1
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Kish M, Ivory DP, Phillips JJ. Transient Structural Dynamics of Glycogen Phosphorylase from Nonequilibrium Hydrogen/Deuterium-Exchange Mass Spectrometry. J Am Chem Soc 2024; 146:298-307. [PMID: 38158228 PMCID: PMC10786028 DOI: 10.1021/jacs.3c08934] [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: 08/16/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
It remains a major challenge to ascertain the specific structurally dynamic changes that underpin protein functional switching. There is a growing need in molecular biology and drug discovery to complement structural models with the ability to determine the dynamic structural changes that occur as these proteins are regulated and function. The archetypal allosteric enzyme glycogen phosphorylase is a clinical target of great interest to treat type II diabetes and metastatic cancers. Here, we developed a time-resolved nonequilibrium millisecond hydrogen/deuterium-exchange mass spectrometry (HDX-MS) approach capable of precisely locating dynamic structural changes during allosteric activation and inhibition of glycogen phosphorylase. We resolved obligate transient changes in the localized structure that are absent when directly comparing active/inactive states of the enzyme and show that they are common to allosteric activation by AMP and inhibition by caffeine, operating at different sites. This indicates that opposing allosteric regulation by inhibitor and activator ligands is mediated by pathways that intersect with a common structurally dynamic motif. This mass spectrometry approach uniquely stands to discover local transient structural dynamics and could be used broadly to identify features that influence the structural transitions of proteins.
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Affiliation(s)
- Monika Kish
- Living
Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4
4QD, U.K.
| | - Dylan P. Ivory
- 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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2
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Hatvany JB, Gallagher ES. Hydrogen/deuterium exchange for the analysis of carbohydrates. Carbohydr Res 2023; 530:108859. [PMID: 37290371 DOI: 10.1016/j.carres.2023.108859] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/10/2023]
Abstract
Carbohydrates and glycans are integral to many biological processes, including cell-cell recognition and energy storage. However, carbohydrates are often difficult to analyze due to the high degree of isomerism present. One method being developed to distinguish these isomeric species is hydrogen/deuterium exchange-mass spectrometry (HDX-MS). In HDX-MS, carbohydrates are exposed to a deuterated reagent and the functional groups with labile hydrogen atoms, including hydroxyls and amides, exchange with the 1 amu heavier isotope, deuterium. These labels can then be detected by MS, which monitors the mass increase with the addition of D-labels. The observed rate of exchange is dependent on the exchanging functional group, the accessibility of the exchanging functional group, and the presence of hydrogen bonds. Herein, we discuss how HDX has been applied in the solution-phase, gas-phase, and during MS ionization to label carbohydrates and glycans. Additionally, we compare differences in the conformations that are labeled, the labeling timeframes, and applications of each of these methods. Finally, we comment on future opportunities for development and use of HDX-MS to analyze glycans and glycoconjugates.
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Affiliation(s)
- Jacob B Hatvany
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA.
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3
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Kish M, Smith V, Lethbridge N, Cole L, Bond NJ, Phillips JJ. Online Fully Automated System for Hydrogen/Deuterium-Exchange Mass Spectrometry with Millisecond Time Resolution. Anal Chem 2023; 95:5000-5008. [PMID: 36896500 PMCID: PMC10034745 DOI: 10.1021/acs.analchem.2c05310] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Amide hydrogen/deuterium-exchange mass spectrometry (HDX-MS) is a powerful tool for analyzing the conformational dynamics of proteins in a solution. Current conventional methods have a measurement limit starting from several seconds and are solely reliant on the speed of manual pipetting or a liquid handling robot. Weakly protected regions of polypeptides, such as in short peptides, exposed loops and intrinsically disordered the protein exchange on the millisecond timescale. Typical HDX methods often cannot resolve the structural dynamics and stability in these cases. Numerous academic laboratories have demonstrated the considerable utility of acquiring HDX-MS data in the sub-second regimes. Here, we describe the development of a fully automated HDX-MS apparatus to resolve amide exchange on the millisecond timescale. Like conventional systems, this instrument boasts automated sample injection with software selection of labeling times, online flow mixing and quenching, while being fully integrated with a liquid chromatography-MS system for existing standard "bottom-up" workflows. HDX-MS's rapid exchange kinetics of several peptides demonstrate the repeatability, reproducibility, back-exchange, and mixing kinetics achieved with the system. Comparably, peptide coverage of 96.4% with 273 peptides was achieved, supporting the equivalence of the system to standard robotics. Additionally, time windows of 50 ms-300 s allowed full kinetic transitions to be observed for many amide groups; especially important are short time points (50-150 ms) for regions that are likely highly dynamic and solvent- exposed. We demonstrate that information on structural dynamics and stability can be measured for stretches of weakly stable polypeptides in small peptides and in local regions of a large enzyme, glycogen phosphorylase.
