1
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Attanayake K, Mahmud S, Banerjee C, Sharif D, Rahman M, Majuta S, DeBastiani A, Sultana MN, Foroushani SH, Li C, Li P, Valentine SJ. Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 499:117231. [PMID: 38854816 PMCID: PMC11156224 DOI: 10.1016/j.ijms.2024.117231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Capillary vibrating sharp-edge spray ionization (cVSSI) combined with hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has been utilized to characterize different solution-phase DNA conformers including DNA G-quadruplex topologies as well as triplex DNA and duplex DNA. In general, G-quadruplex DNA shows a wide range of protection of hydrogens extending from ~12% to ~21% deuterium incorporation. Additionally, the DNA sequences selected to represent parallel, antiparallel, and hybrid G-quadruplex topologies exhibit slight differences in deuterium uptake levels which appear to loosely relate to overall conformer stability. Notably, the exchange level for one of the hybrid sequence sub topologies of G-quadruplex DNA (24 TTG) is significantly different (compared with the others studied here) despite the DNA sequences being highly comparable. For the quadruplex-forming sequences, correlation analysis suggests protection of base hydrogens involved in tetrad hydrogen bonding. For duplex DNA ~19% deuterium incorporation is observed while only ~16% is observed for triplex DNA. This increased protection of hydrogens may be due to the added backbone scaffolding and Hoogsteen base pairing of the latter species. These experiments lay the groundwork for future studies aimed at determining the structural source of this protection as well as the applicability of the approach for ascertaining different oligonucleotide folds, co-existing conformations, and/or overall conformer flexibility.
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Affiliation(s)
- Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Sultan Mahmud
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Chandrima Banerjee
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Daud Sharif
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Mohammad Rahman
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Sandra Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Mst Nigar Sultana
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | | | - Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
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2
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Miyagi M, Nakazawa T. Significance of Histidine Hydrogen-Deuterium Exchange Mass Spectrometry in Protein Structural Biology. BIOLOGY 2024; 13:37. [PMID: 38248468 PMCID: PMC10813008 DOI: 10.3390/biology13010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/23/2024]
Abstract
Histidine residues play crucial roles in shaping the function and structure of proteins due to their unique ability to act as both acids and bases. In other words, they can serve as proton donors and acceptors at physiological pH. This exceptional property is attributed to the side-chain imidazole ring of histidine residues. Consequently, determining the acid-base dissociation constant (Ka) of histidine imidazole rings in proteins often yields valuable insights into protein functions. Significant efforts have been dedicated to measuring the pKa values of histidine residues in various proteins, with nuclear magnetic resonance (NMR) spectroscopy being the most commonly used technique. However, NMR-based methods encounter challenges in assigning signals to individual imidazole rings and require a substantial amount of proteins. To address these issues associated with NMR-based approaches, a mass-spectrometry-based method known as histidine hydrogen-deuterium exchange mass spectrometry (His-HDX-MS) has been developed. This technique not only determines the pKa values of histidine imidazole groups but also quantifies their solvent accessibility. His-HDX-MS has proven effective across diverse proteins, showcasing its utility. This review aims to clarify the fundamental principles of His-HDX-MS, detail the experimental workflow, explain data analysis procedures and provide guidance for interpreting the obtained results.
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Affiliation(s)
- Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4988, USA
| | - Takashi Nakazawa
- Department of Chemistry, Nara Women’s University, Nara 630-8506, Japan
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3
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Code C, Qiu D, Solov’yov IA, Lee JG, Shin HC, Roland C, Sagui C, Houde D, Rand KD, Jørgensen TJD. Conformationally Restricted Glycopeptide Backbone Inhibits Gas-Phase H/D Scrambling between Glycan and Peptide Moieties. J Am Chem Soc 2023; 145:23925-23938. [PMID: 37883679 PMCID: PMC10636759 DOI: 10.1021/jacs.3c04068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
Protein glycosylation is a common post-translational modification on extracellular proteins. The conformational dynamics of several glycoproteins have been characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS). However, it is, in most cases, not possible to extract information about glycan conformation and dynamics due to the general difficulty of separating the deuterium content of the glycan from that of the peptide (in particular, for O-linked glycans). Here, we investigate whether the fragmentation of protonated glycopeptides by collision-induced dissociation (CID) can be used to determine the solution-specific deuterium content of the glycan. Central to this concept is that glycopeptides can undergo a facile loss of glycans upon CID, thereby allowing for the determination of their masses. However, an essential prerequisite is that hydrogen and deuterium (H/D) scrambling can be kept in check. Therefore, we have measured the degree of scrambling upon glycosidic bond cleavage in glycopeptides that differ in the conformational flexibility of their backbone and glycosylation pattern. Our results show that complete scrambling precedes the glycosidic bond cleavage in normal glycopeptides derived from a glycoprotein; i.e., all labile hydrogens have undergone positional randomization prior to loss of the glycan. In contrast, the glycosidic bond cleavage occurs without any scrambling in the glycopeptide antibiotic vancomycin, reflecting that the glycan cannot interact with the peptide moiety due to a conformationally restricted backbone as revealed by molecular dynamics simulations. Scrambling is also inhibited, albeit to a lesser degree, in the conformationally restricted glycopeptides ristocetin and its pseudoaglycone, demonstrating that scrambling depends on an intricate interplay between the flexibility and proximity of the glycan and the peptide backbone.
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Affiliation(s)
- Christian Code
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Danwen Qiu
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ilia A. Solov’yov
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Department
of Physics, Carl von Ossietzky University
Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Research
Centre for Neurosensory Science, Carl von
Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Center
for Nanoscale Dynamics (CENAD), Carl von
Ossietzky Universität Oldenburg Institut für Physik, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
| | - Jung-Goo Lee
- Center for
Molecular Intelligence, The State University
of New York (SUNY), Korea,
119 Songdo Munwha-ro, Yeonsu-gu, 21985 Incheon, Korea
| | - Hyeon-Cheol Shin
- Center for
Molecular Intelligence, The State University
of New York (SUNY), Korea,
119 Songdo Munwha-ro, Yeonsu-gu, 21985 Incheon, Korea
| | - Christopher Roland
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Celeste Sagui
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Damian Houde
- Department
of Protein Pharmaceutical Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Kasper D. Rand
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University
of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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4
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Sharif D, Rahman M, Mahmud S, Sultana MN, Attanayake K, DeBastiani A, Foroushani SH, Li P, Valentine SJ. In-droplet hydrogen-deuterium exchange to examine protein/peptide solution conformer heterogeneity. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9593. [PMID: 37430450 DOI: 10.1002/rcm.9593] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/25/2023] [Accepted: 05/22/2023] [Indexed: 07/12/2023]
Abstract
RATIONALE Many different structure analysis techniques are not capable of probing the heterogeneity of solution conformations. Here, we examine the ability of in-droplet hydrogen-deuterium exchange (HDX) to directly probe solution conformer heterogeneity of a protein with mass spectrometry (MS) detection. METHODS Two vibrating capillary vibrating sharp-edge spray ionization (cVSSI) devices have been arranged such that they generate microdroplet plumes of the analyte and D2 O reagent, which coalesce to form reaction droplets where HDX takes place in the solution environment. The native HDX-MS setup has been first explored for two model peptides that have distinct structural compositions in solution. The effectiveness of the multidevice cVSSI-HDX in illustrating structural details has been further exploited to investigate coexisting solution-phase conformations of the protein ubiquitin. RESULTS In-droplet HDX reveals decreased backbone exchange for a model peptide that has a greater helix-forming propensity. Differences in intrinsic rates of the alanine and serine residues may account for much of the observed protection. The data allow the first estimates of backbone exchange rates for peptides undergoing in-droplet HDX. That said, the approach may hold greater potential for investigating the tertiary structure and structural transitions of proteins. For ubiquitin protein, HDX reactivity differences suggest that multiple conformers are present in native solutions. The addition of methanol to buffered aqueous solutions of ubiquitin results in increased populations of solution conformers of higher reactivity. Data analysis suggests that partially folded conformers such as the A-state of ubiquitin increase with methanol content; the native state may be preserved to a limited degree even under stronger denaturation conditions. CONCLUSION The deuterium uptake after in-droplet HDX has been observed to correspond to some degree with peptide backbone hydrogen protection based on differences in intrinsic rates of exchange. The presence of coexisting protein solution structures under native and denaturing solution conditions has been distinguished by the isotopic distributions of deuterated ubiquitin ions.
