcNAc) residues. It is the first time that this combined approach with a unique mass spectrometer was used to measure 146 Da differences as part of a large intact dimeric antibody. Results showed that in the dimer, both heavy chains were fucosylated on the core GlcNAc of the Fc Asn site equivalent to Asn297. In the presence of the fucosylation inhibitor, fucosylation was lost on both subunits. Following reduction, monomers were analyzed and the masses obtained corroborated the dimer results. Dimeric EG2-hFc Mab treated with PNGase F, to deglycosylate the protein, was also measured by MS for mass comparison. In spite of the success of fucosylation level measurements, the experimental masses of deglycosylated dimers and GlcNAc-Fuc bearing dimers did not correspond to masses of our sequence of reference (A. Bell et al., Cancer Lett., 2010, 289(1), 81-90; ; ), which prompted experiments to determine the protein backbone sequence. Digest mixtures from trypsin, GluC, as well as trypsin + GluC proteolysis were analyzed by matrix-assisted laser desorption/ionization (MALDI) MS and MS/MS. A few variations were found relative to the reference sequence, which are discussed in detail herein. These measurements allowed us to build a new "experimental" sequence for the EG2-hFc samples investigated in this work, although there are still ambiguities to be resolved in this new sequence. MALDI-MS/MS also confirmed the fucosylation pattern in the Fc tryptic peptide EEQYNSTYR.
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Affiliation(s)
- Lynda J Donald
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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