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Affiliation(s)
- Monika Kish
- Living Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, U.K
| | | | | | - Lindsay Cole
- Applied Photophysics Ltd, Leatherhead KT227BA, U.K
| | - Nicholas J Bond
- Analytical Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Milstein Building, Granta Park, Cambridge CB21 6GH, 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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4
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Anacleto J, Lento C, Sarpe V, Maqsood A, Mehrazma B, Schriemer D, Wilson DJ. Apparatus for Automated Continuous Hydrogen Deuterium Exchange Mass Spectrometry Measurements from Milliseconds to Hours. Anal Chem 2023; 95:4421-4428. [PMID: 36880265 PMCID: PMC9996604 DOI: 10.1021/acs.analchem.2c05003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a rapidly growing technique for protein characterization in industry and academia, complementing the "static" picture provided by classical structural biology with information about the dynamic structural changes that accompany biological function. Conventional hydrogen deuterium exchange experiments, carried out on commercially available systems, typically collect 4-5 exchange timepoints on a timescale ranging from tens of seconds to hours using a workflow that can require 24 h or more of continuous data collection for triplicate measurements. A small number of groups have developed setups for millisecond timescale HDX, allowing for the characterization of dynamic shifts in weakly structured or disordered regions of proteins. This capability is particularly important given the central role that weakly ordered protein regions often play in protein function and pathogenesis. In this work, we introduce a new continuous flow injection setup for time-resolved HDX-MS (CFI-TRESI-HDX) that allows automated, continuous or discrete labeling time measurements from milliseconds to hours. The device is composed almost entirely of "off-the-shelf" LC components and can acquire an essentially unlimited number of timepoints with substantially reduced runtimes compared to conventional systems.
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Affiliation(s)
- Joseph Anacleto
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology, Calgary, Alberta T2N 4N1, Canada
| | - Ayesha Maqsood
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Banafsheh Mehrazma
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - David Schriemer
- Department of Biochemistry and Molecular Biology, Calgary, Alberta T2N 4N1, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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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: 3] [Impact Index Per Article: 3.0] [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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Shao X, Huang Y, Wang G. Microfluidic devices for protein analysis using intact and top‐down mass spectrometry. VIEW 2022. [DOI: 10.1002/viw.20220032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Xinyang Shao
- Institute for Cell Analysis Shenzhen Bay Laboratory Shenzhen China
- Biomedical Pioneering Innovation Center Peking University Beijing China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing China
| | - Yanyi Huang
- Institute for Cell Analysis Shenzhen Bay Laboratory Shenzhen China
- Biomedical Pioneering Innovation Center Peking University Beijing China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing China
- College of Chemistry and Molecular Engineering and Beijing National Laboratory for Molecular Sciences Peking University Beijing China
| | - Guanbo Wang
- Institute for Cell Analysis Shenzhen Bay Laboratory Shenzhen China
- Biomedical Pioneering Innovation Center Peking University Beijing China
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7
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Investigating how intrinsically disordered regions contribute to protein function using HDX-MS. Biochem Soc Trans 2022; 50:1607-1617. [DOI: 10.1042/bst20220206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022]
Abstract
A large amount of the human proteome is composed of highly dynamic regions that do not adopt a single static conformation. These regions are defined as intrinsically disordered, and they are found in a third of all eukaryotic proteins. They play instrumental roles in many aspects of protein signaling, but can be challenging to characterize by biophysical methods. Intriguingly, many of these regions can adopt stable secondary structure upon interaction with a variety of binding partners, including proteins, lipids, and ligands. This review will discuss the application of Hydrogen-deuterium exchange mass spectrometry (HDX-MS) as a powerful biophysical tool that is particularly well suited for structural and functional characterization of intrinsically disordered regions in proteins. A focus will be on the theory of hydrogen exchange, and its practical application to identify disordered regions, as well as characterize how they participate in protein–protein and protein–membrane interfaces. A particular emphasis will be on how HDX-MS data can be presented specifically tailored for analysis of intrinsically disordered regions, as well as the technical aspects that are critical to consider when designing HDX-MS experiments for proteins containing intrinsically disordered regions.