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Affiliation(s)
- Daud Sharif
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Mohammad Rahman
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Sultan Mahmud
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Mst Nigar Sultana
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Samira Hajian Foroushani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
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5
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Developments in rapid hydrogen-deuterium exchange methods. Essays Biochem 2023; 67:165-174. [PMID: 36636941 DOI: 10.1042/ebc20220174] [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: 10/19/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 01/14/2023]
Abstract
Biological macromolecules, such as proteins, nucleic acids, and carbohydrates, contain heteroatom-bonded hydrogens that undergo exchange with solvent hydrogens on timescales ranging from microseconds to hours. In hydrogen-deuterium exchange mass spectrometry (HDX-MS), this exchange process is used to extract information about biomolecular structure and dynamics. This minireview focuses on millisecond timescale HDX-MS measurements, which, while less common than 'conventional' timescale (seconds to hours) HDX-MS, provide a unique window into weakly structured species, weak (or fast cycling) binding interactions, and subtle shifts in conformational dynamics. This includes intrinsically disordered proteins and regions (IDPs/IDRs) that are associated with cancer and amyloidotic neurodegenerative disease. For nucleic acids and carbohydrates, structures such as isomers, stems, and loops, can be elucidated and overall structural rigidity can be assessed. We will provide a brief overview of technical developments in rapid HDX followed by highlights of various applications, emphasising the importance of broadening the HDX timescale to improve throughput and to capture a wider range of function-relevant dynamic and structural shifts.
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6
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Seeing the complete picture: proteins in top-down mass spectrometry. Essays Biochem 2022; 67:283-300. [PMID: 36468679 DOI: 10.1042/ebc20220098] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Abstract
Top-down protein mass spectrometry can provide unique insights into protein sequence and structure, including precise proteoform identification and study of protein–ligand and protein–protein interactions. In contrast with the commonly applied bottom-up approach, top-down approaches do not include digestion of the protein of interest into small peptides, but instead rely on the ionization and subsequent fragmentation of intact proteins. As such, it is fundamentally the only way to fully characterize the composition of a proteoform. Here, we provide an overview of how a top-down protein mass spectrometry experiment is performed and point out recent applications from the literature to the reader. While some parts of the top-down workflow are broadly applicable, different research questions are best addressed with specific experimental designs. The most important divide is between studies that prioritize sequence information (i.e., proteoform identification) versus structural information (e.g., conformational studies, or mapping protein–protein or protein–ligand interactions). Another important consideration is whether to work under native or denaturing solution conditions, and the overall complexity of the sample also needs to be taken into account, as it determines whether (chromatographic) separation is required prior to MS analysis. In this review, we aim to provide enough information to support both newcomers and more experienced readers in the decision process of how to answer a potential research question most efficiently and to provide an overview of the methods that exist to answer these questions.
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7
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Fundamentals of HDX-MS. Essays Biochem 2022; 67:301-314. [PMID: 36251047 PMCID: PMC10070489 DOI: 10.1042/ebc20220111] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is becoming part of the standard repertoire of techniques used by molecular biologists to investigate protein structure and dynamics. This is partly due to the increased use of automation in all stages of the technique and its versatility of application-many proteins that present challenges with techniques such as X-ray crystallography and cryoelectron microscopy are amenable to investigation with HDX-MS. The present review is aimed at scientists who are curious about the technique, and how it may aid their research. It describes the fundamental basis of solvent exchange, the basics of a standard HDX-MS experiment, as well as highlighting emerging novel experimental advances, which point to where the field is heading.
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8
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Vallejo DD, Rojas Ramírez C, Parson KF, Han Y, Gadkari VV, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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9
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Seetaloo N, Kish M, Phillips JJ. HDfleX: Software for Flexible High Structural Resolution of Hydrogen/Deuterium-Exchange Mass Spectrometry Data. Anal Chem 2022; 94:4557-4564. [PMID: 35263087 PMCID: PMC9204700 DOI: 10.1021/acs.analchem.1c05339] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Hydrogen/deuterium-exchange
mass spectrometry (HDX-MS) experiments
on protein structures can be performed at three levels: (1) by enzymatically
digesting labeled proteins and analyzing the peptides (bottom-up),
(2) by further fragmenting peptides following digestion (middle-down),
and (3) by fragmenting the intact labeled protein (top-down) using
soft gas-phase fragmentation methods, such as electron transfer dissociation
(ETD). However, to the best of our knowledge, the software packages
currently available for the analysis of HDX-MS data do not enable
the peptide- and ETD-levels to be combined; they can only be analyzed
separately. Thus, we developed HDfleX, a standalone
application for the analysis of flexible high structural resolution
of HDX-MS data, which allows data at any level of structural resolution
(intact protein, peptide, fragment) to be merged. HDfleX features rapid experimental data fitting, robust statistical significance
analyses, and optional methods for theoretical intrinsic calculations
and a novel empirical correction for comparison between solution conditions.
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Affiliation(s)
- Neeleema Seetaloo
- Living Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
| | - Monika Kish
- Living Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
| | - Jonathan J Phillips
- Living Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K.,Alan Turing Institute, British Library, London NW1 2DB, U.K
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10
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Michaličková D, Kübra Ö, Das D, Osama B, Slanař O. Molecular biomarkers in multiple sclerosis. ARHIV ZA FARMACIJU 2022. [DOI: 10.5937/arhfarm72-36165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Multiple sclerosis (MS) is a highly heterogenous disease regarding radiological, pathological, and clinical characteristics and therapeutic response, including both the efficacy and safety profile of treatments. Accordingly, there is a high demand for biomarkers that sensitively and specifically apprehend the distinctive aspects of the MS heterogeneity, and that can aid in better understanding of the disease diagnosis, prognosis, prediction of the treatment response, and, finally, in the development of new treatments. Currently, clinical characteristics (e.g., relapse rate and disease progression) and magnetic resonance imaging play the most important role in the clinical classification of MS and assessment of its course. Molecular biomarkers (e.g., immunoglobulin G (IgG) oligoclonal bands, IgG index, anti-aquaporin-4 antibodies, neutralizing antibodies against interferon-beta and natalizumab, anti-varicella zoster virus and anti-John Cunningham (JC) virus antibodies) complement these markers excellently. This review provides an overview of exploratory, validated and clinically useful molecular biomarkers in MS which are used for prediction, diagnosis, disease activity and treatment response.
