1
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Oney-Hawthorne SD, Barondeau DP. Fe-S cluster biosynthesis and maturation: Mass spectrometry-based methods advancing the field. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119784. [PMID: 38908802 DOI: 10.1016/j.bbamcr.2024.119784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
Iron‑sulfur (FeS) clusters are inorganic protein cofactors that perform essential functions in many physiological processes. Spectroscopic techniques have historically been used to elucidate details of FeS cluster type, their assembly and transfer, and changes in redox and ligand binding properties. Structural probes of protein topology, complex formation, and conformational dynamics are also necessary to fully understand these FeS protein systems. Recent developments in mass spectrometry (MS) instrumentation and methods provide new tools to investigate FeS cluster and structural properties. With the unique advantage of sampling all species in a mixture, MS-based methods can be utilized as a powerful complementary approach to probe native dynamic heterogeneity, interrogate protein folding and unfolding equilibria, and provide extensive insight into protein binding partners within an entire proteome. Here, we highlight key advances in FeS protein studies made possible by MS methodology and contribute an outlook for its role in the field.
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Affiliation(s)
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA.
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2
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Cabrera ER, Schrader RL, Walker TE, Laganowsky A, Russell DH, Clowers BH. Nonlinear Frequency Modulation for Fourier Transform Ion Mobility Mass Spectrometry Improves Experimental Efficiency. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 497:117197. [PMID: 38352886 PMCID: PMC10861183 DOI: 10.1016/j.ijms.2024.117197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Through optimization of terminal frequencies and effective sampling rates, we have developed nonlinear sawtooth-shaped frequency sweeps for efficient Fourier transform ion mobility mass spectrometry (FT-IM-MS) experiments. This is in contrast to conventional FT-IM-MS experiments where ion gates are modulated according to a linear frequency sweep. Linear frequency sweeps are effective but can be hindered by the amount of useful signal obtained using a single sweep over a large frequency range imposed by ion gating inefficiencies, particularly small ion packets, and gate depletion. These negative factors are direct consequences of the inherently low gate pulse widths of high-frequency ion gating events, placing an upper bound on FT-IM-MS performance. Here, we report alternative ion modulation strategies. Sawtooth frequency sweeps may be constructed for the purpose of either extending high-SNR transients or conducting efficient signal-averaging experiments for low-SNR transients. The data obtained using this approach show high-SNR signals for a set of low-mass tetraalkylammonium salts (<1000 m/z) where resolving powers in excess of 500 are achieved. Data for low-SNR obtained for multimeric protein complexes streptavidin (53 kDa) and GroEL (800 kDa) also reveal large increases in the signal-to-noise ratio for reconstructed arrival time distributions.
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Affiliation(s)
- Elvin R. Cabrera
- Department of Chemistry, Washington State University, Pullman, WA 99164, United States
| | - Robert L. Schrader
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | - Thomas E. Walker
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
| | - Brian H. Clowers
- Department of Chemistry, Washington State University, Pullman, WA 99164, United States
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3
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Fisher NP, McGee JP, Bowen KP, Goodwin M, Senko MW, Kelleher NL, Kafader JO. Determining Collisional Cross Sections from Ion Decay with Individual Ion Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2625-2629. [PMID: 38011219 PMCID: PMC10840072 DOI: 10.1021/jasms.3c00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Collision cross section (CCS) measurements determined by ion mobility spectrometry (IMS) provide useful information about gas-phase protein structure that is complementary to mass analysis. Methods for determining CCS without a dedicated IMS system have been developed for Fourier transform mass spectrometry (FT-MS) platforms by measuring the signal decay during detection. Individual ion mass spectrometry (I2MS) provides charge detection and measures ion lifetimes across the length of an FT-MS detection event. By tracking lifetimes for entire ion populations, we demonstrate simultaneous determination of charge, mass, and CCS for proteins and complexes ranging from ∼8 to ∼232 kDa.