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8
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Rainer T, Egger AS, Zeindl R, Tollinger M, Kwiatkowski M, Müller T. 3D-Printed High-Pressure-Resistant Immobilized Enzyme Microreactor (μIMER) for Protein Analysis. Anal Chem 2022; 94:8580-8587. [PMID: 35678765 PMCID: PMC9218953 DOI: 10.1021/acs.analchem.1c05232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Additive manufacturing
(3D printing) has greatly revolutionized
the way researchers approach certain technical challenges. Despite
its outstanding print quality and resolution, stereolithography (SLA)
printing is cost-effective and relatively accessible. However, applications
involving mass spectrometry (MS) are few due to residual oligomers
and additives leaching from SLA-printed devices that interfere with
MS analyses. We identified the crosslinking agent urethane dimethacrylate
as the main contaminant derived from SLA prints. A stringent washing
and post-curing protocol mitigated sample contamination and rendered
SLA prints suitable for MS hyphenation. Thereafter, SLA printing was
used to produce 360 μm I.D. microcolumn chips with excellent
structural properties. By packing the column with polystyrene microspheres
and covalently immobilizing pepsin, an exceptionally effective microscale
immobilized enzyme reactor (μIMER) was created. Implemented
in an online liquid chromatography-MS/MS setup, the protease microcolumn
enabled reproducible protein digestion and peptide mapping with 100%
sequence coverage obtained for three different recombinant proteins.
Additionally, when assessing the μIMER digestion efficiency
for complex proteome samples, it delivered a 144-fold faster and significantly
more efficient protein digestion compared to 24 h for bulk digestion.
The 3D-printed μIMER withstands remarkably high pressures above
130 bar and retains its activity for several weeks. This versatile
platform will enable researchers to produce tailored polymer-based
enzyme reactors for various applications in analytical chemistry and
beyond.
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Affiliation(s)
- Tobias Rainer
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Anna-Sophia Egger
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Ricarda Zeindl
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Thomas Müller
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
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9
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Stofella M, Skinner SP, Sobott F, Houwing-Duistermaat J, Paci E. High-Resolution Hydrogen-Deuterium Protection Factors from Sparse Mass Spectrometry Data Validated by Nuclear Magnetic Resonance Measurements. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:813-822. [PMID: 35385652 PMCID: PMC9074100 DOI: 10.1021/jasms.2c00005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Experimental measurement of time-dependent spontaneous exchange of amide protons with deuterium of the solvent provides information on the structure and dynamical structural variation in proteins. Two experimental techniques are used to probe the exchange: NMR, which relies on different magnetic properties of hydrogen and deuterium, and MS, which exploits the change in mass due to deuteration. NMR provides residue-specific information, that is, the rate of exchange or, analogously, the protection factor (i.e., the unitless ratio between the rate of exchange for a completely unstructured state and the observed rate). MS provides information that is specific to peptides obtained by proteolytic digestion. The spatial resolution of HDX-MS measurements depends on the proteolytic pattern of the protein, the fragmentation method used, and the overlap between peptides. Different computational approaches have been proposed to extract residue-specific information from peptide-level HDX-MS measurements. Here, we demonstrate the advantages of a method recently proposed that exploits self-consistency and classifies the possible sets of protection factors into a finite number of alternative solutions compatible with experimental data. The degeneracy of the solutions can be reduced (or completely removed) by exploiting the additional information encoded in the shape of the isotopic envelopes. We show how sparse and noisy MS data can provide high-resolution protection factors that correlate with NMR measurements probing the same protein under the same conditions.
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Affiliation(s)
- Michele Stofella
- School
of Molecular and Cellular Biology, University
of Leeds, LS2 9JT Leeds, United Kingdom
- Dipartimento
di Fisica e Astronomia, Università
di Bologna, 40127 Bologna, Italy
| | - Simon P. Skinner
- School
of Molecular and Cellular Biology, University
of Leeds, LS2 9JT Leeds, United Kingdom
| | - Frank Sobott
- School
of Molecular and Cellular Biology, University
of Leeds, LS2 9JT Leeds, United Kingdom
| | | | - Emanuele Paci
- School
of Molecular and Cellular Biology, University
of Leeds, LS2 9JT Leeds, United Kingdom
- Dipartimento
di Fisica e Astronomia, Università
di Bologna, 40127 Bologna, Italy
- (E.P.)