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11
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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12
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Simanjuntak Y, Schamoni-Kast K, Grün A, Uetrecht C, Scaturro P. Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology. Viruses 2021; 13:668. [PMID: 33924391 PMCID: PMC8070632 DOI: 10.3390/v13040668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/01/2021] [Accepted: 04/10/2021] [Indexed: 02/06/2023] Open
Abstract
RNA viruses cause a wide range of human diseases that are associated with high mortality and morbidity. In the past decades, the rise of genetic-based screening methods and high-throughput sequencing approaches allowed the uncovering of unique and elusive aspects of RNA virus replication and pathogenesis at an unprecedented scale. However, viruses often hijack critical host functions or trigger pathological dysfunctions, perturbing cellular proteostasis, macromolecular complex organization or stoichiometry, and post-translational modifications. Such effects require the monitoring of proteins and proteoforms both on a global scale and at the structural level. Mass spectrometry (MS) has recently emerged as an important component of the RNA virus biology toolbox, with its potential to shed light on critical aspects of virus-host perturbations and streamline the identification of antiviral targets. Moreover, multiple novel MS tools are available to study the structure of large protein complexes, providing detailed information on the exact stoichiometry of cellular and viral protein complexes and critical mechanistic insights into their functions. Here, we review top-down and bottom-up mass spectrometry-based approaches in RNA virus biology with a special focus on the most recent developments in characterizing host responses, and their translational implications to identify novel tractable antiviral targets.
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Affiliation(s)
- Yogy Simanjuntak
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Kira Schamoni-Kast
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Alice Grün
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Charlotte Uetrecht
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
- European XFEL GmbH, 22869 Schenefeld, Germany
| | - Pietro Scaturro
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
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13
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Modzel M, Wollenberg DTW, Trelle MB, Larsen MR, Jørgensen TJD. Ultraviolet Photodissociation of Protonated Peptides and Proteins Can Proceed with H/D Scrambling. Anal Chem 2021; 93:691-696. [PMID: 33295747 DOI: 10.1021/acs.analchem.0c02957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet photodissociation (UVPD) has recently been introduced as an ion activation method for the determination of single-residue deuterium levels in H/D exchange tandem mass spectrometry experiments. In this regard, it is crucial to know which fragment ion types can be utilized for this purpose. UVPD yields rich product ion spectra where all possible backbone fragment ion types (a/x, b/y, and c/z) are typically observed. Here we provide a detailed investigation of the level of H/D scrambling for all fragment ion types upon UVPD of the peptide scrambling probe P1 (HHHHHHIIKIIK) using an Orbitrap tribrid mass spectrometer equipped with a solid-state 213 nm UV laser. The most abundant UVPD-generated fragment ions (i.e., b/y ions) exhibit extensive H/D scrambling. Similarly, a/x and c/z ions have also undergone H/D scrambling due to UV-induced heating of the precursor ion population. Therefore, dominant b/y ions upon UVPD of protonated peptides are a strong indicator for the occurrence of extensive H/D scrambling of the precursor ion population. In contrast to peptide P1, UV-irradiation of ubiquitin did not induce H/D scrambling in the nonfragmented precursor ion population. However, the UVPD-generated b2 and a4 ions from ubiquitin exhibit extensive H/D scrambling. To minimize H/D scrambling, short UV-irradiation time and high gas pressures are recommended.
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Affiliation(s)
- Maciej Modzel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark.,Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Daniel T Weltz Wollenberg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark.,Novozymes A/S, Krogshøjvej 36, Bagsværd 2880, Denmark
| | - Morten Beck Trelle
- Department of Clinical Biochemistry, Svendborg Hospital, Baagøes Allé 15, SVB Building 17.01, 5700 Svendborg, Denmark
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
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14
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Sun H, Ma L, Wang L, Xiao P, Li H, Zhou M, Song D. Research advances in hydrogen-deuterium exchange mass spectrometry for protein epitope mapping. Anal Bioanal Chem 2021; 413:2345-2359. [PMID: 33404742 DOI: 10.1007/s00216-020-03091-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/01/2022]
Abstract
With the development of biomedical technology, epitope mapping of proteins has become critical for developing and evaluating new protein drugs. The application of hydrogen-deuterium exchange for protein epitope mapping holds great potential. Although several reviews addressed the hydrogen-deuterium exchange, to date, only a few systematic reviews have focused on epitope mapping using this technology. Here, we introduce the basic principles, development history, and review research progress in hydrogen-deuterium exchange epitope mapping technology and discuss its advantages. We summarize the main hurdles in applying hydrogen-deuterium exchange epitope mapping technology, combined with relevant examples to provide specific solutions. We describe the epitope mapping of virus assemblies, disease-associated proteins, and polyclonal antibodies as examples of pattern introduction. Finally, we discuss the outlook of hydrogen-deuterium exchange epitope mapping technology. This review will help researchers studying protein epitopes to gain a more comprehensive understanding of this technology.
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Affiliation(s)
- Haofeng Sun
- National Institute of Metrology, Beijing, 100029, China
- College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lingyun Ma
- National Institute of Metrology, Beijing, 100029, China
| | - Leyu Wang
- College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Peng Xiao
- National Institute of Metrology, Beijing, 100029, China
| | - Hongmei Li
- National Institute of Metrology, Beijing, 100029, China
| | - Min Zhou
- School of Chemical and Engineering, Nanjing University of Science and Technology, Jiangsu, 210094, China.
| | - Dewei Song
- National Institute of Metrology, Beijing, 100029, China.
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15
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Wollenberg DTW, Pengelley S, Mouritsen JC, Suckau D, Jørgensen CI, Jørgensen TJD. Avoiding H/D Scrambling with Minimal Ion Transmission Loss for HDX-MS/MS-ETD Analysis on a High-Resolution Q-TOF Mass Spectrometer. Anal Chem 2020; 92:7453-7461. [PMID: 32427467 DOI: 10.1021/acs.analchem.9b05208] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Hydrogen/deuterium exchange monitored by mass spectrometry (HDX-MS) enables the study of protein dynamics by measuring the time-resolved deuterium incorporation into a protein incubated in D2O. Using electron-based fragmentation in the gas phase it is possible to measure deuterium uptake at single-residue resolution. However, a prerequisite for this approach is that the solution-phase labeling is conserved in the gas phase prior to precursor fragmentation. It is therefore essential to reduce or even avoid intramolecular hydrogen/deuterium migration, which causes randomization of the deuterium labels along the peptide (hydrogen scrambling). Here, we describe an optimization strategy for reducing scrambling to a negligible level while minimizing the impact on sensitivity on a high-resolution Q-TOF equipped with ETD and an electrospray ionization interface consisting of a glass transfer capillary followed by a dual ion funnel. In our strategy we narrowed down the optimization to two accelerating potentials, and we defined the optimization of these in a simple rule by accounting for their interdependency in relation to scrambling and transmission efficiency. Using this rule, we were able to reduce scrambling from 75% to below 5% on average using the highly scrambling-sensitive quadruply charged P1 peptide scrambling probe resulting in a minor 33% transmission loss. To demonstrate the applicability of this approach, we probe the dynamics of certain regions in cytochrome c.