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Affiliation(s)
- Nickolas P Fisher
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - John P McGee
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Kyle P Bowen
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Michael Goodwin
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Michael W Senko
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
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4
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Cajahuaringa S, Caetano DLZ, Zanotto LN, Araujo G, Skaf MS. MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies. J Chem Inf Model 2023; 63:3557-3566. [PMID: 37184925 PMCID: PMC10269586 DOI: 10.1021/acs.jcim.3c00405] [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: 03/15/2023] [Indexed: 05/16/2023]
Abstract
Ion mobility mass spectrometry (IM-MS) techniques have become highly valued as a tool for structural characterization of biomolecular systems since they yield accurate measurements of the rotationally averaged collision cross-section (CCS) against a buffer gas. Despite its enormous potential, IM-MS data interpretation is often challenging due to the conformational isomerism of metabolites, lipids, proteins, and other biomolecules in the gas phase. Therefore, reliable and fast CCS calculations are needed to help interpret IM-MS data. In this work, we present MassCCS, a parallelized open-source code for computing CCS of molecules ranging from small organic compounds to massive protein assemblies at the trajectory method level of description using atomic and molecular buffer gas particles. The performance of the code is comparable to other available software for small molecules and proteins but is significantly faster for larger macromolecular assemblies. We performed extensive tests regarding accuracy, performance, and scalability with system size and number of CPU cores. MassCCS has proven highly accurate and efficient, with execution times under a few minutes, even for large (84.87 MDa) virus capsid assemblies with very modest computational resources. MassCCS is freely available at https://github.com/cces-cepid/massccs.
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Affiliation(s)
- Samuel Cajahuaringa
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Daniel L. Z. Caetano
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
- Institute
of Chemistry, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Leandro N. Zanotto
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Guido Araujo
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Munir S. Skaf
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
- Institute
of Chemistry, University of Campinas, Campinas, São Paulo 13083-970, Brazil
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5
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Henderson LW, Sharon EM, Gautam AKS, Anthony AJ, Jarrold MF, Russell DH, Matouschek A, Clemmer DE. Stability of 20S Proteasome Configurations: Preopening the Axial Gate. J Phys Chem Lett 2023; 14:5014-5017. [PMID: 37224454 PMCID: PMC10916758 DOI: 10.1021/acs.jpclett.3c01040] [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] [Indexed: 05/26/2023]
Abstract
Mass spectrometry studies of the stability of the S. cerevisiae 20S proteasome from 11 to 55 °C reveal a series of related configurations and coupled transitions that appear to be associated with opening of the proteolytic core. We find no evidence for dissociation, and all transitions are reversible. A thermodynamic analysis indicates that configurations fall into three general types of structures: enthalpically stabilized, tightly closed (observed as the +54 to +58 charge states) configurations; high-entropy (+60 to +66) states that are proposed as precursors to pore opening; and larger (+70 to +79) partially and fully open pore structures. In the absence of the 19S regulatory unit, the mechanism for opening the 20S pore appears to involve a charge-priming process that loosens the closed-pore configuration. Only a small fraction (≤2%) of these 20S precursor configurations appear to open and thus expose the catalytic cavity.
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Affiliation(s)
- Lucas W Henderson
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Edie M Sharon
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Amit K S Gautam
- Department of Molecular Biosciences, University of Texas, Austin, Texas 78712, United States
| | - Adam J Anthony
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Andreas Matouschek
- Department of Molecular Biosciences, University of Texas, Austin, Texas 78712, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
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6
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James VK, Sanders JD, Aizikov K, Fort KL, Grinfeld D, Makarov A, Brodbelt JS. Expanding Orbitrap Collision Cross-Section Measurements to Native Protein Applications Through Kinetic Energy and Signal Decay Analysis. Anal Chem 2023; 95:7656-7664. [PMID: 37133913 DOI: 10.1021/acs.analchem.3c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The measurement of collision cross sections (CCS, σ) offers supplemental information about sizes and conformations of ions beyond mass analysis alone. We have previously shown that CCSs can be determined directly from the time-domain transient decay of ions in an Orbitrap mass analyzer as ions oscillate around the central electrode and collide with neutral gas, thus removing them from the ion packet. Herein, we develop the modified hard collision model, thus deviating from the prior FT-MS hard sphere model, to determine CCSs as a function of center-of-mass collision energy in the Orbitrap analyzer. With this model, we aim to increase the upper mass limit of CCS measurement for native-like proteins, characterized by low charge states and presumed to be in more compact conformations. We also combine CCS measurements with collision induced unfolding and tandem mass spectrometry experiments to monitor protein unfolding and disassembly of protein complexes and measure CCSs of ejected monomers from protein complexes.