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10
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Sun H, Liu J, Xiao P, Zhou Y, Li H, Shen M, Sun K, Wang X, Zhou M, Song D. Epitope mapping of antibodies in C-reactive protein assay kits by hydrogen-deuterium exchange mass spectrometry explains differential results across kits. Anal Bioanal Chem 2022; 414:3875-3884. [PMID: 35389096 DOI: 10.1007/s00216-022-04029-z] [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: 12/29/2021] [Revised: 03/09/2022] [Accepted: 03/17/2022] [Indexed: 01/08/2023]
Abstract
C-Reactive protein (CRP) is an important marker for in vitro diagnosis (IVD) of inflammation. However, CRP immunoturbidimetric kits from different manufacturers exhibit inconsistency in evaluation, making clinical diagnosis challenging. The use of immunological methods in diagnosis means that the differences in epitopes across kits may directly lead to inconsistent results. Therefore, to provide consistent results, it is essential to perform epitope mapping of different kits. The composition of antibodies in a single kit is typically complex, with a combination of polyclonal antibodies or monoclonal antibodies. Here, we show an epitope screening strategy for complex antibodies in a kit based on hydrogen-deuterium exchange mass spectrometry (HDX-MS). We applied this workflow to successfully map the epitopes for three kits from three different manufacturers and compared their quantitative results. We obtained different quantitative results using kits from different manufacturers upon epitope mapping, confirming the correlation between the quantitative results and the epitopes. Thus, we have established a workflow based on HDX-MS to screen epitopes in IVD kits. This work helps determine the quantitative accuracy of a kit based on structural information, can guide the design and production of IVD reagents, and further improves the accuracy of IVD.
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Affiliation(s)
- Haofeng Sun
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, China.,School of Chemical and Engineering, Nanjing University of Science and Technology, Jiangsu, 210094, China
| | - Jianyi Liu
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, China
| | - Peng Xiao
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, China
| | - Yi Zhou
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, China.,School of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hongmei Li
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, China
| | - Min Shen
- Reference Laboratory, Medical System Biotechnology Co., Ltd., Ningbo, 315104, China
| | - Keqi Sun
- Reference System Department, Maccura Biotechnology Co., Ltd., Chengdu, 611713, China
| | - Xiaojian Wang
- Reference Laboratory, Beijing Strong Biotechnologies, Inc., Beijing, 101400, Huairou, China
| | - Min Zhou
- School of Chemical and Engineering, Nanjing University of Science and Technology, Jiangsu, 210094, China.
| | - Dewei Song
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, China.
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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: 101] [Impact Index Per Article: 33.7] [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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Lento C, Wilson DJ. Subsecond Time-Resolved Mass Spectrometry in Dynamic Structural Biology. Chem Rev 2021; 122:7624-7646. [PMID: 34324314 DOI: 10.1021/acs.chemrev.1c00222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Life at the molecular level is a dynamic world, where the key players-proteins, oligonucleotides, lipids, and carbohydrates-are in a perpetual state of structural flux, shifting rapidly between local minima on their conformational free energy landscapes. The techniques of classical structural biology, X-ray crystallography, structural NMR, and cryo-electron microscopy (cryo-EM), while capable of extraordinary structural resolution, are innately ill-suited to characterize biomolecules in their dynamically active states. Subsecond time-resolved mass spectrometry (MS) provides a unique window into the dynamic world of biological macromolecules, offering the capacity to directly monitor biochemical processes and conformational shifts with a structural dimension provided by the electrospray charge-state distribution, ion mobility, covalent labeling, or hydrogen-deuterium exchange. Over the past two decades, this suite of techniques has provided important insights into the inherently dynamic processes that drive function and pathogenesis in biological macromolecules, including (mis)folding, complexation, aggregation, ligand binding, and enzyme catalysis, among others. This Review provides a comprehensive account of subsecond time-resolved MS and the advances it has enabled in dynamic structural biology, with an emphasis on insights into the dynamic drivers of protein function.