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Affiliation(s)
- Daniel T Weltz Wollenberg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark.,Novozymes A/S, Krogshøjvej 36, Bagsværd 2280, Denmark
| | - Stuart Pengelley
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, Bremen, 28359, Germany
| | | | - Detlev Suckau
- Bruker Daltonik GmbH, Fahrenheitstrasse 4, Bremen, 28359, Germany
| | | | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
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16
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Sanguantrakun N, Chanthamontri C, Gross ML. Top-Down Analysis of In-Source HDX of Native Protein Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1151-1154. [PMID: 32275420 PMCID: PMC7489294 DOI: 10.1021/jasms.9b00149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hydrogen/deuterium exchange (HDX) is used in protein biophysics to probe folding dynamics, intermolecular interactions, epitope and other mapping. A typical procedure often involves HDX in buffered D2O solution followed by pepsin digestion, and liquid chromatography/electrospray ionization mass spectrometry analysis. In this work, HDX of protein ions was conducted in the ESI source. Both native electrospray droplets of ubiquitin and denatured myoglobin were exposed to D2O vapor in the source region of a Bruker SolariX 12T FTICR-mass spectrometer. Electron capture dissociation was used to assess deuterium incorporation at the residue level. This in-source HDX, on the millisecond-time scale, exchanges side-chain hydrogens and fast-exchanging amides compared to conventional minutes-to-hours HDX of backbone hydrogens in solution with less sample preparation (i.e., no D2O/protein mixing and incubation, no quenching, protein digestion, or LC separation).
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Affiliation(s)
- Nawaporn Sanguantrakun
- Department of Basic Sciences, St. Louis College of Pharmacy, St. Louis, MO 63110
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Chamnongsak Chanthamontri
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
- Millipore Sigma, 2909 Laclede Avenue, St. Louis, MO 63103
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
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17
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Kaltashov IA, Bobst CE, Pawlowski J, Wang G. Mass spectrometry-based methods in characterization of the higher order structure of protein therapeutics. J Pharm Biomed Anal 2020; 184:113169. [PMID: 32092629 DOI: 10.1016/j.jpba.2020.113169] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/31/2022]
Abstract
Higher order structure of protein therapeutics is an important quality attribute, which dictates both potency and safety. While modern experimental biophysics offers an impressive arsenal of state-of-the-art tools that can be used for the characterization of higher order structure, many of them are poorly suited for the characterization of biopharmaceutical products. As a result, these analyses were traditionally carried out using classical techniques that provide relatively low information content. Over the past decade, mass spectrometry made a dramatic debut in this field, enabling the characterization of higher order structure of biopharmaceuticals as complex as monoclonal antibodies at a level of detail that was previously unattainable. At present, mass spectrometry is an integral part of the analytical toolbox across the industry, which is critical not only for quality control efforts, but also for discovery and development.
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Affiliation(s)
- Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA.
| | - Cedric E Bobst
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Jake Pawlowski
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Guanbo Wang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu Province, PR China
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18
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Xia D, Liu B, Xu X, Ding Y, Zheng Q. Drug target discovery by magnetic nanoparticles coupled mass spectrometry. J Pharm Anal 2020; 11:122-127. [PMID: 33717618 PMCID: PMC7930636 DOI: 10.1016/j.jpha.2020.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/24/2019] [Accepted: 02/04/2020] [Indexed: 11/25/2022] Open
Abstract
Drug target discovery is the basis of drug screening. It elucidates the cause of disease and the mechanism of drug action, which is the essential of drug innovation. Target discovery performed in biological systems is complicated as proteins are in low abundance and endogenous compounds may interfere with drug binding. Therefore, methods to track drug-target interactions in biological matrices are urgently required. In this work, a Fe3O4 nanoparticle-based approach was developed for drug-target screening in biofluids. A known ligand-protein complex was selected as a principle-to-proof example to validate the feasibility. After incubation in cell lysates, ligand-modified Fe3O4 nanoparticles bound to the target protein and formed complexes that were separated from the lysates by a magnet for further analysis. The large surface-to-volume ratio of the nanoparticles provides more active sites for the modification of chemical drugs. It enhances the opportunity for ligand-protein interactions, which is beneficial for capturing target proteins, especially for those with low abundance. Additionally, a one-step magnetic separation simplifies the pre-processing of ligand-protein complexes, so it effectively reduces the endogenous interference. Therefore, the present nanoparticle-based approach has the potential to be used for drug target screening in biological systems. Fe3O4 NPs were made hydrophilic to adequately disperse in the cell lysate and fully contact with target proteins. The magnetic property of the NPs allowed one-step isolation while maintaining ligand-protein non-covalent bindings. It enabled the capture of low abundant targets in biological matrices while eliminated the endogenous interference.
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Affiliation(s)
- Dandan Xia
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Baoling Liu
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiaowei Xu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.,Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, 210009, China
| | - Ya Ding
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qiuling Zheng
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
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19
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Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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20
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Kaldmäe M, Leppert A, Chen G, Sarr M, Sahin C, Nordling K, Kronqvist N, Gonzalvo-Ulla M, Fritz N, Abelein A, Laίn S, Biverstål H, Jörnvall H, Lane DP, Rising A, Johansson J, Landreh M. High intracellular stability of the spidroin N-terminal domain in spite of abundant amyloidogenic segments revealed by in-cell hydrogen/deuterium exchange mass spectrometry. FEBS J 2019; 287:2823-2833. [PMID: 31815338 PMCID: PMC7383493 DOI: 10.1111/febs.15169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/01/2019] [Accepted: 12/05/2019] [Indexed: 12/22/2022]
Abstract
Proteins require an optimal balance of conformational flexibility and stability in their native environment to ensure their biological functions. A striking example is spidroins, spider silk proteins, which are stored at extremely high concentrations in soluble form, yet undergo amyloid-like aggregation during spinning. Here, we elucidate the stability of the highly soluble N-terminal domain (NT) of major ampullate spidroin 1 in the Escherichia coli cytosol as well as in inclusion bodies containing fibrillar aggregates. Surprisingly, we find that NT, despite being largely composed of amyloidogenic sequences, showed no signs of concentration-dependent aggregation. Using a novel intracellular hydrogen/deuterium exchange mass spectrometry (HDX-MS) approach, we reveal that NT adopts a tight fold in the E. coli cytosol and in this manner conceals its aggregation-prone regions by maintaining a tight fold under crowded conditions. Fusion of NT to the unstructured amyloid-forming Aβ40 peptide, on the other hand, results in the formation of fibrillar aggregates. However, HDX-MS indicates that the NT domain is only partially incorporated into these aggregates in vivo. We conclude that NT is able to control its aggregation to remain functional under the extreme conditions in the spider silk gland.
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Affiliation(s)
- Margit Kaldmäe
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Axel Leppert
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Gefei Chen
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Medoune Sarr
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Kerstin Nordling
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Nina Kronqvist
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Marta Gonzalvo-Ulla
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nicolas Fritz
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Axel Abelein
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Sonia Laίn
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Henrik Biverstål
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden.,Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Hans Jörnvall
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - David P Lane
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Anna Rising
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden.,Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Johansson
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
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21
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Johnson DT, Di Stefano LH, Jones LM. Fast photochemical oxidation of proteins (FPOP): A powerful mass spectrometry-based structural proteomics tool. J Biol Chem 2019; 294:11969-11979. [PMID: 31262727 DOI: 10.1074/jbc.rev119.006218] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fast photochemical oxidation of proteins (FPOP) is a MS-based method that has proved useful in studies of protein structures, interactions, conformations, and protein folding. The success of this method relies on the irreversible labeling of solvent-exposed amino acid side chains by hydroxyl radicals. FPOP generates these radicals through laser-induced photolysis of hydrogen peroxide. The data obtained provide residue-level resolution of protein structures and interactions on the microsecond timescale, enabling investigations of fast processes such as protein folding and weak protein-protein interactions. An extensive comparison between FPOP and other footprinting techniques gives insight on their complementarity as well as the robustness of FPOP to provide unique structural information once unattainable. The versatility of this method is evidenced by both the heterogeneity of samples that can be analyzed by FPOP and the myriad of applications for which the method has been successfully used: from proteins of varying size to intact cells. This review discusses the wide applications of this technique and highlights its high potential. Applications including, but not limited to, protein folding, membrane proteins, structure elucidation, and epitope mapping are showcased. Furthermore, the use of FPOP has been extended to probing proteins in cells and in vivo These promising developments are also presented herein.