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Affiliation(s)
- Virginia K James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Kyle L Fort
- Thermo Fisher Scientific, Bremen 28199, Germany
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584, The Netherlands
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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7
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Yang L, Zhang W, Xu W. Efficient protein conformation dynamics characterization enabled by mobility-mass spectrometry. Anal Chim Acta 2023; 1243:340800. [PMID: 36697173 DOI: 10.1016/j.aca.2023.340800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/25/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023]
Abstract
Protein structure dynamics in solution and from solution to gas phase are important but challenging topics. Great efforts and advances have been made especially since the wide application of ion mobility mass spectrometry (IM-MS), by which protein collision cross section (CCS) in gas phase could be measured. Due to the lack of efficient experimental methods, protein structures in protein databank are typically referred as their structures in solution. Although conventional structural biology techniques provide high-resolution protein structures, complicated and stringent processes also limit their applicability under different solvent conditions, thus preventing the capture of protein dynamics in solution. Enabled by the combination of mobility capillary electrophoresis (MCE) and IM-MS, an efficient experimental protocol was developed to characterize protein conformation dynamics in solution and from solution to gas phase. As a first attempt, key factors that affecting protein conformations were distinguished and evaluated separately, including pH, temperature, softness of ionization process, presence and specific location of disulfide bonds. Although similar extent of unfolding could be observed for different proteins, in-depth analysis reveals that pH decrease from 7.0 to 3.0 dominates the unfolding of proteins without disulfide bonds in conventional ESI-MS experiments; while harshness of the ionization process dominates the unfolding of proteins with disulfide bonds. Second, disulfide bonds show capability of preserving protein conformations in acidic solution environments. However, by monitoring protein conformation dynamics and comparing results from different proteins, it is also found that their capability is position dependent. Surprisingly, disulfide bonds did not show the capability of preserving protein conformations during ionization processes.
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Affiliation(s)
- Lei Yang
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Wenjing Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
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8
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Butalewicz JP, Sanders JD, Clowers BH, Brodbelt JS. Improving Ion Mobility Mass Spectrometry of Proteins through Tristate Gating and Optimization of Multiplexing Parameters. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:101-108. [PMID: 36469482 DOI: 10.1021/jasms.2c00274] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Coupling drift tube ion mobility (IM) to Fourier transform mass spectrometry (FT-MS) affords the opportunity for gas-phase separation of ions based on size and conformation with high-resolution mass analysis. However, combining IM and FT-MS is challenging because ions exit the drift tube on a much faster time scale than the rate of mass analysis. Fourier transform (FT) and Hadamard transform multiplexing methods have been implemented to overcome the duty-cycle mismatch, offering new avenues for obtaining high-resolution, high-mass-accuracy analysis of mobility-selected ions. The gating methods used to integrate the drift tube with the FT mass analyzer discriminate against the transmission of large, low-mobility ions owing to the well-known gate depletion effect. Tristate gating strategies have been shown to increase ion transmission for drift tube IM-FT-MS systems through implementation of dual ion gating, controlling the quantity and timing of ions through the drift tube to reduce losses of slow-moving ions. Here we present an optimized set of multiplexing parameters for tristate gating ion mobility of several proteins on an Orbitrap mass spectrometer and further report parameters for increased ion transmission and mobility resolution as well as decreased experimental times from 15 min down to 30 s. On average, peak intensities in the arrival time distributions (ATDs) for ubiquitin increased 2.1× on average, while those of myoglobin increased by 1.5× with a resolving power increase on average of 11%.