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Affiliation(s)
- Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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13
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Cornwell O, Ault JR, Bond NJ, Radford SE, Ashcroft AE. Investigation of D76N β 2-Microglobulin Using Protein Footprinting and Structural Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1583-1592. [PMID: 33586970 PMCID: PMC9282677 DOI: 10.1021/jasms.0c00438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
NMR studies and X-ray crystallography have shown that the structures of the 99-residue amyloidogenic protein β2-microglobulin (β2m) and its more aggregation-prone variant, D76N, are indistinguishable, and hence, the reason for the striking difference in their aggregation propensities remains elusive. Here, we have employed two protein footprinting methods, hydrogen-deuterium exchange (HDX) and fast photochemical oxidation of proteins (FPOP), in conjunction with ion mobility-mass spectrometry, to probe the differences in conformational dynamics of the two proteins. Using HDX-MS, a clear difference in HDX protection is observed between these two proteins in the E-F loop (residues 70-77) which contains the D76N substitution, with a significantly higher deuterium uptake being observed in the variant protein. Conversely, following FPOP-MS only minimal differences in the level of oxidation between the two proteins are observed in the E-F loop region, suggesting only modest side-chain movements in that area. Together the HDX-MS and FPOP-MS data suggest that a tangible perturbation to the hydrogen-bonding network in the E-F loop has taken place in the D76N variant and furthermore illustrate the benefit of using multiple complementary footprinting methods to address subtle, but possibly biologically important, differences between highly similar proteins.
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Affiliation(s)
- Owen Cornwell
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - James R. Ault
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Nicholas J. Bond
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Alison E. Ashcroft
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
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14
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Fairbanks BD, Macdougall LJ, Mavila S, Sinha J, Kirkpatrick BE, Anseth KS, Bowman CN. Photoclick Chemistry: A Bright Idea. Chem Rev 2021; 121:6915-6990. [PMID: 33835796 PMCID: PMC9883840 DOI: 10.1021/acs.chemrev.0c01212] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
At its basic conceptualization, photoclick chemistry embodies a collection of click reactions that are performed via the application of light. The emergence of this concept has had diverse impact over a broad range of chemical and biological research due to the spatiotemporal control, high selectivity, and excellent product yields afforded by the combination of light and click chemistry. While the reactions designated as "photoclick" have many important features in common, each has its own particular combination of advantages and shortcomings. A more extensive realization of the potential of this chemistry requires a broader understanding of the physical and chemical characteristics of the specific reactions. This review discusses the features of the most frequently employed photoclick reactions reported in the literature: photomediated azide-alkyne cycloadditions, other 1,3-dipolarcycloadditions, Diels-Alder and inverse electron demand Diels-Alder additions, radical alternating addition chain transfer additions, and nucleophilic additions. Applications of these reactions in a variety of chemical syntheses, materials chemistry, and biological contexts are surveyed, with particular attention paid to the respective strengths and limitations of each reaction and how that reaction benefits from its combination with light. Finally, challenges to broader employment of these reactions are discussed, along with strategies and opportunities to mitigate such obstacles.
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Affiliation(s)
- Benjamin D Fairbanks
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Laura J Macdougall
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Sudheendran Mavila
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Jasmine Sinha
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Bruce E Kirkpatrick
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- The BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
- Medical Scientist Training Program, School of Medicine, University of Colorado, Aurora, Coorado 80045, United States
| | - Kristi S Anseth
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- The BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Christopher N Bowman
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- Materials Science and Engineering Program, University of Colorado, Boulder, Colorado 80303, United States
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15
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Beveridge R, Calabrese AN. Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins. Front Chem 2021; 9:603639. [PMID: 33791275 PMCID: PMC8006314 DOI: 10.3389/fchem.2021.603639] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and regions of intrinsic disorder (IDRs) are abundant in proteomes and are essential for many biological processes. Thus, they are often implicated in disease mechanisms, including neurodegeneration and cancer. The flexible nature of IDPs and IDRs provides many advantages, including (but not limited to) overcoming steric restrictions in binding, facilitating posttranslational modifications, and achieving high binding specificity with low affinity. IDPs adopt a heterogeneous structural ensemble, in contrast to typical folded proteins, making it challenging to interrogate their structure using conventional tools. Structural mass spectrometry (MS) methods are playing an increasingly important role in characterizing the structure and function of IDPs and IDRs, enabled by advances in the design of instrumentation and the development of new workflows, including in native MS, ion mobility MS, top-down MS, hydrogen-deuterium exchange MS, crosslinking MS, and covalent labeling. Here, we describe the advantages of these methods that make them ideal to study IDPs and highlight recent applications where these tools have underpinned new insights into IDP structure and function that would be difficult to elucidate using other methods.