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Affiliation(s)
- Danté T Johnson
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201
| | - Luciano H Di Stefano
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201.
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22
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Masson GR, Burke JE, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC, Rand KD. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods 2019; 16:595-602. [PMID: 31249422 PMCID: PMC6614034 DOI: 10.1038/s41592-019-0459-y] [Citation(s) in RCA: 382] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful biophysical technique being increasingly applied to a wide variety of problems. As the HDX-MS community continues to grow, adoption of best practices in data collection, analysis, presentation and interpretation will greatly enhance the accessibility of this technique to nonspecialists. Here we provide recommendations arising from community discussions emerging out of the first International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX; 2017). It is meant to represent both a consensus viewpoint and an opportunity to stimulate further additions and refinements as the field advances.
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Affiliation(s)
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ganesh S Anand
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Christoph Borchers
- Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Sébastien Brier
- Institut Pasteur, Chemistry and Structural Biology Department, Paris, France
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - S Walter Englander
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Yoshitomo Hamuro
- Johnson & Johnson Pharmaeutical Research and Development, Jersey City, NJ, USA
| | - Albert J R Heck
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | | | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej, Odense, Denmark
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Leland Mayne
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Dana Reichmann
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Joost Snijder
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Timothy S Strutzenberg
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | | | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Benjamin T Walters
- Department of Early Stage Pharmaceutical Development, Genentech, Inc., South San Francisco, CA, USA
| | - David D Weis
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, ON, Canada
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | | | - Jie Zheng
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB, Canada.
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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23
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Shen Y, Zhao X, Wang G, Chen DDY. Differential Hydrogen/Deuterium Exchange during Proteoform Separation Enables Characterization of Conformational Differences between Coexisting Protein States. Anal Chem 2019; 91:3805-3809. [DOI: 10.1021/acs.analchem.9b00558] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Yue Shen
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Xiuxiu Zhao
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - Guanbo Wang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu Province 210023, China
| | - David D. Y. Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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24
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Hamuro Y, Zhang T. High-Resolution HDX-MS of Cytochrome c Using Pepsin/Fungal Protease Type XIII Mixed Bed Column. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:227-234. [PMID: 30374663 DOI: 10.1007/s13361-018-2087-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 06/08/2023]
Abstract
A pepsin/FPXIII (protease from Aspergillus saitoi, type XIII) mixed bed column significantly improved the resolution of bottom-up hydrogen/deuterium exchange mass spectrometry (HDX-MS) data compared with a pepsin-only column. The HDX-MS method using the mixed bed column determined 65 amide hydrogen exchange rates out of one hundred cytochrome c backbone amide hydrogens. Different cleavage specificities of the two enzymes generated 138 unique high-quality peptic fragments, which allows fine sub-localization of deuterium. The exchange rates determined in this method are consistent within the current study as well as with the previous HDX-NMR study. High-resolution HDX-MS data can determine the exchange rate of each residue not the deuterium buildup curve of a peptic fragment. The exchange rates provide more precise and quantitative measurements of protein dynamics in a more reproducible manner. Graphical Abstract ᅟ.
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Affiliation(s)
- Yoshitomo Hamuro
- SGS Life North America, 606 Brandywine Parkway, West Chester, PA, 19380, USA.
- Janssen Pharmaceutical, 1400 McKean Road, Spring House, PA, 19477, USA.
| | - Terry Zhang
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA, 95134, USA
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25
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Benhaim M, Lee KK, Guttman M. Tracking Higher Order Protein Structure by Hydrogen-Deuterium Exchange Mass Spectrometry. Protein Pept Lett 2019; 26:16-26. [PMID: 30543159 PMCID: PMC6386625 DOI: 10.2174/0929866526666181212165037] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/30/2018] [Accepted: 11/17/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Structural biology has provided a fundamental understanding of protein structure and mechanistic insight into their function. However, high-resolution structures alone are insufficient for a complete understanding of protein behavior. Higher energy conformations, conformational changes, and subtle structural fluctuations that underlie the proper function of proteins are often difficult to probe using traditional structural approaches. Hydrogen/Deuterium Exchange with Mass Spectrometry (HDX-MS) provides a way to probe the accessibility of backbone amide protons under native conditions, which reports on local structural dynamics of solution protein structure that can be used to track complex structural rearrangements that occur in the course of a protein's function. CONCLUSION In the last 20 years the advances in labeling techniques, sample preparation, instrumentation, and data analysis have enabled HDX to gain insights into very complex biological systems. Analysis of challenging targets such as membrane protein complexes is now feasible and the field is paving the way to the analysis of more and more complex systems.
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Affiliation(s)
- Mark Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
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26
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Lermyte F, Valkenborg D, Loo JA, Sobott F. Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure. MASS SPECTROMETRY REVIEWS 2018; 37:750-771. [PMID: 29425406 PMCID: PMC6131092 DOI: 10.1002/mas.21560] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 05/11/2023]
Abstract
In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation. Although we focus on the two most widely used methods-ECD and ETD-we also discuss the use of other ion/electron, ion/ion, and ion/neutral fragmentation methods, useful for interrogation of a range of classes of biomolecules in positive- and negative-ion mode, and speculate about how this exciting field might evolve in the coming years.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Agoralaan, Diepenbeek, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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27
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Karch KR, Coradin M, Zandarashvili L, Kan ZY, Gerace M, Englander SW, Black BE, Garcia BA. Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly. Structure 2018; 26:1651-1663.e3. [PMID: 30293810 DOI: 10.1016/j.str.2018.08.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/21/2018] [Accepted: 08/08/2018] [Indexed: 10/28/2022]
Abstract
Until recently, a major limitation of hydrogen-deuterium exchange mass spectrometry (HDX-MS) was that resolution of deuterium localization was limited to the length of the peptide generated during proteolysis. However, electron transfer dissociation (ETD) has been shown to preserve deuterium label in the gas phase, enabling better resolution. To date, this technology remains mostly limited to small, already well-characterized proteins. Here, we optimize, expand, and adapt HDX-MS tandem MS (MS/MS) capabilities to accommodate histone and nucleosomal complexes on top-down HDX-MS/MS and middle-down HDX-MS/MS platforms and demonstrate that near site-specific resolution of deuterium localization can be obtained with high reproducibility. We are able to study histone tail dynamics in unprecedented detail, which have evaded analysis by traditional structural biology techniques for decades, revealing important insights into chromatin biology. Together, the results of these studies highlight the versatility, reliability, and reproducibility of ETD-based HDX-MS/MS methodology to interrogate large protein and protein/DNA complexes.
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Affiliation(s)
- Kelly R Karch
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia 19104, USA
| | - Mariel Coradin
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia 19104, USA
| | - Levani Zandarashvili
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia 19104, USA
| | - Zhong-Yuan Kan
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - Morgan Gerace
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia 19104, USA
| | - S Walter Englander
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - Ben E Black
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia 19104, USA.