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Affiliation(s)
- Jamie P Butalewicz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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9
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Lin CW, Oney-Hawthorne SD, Kuo ST, Barondeau DP, Russell DH. Mechanistic Insights into IscU Conformation Regulation for Fe-S Cluster Biogenesis Revealed by Variable Temperature Electrospray Ionization Native Ion Mobility Mass Spectrometry. Biochemistry 2022; 61:2733-2741. [PMID: 36351081 PMCID: PMC10009881 DOI: 10.1021/acs.biochem.2c00429] [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] [Indexed: 11/10/2022]
Abstract
Iron-sulfur (Fe-S) cluster (ISC) cofactors are required for the function of many critical cellular processes. In the ISC Fe-S cluster biosynthetic pathway, IscU assembles Fe-S cluster intermediates from iron, electrons, and inorganic sulfur, which is provided by the cysteine desulfurase enzyme IscS. IscU also binds to Zn, which mimics and competes for binding with the Fe-S cluster. Crystallographic and nuclear magnetic resonance spectroscopic studies reveal that IscU is a metamorphic protein that exists in multiple conformational states, which include at least a structured form and a disordered form. The structured form of IscU is favored by metal binding and is stable in a narrow temperature range, undergoing both cold and hot denaturation. Interestingly, the form of IscU that binds IscS and functions in Fe-S cluster assembly remains controversial. Here, results from variable temperature electrospray ionization (vT-ESI) native ion mobility mass spectrometry (nIM-MS) establish that IscU exists in structured, intermediate, and disordered forms that rearrange to more extended conformations at higher temperatures. A comparison of Zn-IscU and apo-IscU reveals that Zn(II) binding attenuates the cold/heat denaturation of IscU, promotes refolding of IscU, favors the structured and intermediate conformations, and inhibits the disordered high charge states. Overall, these findings provide a structural rationalization for the role of Zn(II) in stabilizing IscU conformations and IscS in altering the IscU active site to prepare for Zn(II) release and cluster synthesis. This work highlights how vT-ESI-nIM-MS can be applied as a powerful tool in mechanistic enzymology by providing details of relationships among temperature, protein conformations, and ligand/protein binding.
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Affiliation(s)
- Cheng-Wei Lin
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Shelby D Oney-Hawthorne
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Syuan-Ting Kuo
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David P Barondeau
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
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10
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Blevins MS, Juetten KJ, James VK, Butalewicz JP, Escobar EE, Lanzillotti MB, Sanders JD, Fort KL, Brodbelt JS. Nanohydrophobic Interaction Chromatography Coupled to Ultraviolet Photodissociation Mass Spectrometry for the Analysis of Intact Proteins in Low Charge States. J Proteome Res 2022; 21:2493-2503. [PMID: 36043517 DOI: 10.1021/acs.jproteome.2c00450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The direct correlation between proteoforms and biological phenotype necessitates the exploration of mass spectrometry (MS)-based methods more suitable for proteoform detection and characterization. Here, we couple nano-hydrophobic interaction chromatography (nano-HIC) to ultraviolet photodissociation MS (UVPD-MS) for separation and characterization of intact proteins and proteoforms. High linearity, sensitivity, and sequence coverage are obtained with this method for a variety of proteins. Investigation of collisional cross sections of intact proteins during nano-HIC indicates semifolded conformations in low charge states, enabling a different dimension of separation in comparison to traditional, fully denaturing reversed-phase separations. This method is demonstrated for a mixture of intact proteins from Escherichia coli ribosomes; high sequence coverage is obtained for a variety of modified and unmodified proteoforms.