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Affiliation(s)
- Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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16
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Svejdal RR, Sticker D, Sønderby C, Kutter JP, Rand KD. Thiol-ene microfluidic chip for fast on-chip sample clean-up, separation and ESI mass spectrometry of peptides and proteins. Anal Chim Acta 2020; 1140:168-177. [DOI: 10.1016/j.aca.2020.09.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 01/13/2023]
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17
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Pino LK, Rose J, O'Broin A, Shah S, Schilling B. Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications. Biochem Soc Trans 2020; 48:1953-1966. [PMID: 33079175 PMCID: PMC7609030 DOI: 10.1042/bst20191091] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022]
Abstract
Research into the basic biology of human health and disease, as well as translational human research and clinical applications, all benefit from the growing accessibility and versatility of mass spectrometry (MS)-based proteomics. Although once limited in throughput and sensitivity, proteomic studies have quickly grown in scope and scale over the last decade due to significant advances in instrumentation, computational approaches, and bio-sample preparation. Here, we review these latest developments in MS and highlight how these techniques are used to study the mechanisms, diagnosis, and treatment of human diseases. We first describe recent groundbreaking technological advancements for MS-based proteomics, including novel data acquisition techniques and protein quantification approaches. Next, we describe innovations that enable the unprecedented depth of coverage in protein signaling and spatiotemporal protein distributions, including studies of post-translational modifications, protein turnover, and single-cell proteomics. Finally, we explore new workflows to investigate protein complexes and structures, and we present new approaches for protein-protein interaction studies and intact protein or top-down MS. While these approaches are only recently incipient, we anticipate that their use in biomedical MS proteomics research will offer actionable discoveries for the improvement of human health.
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Affiliation(s)
- Lindsay K. Pino
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, CA, U.S.A
| | - Amy O'Broin
- Buck Institute for Research on Aging, Novato, CA, U.S.A
| | - Samah Shah
- Buck Institute for Research on Aging, Novato, CA, U.S.A
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18
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Engen JR, Botzanowski T, Peterle D, Georgescauld F, Wales TE. Developments in Hydrogen/Deuterium Exchange Mass Spectrometry. Anal Chem 2020; 93:567-582. [DOI: 10.1021/acs.analchem.0c04281] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas Botzanowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Florian Georgescauld
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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19
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Bickham AV, Pang C, George BQ, Topham DJ, Nielsen JB, Nordin GP, Woolley AT. 3D Printed Microfluidic Devices for Solid-Phase Extraction and On-Chip Fluorescent Labeling of Preterm Birth Risk Biomarkers. Anal Chem 2020; 92:12322-12329. [PMID: 32829631 DOI: 10.1021/acs.analchem.0c01970] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Solid-phase extraction (SPE) is a general preconcentration method for sample preparation that can be performed on a variety of specimens. The miniaturization of SPE within a 3D printed microfluidic device further allows for fast and simple extraction of analytes while also enabling integration of SPE with other sample preparation and separation methods. Here, we present the development and application of a reversed-phase lauryl methacrylate-based monolith, formed in 3D printed microfluidic devices, which can selectively retain peptides and proteins. The effectiveness of these SPE monoliths and 3D printed microfluidic devices was tested using a panel of nine preterm birth biomarkers of varying hydrophobicities and ranging in mass from 2 to 470 kDa. The biomarkers were selectively retained, fluorescently labeled, and eluted separately from the excess fluorescent label in 3D printed microfluidic systems. These are the first results demonstrating microfluidic analysis processes on a complete panel of preterm birth biomarkers, an important step toward developing a miniaturized, fully integrated analysis system.