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28
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Háda V, Bagdi A, Bihari Z, Timári SB, Fizil Á, Szántay C. Recent advancements, challenges, and practical considerations in the mass spectrometry-based analytics of protein biotherapeutics: A viewpoint from the biosimilar industry. J Pharm Biomed Anal 2018; 161:214-238. [PMID: 30205300 DOI: 10.1016/j.jpba.2018.08.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 01/22/2023]
Abstract
The extensive analytical characterization of protein biotherapeutics, especially of biosimilars, is a critical part of the product development and registration. High-resolution mass spectrometry became the primary analytical tool used for the structural characterization of biotherapeutics. Its high instrumental sensitivity and methodological versatility made it possible to use this technique to characterize both the primary and higher-order structure of these proteins. However, even by using high-end instrumentation, analysts face several challenges with regard to how to cope with industrial and regulatory requirements, that is, how to obtain accurate and reliable analytical data in a time- and cost-efficient way. New sample preparation approaches, measurement techniques and data evaluation strategies are available to meet those requirements. The practical considerations of these methods are discussed in the present review article focusing on hot topics, such as reliable and efficient sequencing strategies, minimization of artefact formation during sample preparation, quantitative peptide mapping, the potential of multi-attribute methodology, the increasing role of mass spectrometry in higher-order structure characterization and the challenges of MS-based identification of host cell proteins. On the basis of the opportunities in new instrumental techniques, methodological advancements and software-driven data evaluation approaches, for the future one can envision an even wider application area for mass spectrometry in the biopharmaceutical industry.
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Affiliation(s)
- Viktor Háda
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary.
| | - Attila Bagdi
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | - Zsolt Bihari
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | | | - Ádám Fizil
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | - Csaba Szántay
- Spectroscopic Research Department, Gedeon Richter Plc, Hungary.
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29
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MS methods to study macromolecule-ligand interaction: Applications in drug discovery. Methods 2018; 144:152-174. [PMID: 29890284 DOI: 10.1016/j.ymeth.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022] Open
Abstract
The interaction of small compounds (i.e. ligands) with macromolecules or macromolecule assemblies (i.e. targets) is the mechanism of action of most of the drugs available today. Mass spectrometry is a popular technique for the interrogation of macromolecule-ligand interactions and therefore is also widely used in drug discovery and development. Thanks to its versatility, mass spectrometry is used for multiple purposes such as biomarker screening, identification of the mechanism of action, ligand structure optimization or toxicity assessment. The evolution and automation of the instruments now allows the development of high throughput methods with high sensitivity and a minimized false discovery rate. Herein, all these approaches are described with a focus on the methods for studying macromolecule-ligand interaction aimed at defining the structure-activity relationships of drug candidates, along with their mechanism of action, metabolism and toxicity.
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30
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Hamuro Y, E SY. Determination of Backbone Amide Hydrogen Exchange Rates of Cytochrome c Using Partially Scrambled Electron Transfer Dissociation Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:989-1001. [PMID: 29500740 DOI: 10.1007/s13361-018-1892-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/08/2018] [Accepted: 01/08/2018] [Indexed: 06/08/2023]
Abstract
The technological goal of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is to determine backbone amide hydrogen exchange rates. The most critical challenge to achieve this goal is obtaining the deuterium incorporation in single-amide resolution, and gas-phase fragmentation may provide a universal solution. The gas-phase fragmentation may generate the daughter ions which differ by a single amino acid and the difference in deuterium incorporations in the two analogous ions can yield the deuterium incorporation at the sub-localized site. Following the pioneering works by Jørgensen and Rand, several papers utilized the electron transfer dissociation (ETD) to determine the location of deuterium in single-amide resolution. This paper demonstrates further advancement of the strategy by determining backbone amide hydrogen exchange rates, instead of just determining deuterium incorporation at a single time point, in combination with a wide time window monitoring. A method to evaluate the effects of scrambling and to determine the exchange rates from partially scrambled HDX-ETD-MS data is described. All parent ions for ETD fragmentation were regio-selectively scrambled: The deuterium in some regions of a peptide ion was scrambled while that in the other regions was not scrambled. The method determined 31 backbone amide hydrogen exchange rates of cytochrome c in the non-scrambled regions. Good fragmentation of a parent ion, a low degree of scrambling, and a low number of exchangeable hydrogens in the preceding side chain are the important factors to determine the exchange rate. The exchange rates determined by the HDX-MS are in good agreement with those determined by NMR. Graphical Abstract ᅟ.
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Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, NJ, 08852, USA.
- SGS Life North America, 606 Brandywine Parkway, West Chester, PA, 19380, USA.
| | - Sook Yen E
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, NJ, 08852, USA
- Regeneron, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
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31
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Hollerweger JC, Hoppe IJ, Regl C, Stock LG, Huber CG, Lohrig U, Stutz H, Brandstetter H. Analytical Cascades of Enzymes for Sensitive Detection of Structural Variations in Protein Samples. Anal Chem 2018; 90:5055-5065. [PMID: 29582994 DOI: 10.1021/acs.analchem.7b04874] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein function critically depends on structure. However, current analytical tools to monitor consistent higher-order structure with high sensitivity, as for instance required in the development of biopharmaceuticals, are limited. To complement existing assays, we present the analytical cascade of enzymes (ACE), a method based on enzymatic modifications of target proteins, which serve to exponentially amplify structural differences between them. The method enables conformational and chemical fingerprinting of closely related proteins, allowing for the sensitive detection of heterogeneities in protein preparations with high precision. Using this method, we detect protein variants differing in conformation only, as well as structural changes induced by diverse covalent modifications. Additionally, we employ this method to identify the nature of structural variants. Moreover, the ACE method should help to address the limited reproducibility in fundamental research, which partly relates to sample heterogeneities.
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Affiliation(s)
- Julia C Hollerweger
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Isabel J Hoppe
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Christof Regl
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Lorenz G Stock
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Christian G Huber
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Urs Lohrig
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria.,Physical and Chemical Characterization Biosimilars , Sandoz GmbH , A-6250 Kundl , Austria
| | - Hanno Stutz
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
| | - Hans Brandstetter
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , 5020 Salzburg , Austria
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32
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Wang H, Yong G, Brown SL, Lee HE, Zenaidee MA, Supuran CT, Donald WA. Supercharging protein ions in native mass spectrometry using theta capillary nanoelectrospray ionization mass spectrometry and cyclic alkylcarbonates. Anal Chim Acta 2018; 1003:1-9. [DOI: 10.1016/j.aca.2017.11.075] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/22/2017] [Accepted: 11/25/2017] [Indexed: 12/27/2022]
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33
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Brodie NI, Huguet R, Zhang T, Viner R, Zabrouskov V, Pan J, Petrotchenko EV, Borchers CH. Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation. Anal Chem 2018; 90:3079-3082. [PMID: 29336549 DOI: 10.1021/acs.analchem.7b03655] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Top-down hydrogen-deuterium exchange (HDX) analysis using electron capture or transfer dissociation Fourier transform mass spectrometry (FTMS) is a powerful method for the analysis of secondary structure of proteins in solution. The resolution of the method is a function of the degree of fragmentation of backbone bonds in the proteins. While fragmentation is usually extensive near the N- and C-termini, electron capture (ECD) or electron transfer dissociation (ETD) fragmentation methods sometimes lack good coverage of certain regions of the protein, most often in the middle of the sequence. Ultraviolet photodissociation (UVPD) is a recently developed fast-fragmentation technique, which provides extensive backbone fragmentation that can be complementary in sequence coverage to the aforementioned electron-based fragmentation techniques. Here, we explore the application of electrospray ionization (ESI)-UVPD FTMS on an Orbitrap Fusion Lumos Tribrid mass spectrometer to top-down HDX analysis of proteins. We have incorporated UVPD-specific fragment-ion types and fragment-ion mixtures into our isotopic envelope fitting software (HDX Match) for the top-down HDX analysis. We have shown that UVPD data is complementary to ETD, thus improving the overall resolution when used as a combined approach.