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Affiliation(s)
- Molly S Blevins
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Kyle J Juetten
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Virginia K James
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jamie P Butalewicz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Edwin E Escobar
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Michael B Lanzillotti
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Kyle L Fort
- Thermo Fisher Scientific, Bremen 28199, Germany
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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11
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Walker TE, Laganowsky A, Russell DH. Surface Activity of Amines Provides Evidence for the Combined ESI Mechanism of Charge Reduction for Protein Complexes. Anal Chem 2022; 94:10824-10831. [PMID: 35862200 PMCID: PMC9357154 DOI: 10.1021/acs.analchem.2c01814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Charge reduction reactions are important for native mass spectrometry (nMS) because lower charge states help retain native-like conformations and preserve noncovalent interactions of protein complexes. While mechanisms of charge reduction reactions are not well understood, they are generally achieved through the addition of small molecules, such as polyamines, to traditional nMS buffers. Here, we present new evidence that surface-active, charge reducing reagents carry away excess charge from the droplet after being emitted due to Coulombic repulsion, thereby reducing the overall charge of the droplet. Furthermore, these processes are directly linked to two mechanisms for electrospray ionization, specifically the charge residue and ion evaporation models (CRM and IEM). Selected protein complexes were analyzed in solutions containing ammonium acetate and selected trialkylamines or diaminoalkanes of increasing alkyl chain lengths. Results show that amines with higher surface activity have increased propensities for promoting charge reduction of the protein ions. The electrospray ionization (ESI) emitter potential was also found to be a major contributing parameter to the prevalence of charge reduction; higher emitter potentials consistently coincided with lower average charge states among all protein complexes analyzed. These results offer experimental evidence for the mechanism of charge reduction in ESI and also provide insight into the final stages of the ESI and their impact on biological ions.
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Affiliation(s)
- Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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12
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Sipe SN, Sanders JD, Reinecke T, Clowers BH, Brodbelt JS. Separation and Collision Cross Section Measurements of Protein Complexes Afforded by a Modular Drift Tube Coupled to an Orbitrap Mass Spectrometer. Anal Chem 2022; 94:9434-9441. [PMID: 35736993 PMCID: PMC9302900 DOI: 10.1021/acs.analchem.2c01653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
New developments in analytical technologies and biophysical methods have advanced the characterization of increasingly complex biomolecular assemblies using native mass spectrometry (MS). Ion mobility methods, in particular, have enabled a new dimension of structural information and analysis of proteins, allowing separation of conformations and providing size and shape insights based on collision cross sections (CCSs). Based on the concepts of absorption-mode Fourier transform (aFT) multiplexing ion mobility spectrometry (IMS), here, a modular drift tube design proves capable of separating native-like proteins up to 148 kDa with resolution up to 45. Coupled with high-resolution Orbitrap MS, binding of small ligands and cofactors can be resolved in the mass domain and correlated to changes in structural heterogeneity observed in the ion-neutral CCS distributions. We also demonstrate the ability to rapidly determine accurate CCSs for proteins with 1-min aFT-IMS-MS sweeps without the need for calibrants or correction factors.
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Affiliation(s)
- Sarah N. Sipe
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D. Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Tobias Reinecke
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Brian H. Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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13
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Abstract
Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed.
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Affiliation(s)
- Kelly R Karch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Dalton T Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
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14
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Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210,Corresponding author:
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15
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Tomlinson L, Batchelor M, Sarsby J, Byrne DP, Brownridge PJ, Bayliss R, Eyers PA, Eyers CE. Exploring the Conformational Landscape and Stability of Aurora A Using Ion-Mobility Mass Spectrometry and Molecular Modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:420-435. [PMID: 35099954 PMCID: PMC9007459 DOI: 10.1021/jasms.1c00271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 05/06/2023]
Abstract
Protein kinase inhibitors are highly effective in treating diseases driven by aberrant kinase signaling and as chemical tools to help dissect the cellular roles of kinase signaling complexes. Evaluating the effects of binding of small molecule inhibitors on kinase conformational dynamics can assist in understanding both inhibition and resistance mechanisms. Using gas-phase ion-mobility mass spectrometry (IM-MS), we characterize changes in the conformational landscape and stability of the protein kinase Aurora A (Aur A) driven by binding of the physiological activator TPX2 or small molecule inhibition. Aided by molecular modeling, we establish three major conformations, the relative abundances of which were dependent on the Aur A activation status: one highly populated compact conformer similar to that observed in most crystal structures, a second highly populated conformer possessing a more open structure infrequently found in crystal structures, and an additional low-abundance conformer not currently represented in the protein databank. Notably, inhibitor binding induces more compact configurations of Aur A, as adopted by the unbound enzyme, with both IM-MS and modeling revealing inhibitor-mediated stabilization of active Aur A.