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Affiliation(s)
- Anna V Bickham
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
| | - Chao Pang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
| | - Benjamin Q George
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
| | - David J Topham
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
| | - Jacob B Nielsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
| | - Gregory P Nordin
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, Utah 84602 United States
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 United States
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20
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Tang J, Qiu G, Cao X, Yue Y, Zhang X, Schmitt J, Wang J. Self-aligned 3D microlenses in a chip fabricated with two-photon stereolithography for highly sensitive absorbance measurement. LAB ON A CHIP 2020; 20:2334-2342. [PMID: 32458914 DOI: 10.1039/d0lc00235f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Absorbance measurement is a widely used method to quantify the concentration of an analyte. The integration of absorbance analysis in microfluidic chips could significantly reduce the sample consumption and contribute to the system miniaturization. However, the sensitivity and limit of detection (LoD) of analysis in microfluidic chips with conventional configuration need improvements due to the limited optical pathway and unregulated light propagation. In this work, a 3D-microlens-incorporating microfluidic chip (3D-MIMC) with a greatly extended detection channel was innovatively fabricated using two-photon stereolithography. The fabrication was optimized with a proposed hierarchical modular printing strategy. Due to the incorporation of 3D microlenses, the light coupling efficiency and the signal-to-noise ratio (SNR) were respectively improved approximately 9 and 4 times. An equivalent optical path length (EOL) of 62.9 mm was achieved in a 3.7 μl detection channel for testing tartrazine samples. As a result, the sensitivity and LoD of the 3D-MIMC assay were correspondingly improved by one order of magnitude, compared with those of the 96-well plate assay. Notably, the 3D-MIMC has the potential to be integrated into a general microanalysis platform for multiple applications.
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Affiliation(s)
- Jiukai Tang
- Institute of Environmental Engineering, ETH Zürich, Zürich 8093, Switzerland.
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21
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Sticker D, Geczy R, Häfeli UO, Kutter JP. Thiol-Ene Based Polymers as Versatile Materials for Microfluidic Devices for Life Sciences Applications. ACS APPLIED MATERIALS & INTERFACES 2020; 12:10080-10095. [PMID: 32048822 DOI: 10.1021/acsami.9b22050] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
While there is a steady growth in the number of microfluidics applications, the search for an optimal material that delivers the diverse characteristics needed for the numerous tasks is still nowhere close to being settled. Often overlooked and still underrepresented, the thiol-ene family of polymer materials has an enormous potential for applications in organs-on-a-chip, droplet productions, microanalytics, and point of care testing. In this review, the main characteristics of the thiol-ene materials are given, and advantages and drawbacks with respect to their potential in microfluidic chip fabrication are critically assessed. Select applications, which exploit the versatility of the thiol-ene polymers, are presented and discussed. It is concluded that, in particular, the rapid prototyping possibility combined with the material's resulting mechanical strength, solvent resistance, and biocompatibility, as well as the inherently easy surface functionalization, are strong factors to make thiol-ene polymers strong contenders for promising future materials for many biological, clinical, and technical lab-on-a-chip applications.
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Affiliation(s)
- Drago Sticker
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Reka Geczy
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Urs O Häfeli
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jörg P Kutter
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
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22
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Affiliation(s)
- Iulia M. Lazar
- Department of Biological Sciences, Academy of Integrated Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
- Carilion School of Medicine, Academy of Integrated Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Nicholas S. Gulakowski
- Systems Biology, Academy of Integrated Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
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23
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Kim HJ, Gallagher ES. Achieving multiple hydrogen/deuterium exchange timepoints of carbohydrate hydroxyls using theta-electrospray emitters. Analyst 2020; 145:3056-3063. [DOI: 10.1039/d0an00135j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microsecond reaction times for in-droplet hydrogen/deuterium exchange of carbohydrate hydroxyls have been varied by changing the opening sizes of theta-electrospray emitters.
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Affiliation(s)
- H. Jamie Kim
- Department of Chemistry and Biochemistry
- Baylor University
- Waco
- USA
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24
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Levin VV, Dilman AD. Visible-Light-Mediated Organocatalyzed Thiol-Ene Reaction Initiated by a Proton-Coupled Electron Transfer. J Org Chem 2019; 84:8337-8343. [PMID: 31129962 DOI: 10.1021/acs.joc.9b01331] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A convenient method for performing a thiol-ene reaction is described. The reaction is performed under blue-light irradiation and catalyzed by photoactive Lewis basic molecules such as acridine orange or naphthalene-fused N-acylbenzimidazole. It is believed that the process is initiated by a proton-coupled electron transfer process within the complex between the thiol and the Lewis basic catalyst.
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Affiliation(s)
- Vitalij V Levin
- N. D. Zelinsky Institute of Organic Chemistry , Leninsky Prospect 47 , Moscow 119991 , Russian Federation
| | - Alexander D Dilman
- N. D. Zelinsky Institute of Organic Chemistry , Leninsky Prospect 47 , Moscow 119991 , Russian Federation
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