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Affiliation(s)
- Nicholas I Brodie
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Romain Huguet
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Terry Zhang
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Rosa Viner
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jingxi Pan
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Evgeniy V Petrotchenko
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Christoph H Borchers
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada.,Department of Biochemistry and Microbiology , University of Victoria , Petch Building, Room 270d, 3800 Finnerty Road , Victoria , British Columbia V8P 5C2 , Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montreal , Quebec H3T 1E2 , Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montreal , Quebec H3T 1E2 , Canada
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34
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Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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35
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Mistarz UH, Bellina B, Jensen PF, Brown JM, Barran PE, Rand KD. UV Photodissociation Mass Spectrometry Accurately Localize Sites of Backbone Deuteration in Peptides. Anal Chem 2017; 90:1077-1080. [DOI: 10.1021/acs.analchem.7b04683] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ulrik H. Mistarz
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Bruno Bellina
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Institute, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Pernille F. Jensen
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jeffery M. Brown
- Waters Corporation, Stamford
Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Institute, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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36
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Gessner C, Steinchen W, Bédard S, J Skinner J, Woods VL, Walsh TJ, Bange G, Pantazatos DP. Computational method allowing Hydrogen-Deuterium Exchange Mass Spectrometry at single amide Resolution. Sci Rep 2017. [PMID: 28630467 PMCID: PMC5476592 DOI: 10.1038/s41598-017-03922-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Hydrogen-deuterium exchange (HDX) coupled with mass spectrometry (HDXMS) is a rapid and effective method for localizing and determining protein stability and dynamics. Localization is routinely limited to a peptide resolution of 5 to 20 amino acid residues. HDXMS data can contain information beyond that needed for defining protein stability at single amide resolution. Here we present a method for extracting this information from an HDX dataset to generate a HDXMS protein stability fingerprint. High resolution (HR)-HDXMS was applied to the analysis of a model protein of a spectrin tandem repeat that exemplified an intuitive stability profile based on the linkage of two triple helical repeats connected by a helical linker. The fingerprint recapitulated expected stability maximums and minimums with interesting structural features that corroborate proposed mechanisms of spectrin flexibility and elasticity. HR-HDXMS provides the unprecedented ability to accurately assess protein stability at the resolution of a single amino acid. The determination of HDX stability fingerprints may be broadly applicable in many applications for understanding protein structure and function as well as protein ligand interactions.
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Affiliation(s)
- Chris Gessner
- Indiana University, Department of Informatics and Computing, Bloomington, IN, USA
| | - Wieland Steinchen
- Philipps-University Marburg, Faculty of Chemistry & LOEWE Center for Synthetic Microbiology Hans-Meerwein-Strasse, 35043, Marburg, Germany
| | - Sabrina Bédard
- GlaxoSmithKline, Platform Technology & Science, Collegeville Road, Collegeville, Pennsylvania, 19426, United States
| | - John J Skinner
- iHuman Institute, ShanghaiTech University, 99 Haike Road, Pudong, Shanghai, China
| | - Virgil L Woods
- Indiana University, Department of Informatics and Computing, Bloomington, IN, USA
| | - Thomas J Walsh
- Weill Cornell Medicine, Transplantation-Oncology Infectious Disease Program, Division of Infectious Diseases, 1300 York Ave, New York, NY, 10065, USA
| | - Gert Bange
- Philipps-University Marburg, Faculty of Chemistry & LOEWE Center for Synthetic Microbiology Hans-Meerwein-Strasse, 35043, Marburg, Germany
| | - Dionysios P Pantazatos
- Weill Cornell Medicine, Transplantation-Oncology Infectious Disease Program, Division of Infectious Diseases, 1300 York Ave, New York, NY, 10065, USA.
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37
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Cryar A, Groves K, Quaglia M. Online Hydrogen-Deuterium Exchange Traveling Wave Ion Mobility Mass Spectrometry (HDX-IM-MS): a Systematic Evaluation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1192-1202. [PMID: 28374315 PMCID: PMC5438439 DOI: 10.1007/s13361-017-1633-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 05/11/2023]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an important tool for measuring and monitoring protein structure. A bottom-up approach to HDX-MS provides peptide level deuterium uptake values and a more refined localization of deuterium incorporation compared with global HDX-MS measurements. The degree of localization provided by HDX-MS is proportional to the number of peptides that can be identified and monitored across an exchange experiment. Ion mobility spectrometry (IMS) has been shown to improve MS-based peptide analysis of biological samples through increased separation capacity. The integration of IMS within HDX-MS workflows has been commercialized but presently its adoption has not been widespread. The potential benefits of IMS, therefore, have not yet been fully explored. We herein describe a comprehensive evaluation of traveling wave ion mobility integrated within an online-HDX-MS system and present the first reported example of UDMSE acquisition for HDX analysis. Instrument settings required for optimal peptide identifications are described and the effects of detector saturation due to peak compression are discussed. A model system is utilized to confirm the comparability of HDX-IM-MS and HDX-MS uptake values prior to an evaluation of the benefits of IMS at increasing sample complexity. Interestingly, MS and IM-MS acquisitions were found to identify distinct populations of peptides that were unique to the respective methods, a property that can be utilized to increase the spatial resolution of HDX-MS experiments by >60%. Graphical Abstract ᅟ.
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Affiliation(s)
- Adam Cryar
- LGC, Queens Road, Teddington, London, TW11 0LY, UK.
| | - Kate Groves
- LGC, Queens Road, Teddington, London, TW11 0LY, UK
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38
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Maleki H, Maurer MM, Ronaghi N, Valentine SJ. Ion Mobility, Hydrogen/Deuterium Exchange, and Isotope Scrambling: Tools to Aid Compound Identification in ‘Omics Mixtures. Anal Chem 2017; 89:6399-6407. [PMID: 28505408 DOI: 10.1021/acs.analchem.7b00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hossein Maleki
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Megan M. Maurer
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Nima Ronaghi
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Stephen J. Valentine
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
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39
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Hamuro Y. Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:971-977. [PMID: 28194737 DOI: 10.1007/s13361-017-1612-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 12/29/2016] [Accepted: 01/17/2017] [Indexed: 06/06/2023]
Abstract
Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation. Graphical Abstract ᅟ.
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Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, NJ, 08852, USA.
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40
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Van der Rest G, Rezaei H, Halgand F. Monitoring Conformational Landscape of Ovine Prion Protein Monomer Using Ion Mobility Coupled to Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:303-314. [PMID: 27757822 DOI: 10.1007/s13361-016-1522-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 06/06/2023]
Abstract
Prion protein is involved in deadly neurodegenerative diseases. Its pathogenicity is linked to its structural conversion (α-helix to β-strand transition). However, recent studies suggest that prion protein can follow a plurality of conversion pathways, which hints towards different conformers that might coexist in solution. To gain insights on the plasticity of the ovine prion protein (PrP) monomer, wild type (A136, R154, Q171), mutants and deletions of ARQ were studied by traveling wave ion mobility experiments coupled to mass spectrometry. In order to perform the analysis of a large body of data sets, we designed and evaluated the performance of a processing pipeline based on Driftscope peak detection and a homemade script for automated peak assignment, annotation, and quantification on specific multiply charged protein data. Using this approach, we showed that in the gas phase, PrPs are represented by at least three conformer families differing in both charge state distribution and collisional cross-section, in agreement with the work of Hilton et al. (2010). We also showed that this plasticity is borne both by the N- and C-terminal domains. Effect of protein concentration, pH and temperature were also assessed, showing that (1) pH does not affect conformer distributions, (2) protein concentration modifies the conformational landscape of one mutant (I208M) only, and (3) heating leads to other unfolded species and to a modification of the conformer intensity ratios. Graphical Abstract ᅟ.