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Affiliation(s)
- Lauren
J. Tomlinson
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Matthew Batchelor
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Joscelyn Sarsby
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Dominic P. Byrne
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Philip J. Brownridge
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Richard Bayliss
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Patrick A. Eyers
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Claire E. Eyers
- Centre
for Proteome Research, Department of Biochemistry & Systems Biology,
Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry & Systems Biology, Institute of Systems, Molecular
& Integrative Biology, University of
Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
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16
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McCabe JW, Jones BJ, Walker TE, Schrader RL, Huntley AP, Lyu J, Hoffman NM, Anderson GA, Reilly PTA, Laganowsky A, Wysocki VH, Russell DH. Implementing Digital-Waveform Technology for Extended m/ z Range Operation on a Native Dual-Quadrupole FT-IM-Orbitrap Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2812-2820. [PMID: 34797072 PMCID: PMC9026758 DOI: 10.1021/jasms.1c00245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Here, we describe a digital-waveform dual-quadrupole mass spectrometer that enhances the performance of our drift tube FT-IMS high-resolution Orbitrap mass spectrometer (MS). The dual-quadrupole analyzer enhances the instrument capabilities for studies of large protein and protein complexes. The first quadrupole (q) provides a means for performing low-energy collisional activation of ions to reduce or eliminate noncovalent adducts, viz., salts, buffers, detergents, and/or endogenous ligands. The second quadrupole (Q) is used to mass-select ions of interest for further interrogation by ion mobility spectrometry and/or collision-induced dissociation (CID). Q is operated using digital-waveform technology (DWT) to improve the mass selection compared to that achieved using traditional sinusoidal waveforms at floated DC potentials (>500 V DC). DWT allows for increased precision of the waveform for a fraction of the cost of conventional RF drivers and with readily programmable operation and precision (Hoffman, N. M. . A comparison-based digital-waveform generator for high-resolution duty cycle. Review of Scientific Instruments 2018, 89, 084101).
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Robert L Schrader
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Adam P Huntley
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Nathan M Hoffman
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | | | - Peter T A Reilly
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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17
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Baumer KM, Cook CD, Zahler CT, Beard AA, Chen Z, Koone JC, Dashnaw CM, Villacob RA, Solouki T, Wood JL, Borchelt DR, Shaw BF. Supercharging Prions via Amyloid‐Selective Lysine Acetylation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Katelyn M. Baumer
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Collin T. Zahler
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Zhijuan Chen
- Department of Neuroscience University of Florida Gainesville FL USA
| | - Jordan C. Koone
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Chad M. Dashnaw
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Raul A. Villacob
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - John L. Wood
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Bryan F. Shaw
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
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18
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Chang CH, Yeung D, Spicer V, Ogata K, Krokhin O, Ishihama Y. Sequence-Specific Model for Predicting Peptide Collision Cross Section Values in Proteomic Ion Mobility Spectrometry. J Proteome Res 2021; 20:3600-3610. [PMID: 34133192 DOI: 10.1021/acs.jproteome.1c00185] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The contribution of peptide amino acid sequence to collision cross section values (CCS) has been investigated using a dataset of ∼134 000 peptides of four different charge states (1+ to 4+). The migration data were acquired using a two-dimensional liquid chromatography (LC)/trapped ion mobility spectrometry/quadrupole/time-of-flight mass spectrometry (MS) analysis of HeLa cell digests created using seven different proteases and was converted to CCS values. Following the previously reported modeling approaches using intrinsic size parameters (ISP), we extended this methodology to encode the position of individual residues within a peptide sequence. A generalized prediction model was built by dividing the dataset into eight groups (four charges for both tryptic/nontryptic peptides). Position-dependent ISPs were independently optimized for the eight subsets of peptides, resulting in prediction accuracy of ∼0.981 for the entire population of peptides. We find that ion mobility is strongly affected by the peptide's ability to solvate the positively charged sites. Internal positioning of polar residues and proline leads to decreased CCS values as they improve charge solvation; conversely, this ability decreases with increasing peptide charge due to electrostatic repulsion. Furthermore, higher helical propensity and peptide hydrophobicity result in a preferential formation of extended structures with higher than predicted CCS values. Finally, acidic/basic residues exhibit position-dependent ISP behavior consistent with electrostatic interaction with the peptide macrodipole, which affects the peptide helicity. The MS raw data files have been deposited with the ProteomeXchange Consortium via the jPOST partner repository (http://jpostdb.org) with the dataset identifiers PXD021440/JPST000959, PXD022800/JPST001017, and PXD026087/ JPST001176.
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Affiliation(s)
- Chih-Hsiang Chang
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Darien Yeung
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Oleg Krokhin
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg, Manitoba R3T 2N2, Canada
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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19
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Baumer KM, Cook CD, Zahler CT, Beard AA, Chen Z, Koone JC, Dashnaw CM, Villacob RA, Solouki T, Wood JL, Borchelt DR, Shaw BF. Supercharging Prions via Amyloid-Selective Lysine Acetylation. Angew Chem Int Ed Engl 2021; 60:15069-15079. [PMID: 33876528 DOI: 10.1002/anie.202103548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 11/10/2022]
Abstract
Repulsive electrostatic forces between prion-like proteins are a barrier against aggregation. In neuropharmacology, however, a prion's net charge (Z) is not a targeted parameter. Compounds that selectively boost prion Z remain unreported. Here, we synthesized compounds that amplified the negative charge of misfolded superoxide dismutase-1 (SOD1) by acetylating lysine-NH3 + in amyloid-SOD1, without acetylating native-SOD1. Compounds resembled a "ball and chain" mace: a rigid amyloid-binding "handle" (benzothiazole, stilbene, or styrylpyridine); an aryl ester "ball"; and a triethylene glycol chain connecting ball to handle. At stoichiometric excess, compounds acetylated up to 9 of 11 lysine per misfolded subunit (ΔZfibril =-8100 per 103 subunits). Acetylated amyloid-SOD1 seeded aggregation more slowly than unacetylated amyloid-SOD1 in vitro and organotypic spinal cord (these effects were partially due to compound binding). Compounds exhibited reactivity with other amyloid and non-amyloid proteins (e.g., fibrillar α-synuclein was peracetylated; serum albumin was partially acetylated; carbonic anhydrase was largely unacetylated).
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Affiliation(s)
- Katelyn M Baumer
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Christopher D Cook
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Collin T Zahler
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Alexandra A Beard
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Zhijuan Chen
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Jordan C Koone
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Chad M Dashnaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Raul A Villacob
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - John L Wood
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - David R Borchelt
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
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20
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McCabe JW, Shirzadeh M, Walker TE, Lin CW, Jones BJ, Wysocki VH, Barondeau DP, Clemmer DE, Laganowsky A, Russell DH. Variable-Temperature Electrospray Ionization for Temperature-Dependent Folding/Refolding Reactions of Proteins and Ligand Binding. Anal Chem 2021; 93:6924-6931. [PMID: 33904705 DOI: 10.1021/acs.analchem.1c00870] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Stabilities and structure(s) of proteins are directly coupled to their local environment or Gibbs free energy landscape as defined by solvent, temperature, pressure, and concentration. Solution pH, ionic strength, cofactors, chemical chaperones, and osmolytes perturb the chemical potential and induce further changes in structure, stability, and function. At present, no single analytical technique can monitor these effects in a single measurement. Mass spectrometry and ion mobility-mass spectrometry play increasingly essential roles in studies of proteins, protein complexes, and even membrane protein complexes; however, with few exceptions, the effects of the solution temperature on the stability and structure(s) of analytes have not been thoroughly investigated. Here, we describe a new variable-temperature electrospray ionization (vT-ESI) source that utilizes a thermoelectric chip to cool and heat the solution contained within the static ESI emitter. This design allows for solution temperatures to be varied from ∼5 to 98 °C with short equilibration times (<2 min) between precisely controlled temperature changes. The performance of the apparatus for vT-ESI-mass spectrometry and vT-ESI-ion mobility-mass spectrometry studies of cold- and heat-folding reactions is demonstrated using ubiquitin and frataxin. Instrument performance for studies on temperature-dependent ligand binding is shown using the chaperonin GroEL.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Benjamin J Jones