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Affiliation(s)
- Guillaume Van der Rest
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS 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
| | - Frédéric Halgand
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS UMR 8000, 91405, Orsay, France.
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Pan J, Zhang S, Borchers CH. Comparative higher-order structure analysis of antibody biosimilars using combined bottom-up and top-down hydrogen-deuterium exchange mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1801-1808. [DOI: 10.1016/j.bbapap.2016.08.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/13/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023]
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42
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Parr MK, Montacir O, Montacir H. Physicochemical characterization of biopharmaceuticals. J Pharm Biomed Anal 2016; 130:366-389. [DOI: 10.1016/j.jpba.2016.05.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 12/26/2022]
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43
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Going CC, Xia Z, Williams ER. Real-time HD Exchange Kinetics of Proteins from Buffered Aqueous Solution with Electrothermal Supercharging and Top-Down Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1019-1027. [PMID: 26919868 PMCID: PMC4865425 DOI: 10.1007/s13361-016-1350-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 06/05/2023]
Abstract
Electrothermal supercharging (ETS) with electrospray ionization produces highly charged protein ions from buffered aqueous solutions in which proteins have native folded structures. ETS increases the charge of ribonuclease A by 34%, whereas only a 6% increase in charge occurs for a reduced-alkylated form of this protein, which is unfolded and its structure is ~66% random coil in this solution. These results indicate that protein denaturation that occurs in the ESI droplets is the primary mechanism for ETS. ETS does not affect the extent of solution-phase hydrogen-deuterium exchange (HDX) that occurs for four proteins that have significantly different structures in solution, consistent with a droplet lifetime that is considerably shorter than observable rates of HDX. Rate constants for HDX of ubiquitin are obtained with a spatial resolution of ~1.3 residues with ETS and electron transfer dissociation of the 10+ charge-state using a single capillary containing a few μL of protein solution in which HDX continuously occurs. HDX protection at individual residues with ETS HDX is similar to that with reagent supercharging HDX and with solution-phase NMR, indicating that the high spray potentials required to induce ETS do not lead to HD scrambling. Graphical Abstract ᅟ.
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Affiliation(s)
- Catherine C Going
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Zijie Xia
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA.
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Malhotra P, Udgaonkar JB. Secondary Structural Change Can Occur Diffusely and Not Modularly during Protein Folding and Unfolding Reactions. J Am Chem Soc 2016; 138:5866-78. [DOI: 10.1021/jacs.6b03356] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pooja Malhotra
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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45
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Protein species-specific characterization of conformational change induced by multisite phosphorylation. J Proteomics 2016; 134:138-143. [DOI: 10.1016/j.jprot.2015.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/29/2015] [Accepted: 12/01/2015] [Indexed: 01/29/2023]
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Gallagher ES, Hudgens JW. Mapping Protein–Ligand Interactions with Proteolytic Fragmentation, Hydrogen/Deuterium Exchange-Mass Spectrometry. Methods Enzymol 2016; 566:357-404. [DOI: 10.1016/bs.mie.2015.08.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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47
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Patrie SM. Top-Down Mass Spectrometry: Proteomics to Proteoforms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:171-200. [PMID: 27975217 DOI: 10.1007/978-3-319-41448-5_8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This chapter highlights many of the fundamental concepts and technologies in the field of top-down mass spectrometry (TDMS), and provides numerous examples of contributions that TD is making in biology, biophysics, and clinical investigations. TD workflows include variegated steps that may include non-specific or targeted preparative strategies, orthogonal liquid chromatography techniques, analyte ionization, mass analysis, tandem mass spectrometry (MS/MS) and informatics procedures. This diversity of experimental designs has evolved to manage the large dynamic range of protein expression and diverse physiochemical properties of proteins in proteome investigations, tackle proteoform microheterogeneity, as well as determine structure and composition of gas-phase proteins and protein assemblies.
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Affiliation(s)
- Steven M Patrie
- Computational and Systems Biology & Biomedical Engineering Graduate Programs, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA.
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48
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Going CC, Xia Z, Williams ER. New supercharging reagents produce highly charged protein ions in native mass spectrometry. Analyst 2015; 140:7184-94. [PMID: 26421324 PMCID: PMC4617834 DOI: 10.1039/c5an01710f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effectiveness of two new supercharging reagents for producing highly charged ions by electrospray ionization (ESI) from aqueous solutions in which proteins have native structures and reactivities were investigated. In aqueous solution, 2-thiophenone and 4-hydroxymethyl-1,3-dioxolan-2-one (HD) at a concentration of 2% by volume can increase the average charge of cytochrome c and myoglobin by up to 163%, resulting in even higher charge states than those that are produced from water/methanol/acid solutions in which these proteins are denatured. The greatest extent of supercharging occurs in pure water, but these supercharging reagents are also highly effective in aqueous solutions containing 200 mM ammonium acetate buffer commonly used in native mass spectrometry (MS). These reagents are less effective supercharging reagents than m-nitrobenzyl alcohol (m-NBA) and propylene carbonate (PC) when ions are formed from water/methanol/acid. The extent to which loss of the heme group from myoglobin occurs is related to the extent of supercharging. Results from guanidine melts of cytochrome c monitored with tryptophan fluorescence show that the supercharging reagents PC, sulfolane and HD are effective chemical denaturants in solution. These results provide additional evidence for the role of protein structural changes in the electrospray droplet as the primary mechanism for supercharging with these reagents in native MS. These results also demonstrate that for at least some proteins, the formation of highly charged ions from native MS is no longer a significant barrier for obtaining structural information using conventional tandem MS methods.
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Affiliation(s)
- Catherine C Going
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA.
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49
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Structural analysis of the interleukin-8/glycosaminoglycan interactions by amide hydrogen/deuterium exchange mass spectrometry. Methods 2015; 89:45-53. [DOI: 10.1016/j.ymeth.2015.02.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/12/2015] [Accepted: 02/19/2015] [Indexed: 12/22/2022] Open
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50
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Abstract
The structural analysis of viruses is often a complex task. In many cases, the details of the viral architecture, especially for enveloped viruses, are limited to low-resolution techniques such as electron microscopy. These structural proteins and assemblies of viruses often populate multiple conformational states and undergo dramatic structural changes, making them difficult to study by most structural methods. They also frequently include highly dynamic regions that are of key functional importance. Many viruses present large surface glycoproteins, which have also proved to be challenging for structural biology due to the intrinsic flexibility and heterogeneity of the glycan decorations. Over the past two decades, hydrogen deuterium exchange coupled to mass spectrometry (HDX-MS) has provided a wealth of information on many diverse viral proteins, glycoproteins, and complexes, in many cases, in multiple conformational states. Here, we describe the methodology for using HDX-MS to investigate the rich structural dynamics of viral systems, and we briefly review the type of systems that have been examined through this type of approach. Though the technique is relatively simple, several potential pitfalls exist at both the sample preparation and the data analysis stage that investigators should be aware of for obtaining reliable data.
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Affiliation(s)
- Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
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