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Vicki H Wysocki
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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21
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Fouque KJD, Garabedian A, Leng F, Tse-Dinh YC, Ridgeway ME, Park MA, Fernandez-Lima F. Trapped Ion Mobility Spectrometry of Native Macromolecular Assemblies. Anal Chem 2021; 93:2933-2941. [PMID: 33492949 PMCID: PMC8327357 DOI: 10.1021/acs.analchem.0c04556] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The structural elucidation of native macromolecular assemblies has been a subject of considerable interest in native mass spectrometry (MS), and more recently in tandem with ion mobility spectrometry (IMS-MS), for a better understanding of their biochemical and biophysical functions. In the present work, we describe a new generation trapped ion mobility spectrometer (TIMS), with extended mobility range (K0 = 0.185-1.84 cm2·V-1·s-1), capable of trapping high-molecular-weight (MW) macromolecular assemblies. This compact 4 cm long TIMS analyzer utilizes a convex electrode, quadrupolar geometry with increased pseudopotential penetration in the radial dimension, extending the mobility trapping to high-MW species under native state (i.e., lower charge states). The TIMS capabilities to perform variable scan rate (Sr) mobility measurements over short time (100-500 ms), high-mobility resolution, and ion-neutral collision cross-section (CCSN2) measurements are presented. The trapping capabilities of the convex electrode TIMS geometry and ease of operation over a wide gas flow, rf range, and electric field trapping range are illustrated for the first time using a comprehensive list of standards varying from CsI clusters (n = 6-73), Tuning Mix oligomers (n = 1-5), common proteins (e.g., ubiquitin, cytochrome C, lysozyme, concanavalin (n = 1-4), carbonic anhydrase, β clamp (n = 1-4), topoisomerase IB, bovine serum albumin (n = 1-3), topoisomerase IA, alcohol dehydrogenase), IgG antibody (e.g., avastin), protein-DNA complexes, and macromolecular assemblies (e.g., GroEL and RNA polymerase (n = 1-2)) covering a wide mass (up to m/z 19 000) and CCS range (up to 22 000 Å2 with <0.6% relative standard deviation (RSD)).
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
| | | | - Melvin A. Park
- Bruker Daltonics Inc., Billerica, MA 01821, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
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22
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Mallis CS, Zheng X, Qiu X, McCabe JW, Shirzadeh M, Lyu J, Laganowsky A, Russell DH. Development of Native MS Capabilities on an Extended Mass Range Q-TOF MS. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2020; 458:116451. [PMID: 33162786 PMCID: PMC7641504 DOI: 10.1016/j.ijms.2020.116451] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Native mass spectrometry (nMS) is increasingly used for studies of large biomolecules (>100 kDa), especially proteins and protein complexes. The growth in this area can be attributed to advances in native electrospray ionization as well as instrumentation that is capable of accessing high mass-to-charge (m/z) regimes without significant losses in sensitivity and resolution. Here, we describe modifications to the ESI source of an Agilent 6545XT Q-TOF MS that is tailored for analysis of large biomolecules. The modified ESI source was evaluated using both soluble and membrane protein complexes ranging from ~127 to ~232 kDa and the ~801 kDa protein chaperone GroEL. The increased mass resolution of the instrument affords the ability to resolve small molecule adducts and analyze collision-induced dissociation products of the native complexes.
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Affiliation(s)
| | - Xueyun Zheng
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Xi Qiu
- Agilent Technologies, Inc., Wilmington, DE 19808
| | - Jacob W. McCabe
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Correspondence to David H. Russell;
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