1
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Mertz KL, Jordahl, Hemme CA, Probasco MD, Forbes DS, Ducos PL, Salome AZ, Westphall MS, Quarmby ST, Grant T, Coon JJ. Laser-Induced Rehydration of Cryo-Landed Proteins Restores Native Structure. Mol Cell Proteomics 2025:100987. [PMID: 40349920 DOI: 10.1016/j.mcpro.2025.100987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2025] [Revised: 05/05/2025] [Accepted: 05/06/2025] [Indexed: 05/14/2025] Open
Abstract
The use of native mass spectrometry (MS) to land biological molecules for subsequent cryogenic electron microscopy (cryoEM) imaging and three-dimensional reconstruction has gained momentum in recent years as a means to overcome longstanding challenges posed by traditional cryoEM sample preparation. However, recent results obtained with this approach have been constrained by low resolution and the compaction of cryo-landed particles, likely due to dehydration during exposure to vacuum. Here, we describe a new sample preparation method that uses a laser integrated into a cryogenic soft-landing apparatus to liquefy precisely deposited amorphous ice, rehydrating particles and restoring their solution structure prior to rapid revitrification via the thermal mass of the grid. With this technique, we demonstrate the reconstruction of cryo-landed, rehydrated, and revitrified β-galactosidase that is comparable in resolution to that achieved with plunge freezing. Further, these particles are not compacted, matching the known structure and conformation obtained with traditionally plunge-frozen particles. These results establish the viability of coupling native MS with cryoEM for high-resolution structural determination without the limitations imposed by conventional sample preparation, and they open a path to solving previously inaccessible molecules and to integrating MS capabilities such as gas-phase purification to complex samples such as cell lysates.
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Affiliation(s)
- Keaton L Mertz
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jordahl
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Colin A Hemme
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Morgridge Institute for Research, Madison, Wisconsin 53515, United States
| | | | - Dylan S Forbes
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Peter L Ducos
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Morgridge Institute for Research, Madison, Wisconsin 53515, United States
| | - Austin Z Salome
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Scott T Quarmby
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Timothy Grant
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Morgridge Institute for Research, Madison, Wisconsin 53515, United States.
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Morgridge Institute for Research, Madison, Wisconsin 53515, United States.
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2
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Campuzano IDG, Loo JA. Evolution of Mass Spectrometers for High m/ z Biological Ion Formation, Transmission, Analysis and Detection: A Personal Perspective. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2025; 36:632-652. [PMID: 40043050 DOI: 10.1021/jasms.4c00348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2025]
Abstract
Mass spectrometry (MS) has become an essential tool in virtually all academic, pharmaceutical, and biopharmaceutical analytical laboratories. The specialized and bespoke area of MS research and application of high m/z ion (>m/z 6000 and high mass, >150 kDa) formation, transmission, analysis, and detection is a relatively new area of focus for MS that has seen dramatic acceleration in interest over the last two decades. Herein we delve into this exciting aspect of MS, discussing how MS instrumentation has been refined and evolved for native-MS analysis. We cover the early groundbreaking experiments showing high m/z ion formation, transmission, and preservation of protein structure in the gas phase. Additionally, we discuss specific instrument optimizations and modifications that have advanced high m/z ion generation, transmission, analysis, and detection, contributing to the research area known as gas-phase structural biology. Native-MS sample introduction methods, emerging technologies, and future perspectives are also examined. Finally, we share personal opinions, observations, and experiences that are new to the community or previously unpublished.
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Affiliation(s)
- Iain D G Campuzano
- Large Molecule Discovery and Research Data Science, Amgen Research, Amgen, Thousand Oaks, California 91320, United States
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
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3
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Britt HM, Robinson CV. Traversing the drug discovery landscape using native mass spectrometry. Curr Opin Struct Biol 2025; 91:102993. [PMID: 39893771 DOI: 10.1016/j.sbi.2025.102993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2024] [Revised: 12/10/2024] [Accepted: 01/13/2025] [Indexed: 02/04/2025]
Abstract
As health needs in our society evolve, the field of drug discovery must undergo constant innovation and improvement to identify novel targets and drug candidates. Owing to its ability to simultaneously capture biological interactions and provide in-depth molecular characterisation of the species involved, native mass spectrometry is starting to play an important role in this endeavour. Here, we discuss recent contributions that native mass spectrometry has made to drug discovery including deciphering protein-small molecule interactions, unravelling biochemical pathways, and integrating with complementary structural approaches.
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Affiliation(s)
- Hannah M Britt
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford, OX1 3QU, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford, OX1 3QU, UK.
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4
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Li Y, Li W, Zheng Y, Wang T, Pu R, Zhang Z. Desalting strategies for native mass spectrometry. Talanta 2025; 281:126824. [PMID: 39250868 DOI: 10.1016/j.talanta.2024.126824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 09/02/2024] [Accepted: 09/05/2024] [Indexed: 09/11/2024]
Abstract
In native mass spectrometry (MS) salts are indispensable for preserving the native structures of biomolecules, but detrimental to mass sensitivity, resolution, and accuracy. Such a conflict makes desalting in native MS more challenging, distinctive, and sample-dependent than in peptide-centric MS. This review first briefly introduces the charged residue mechanism whereby native-like gaseous protein ions are released from electrospray droplets, revealing a higher degree of salt adduction than denatured proteins. Subsequently, this review summarizes and explores the existing strategies, underlying mechanisms and future perspectives of desalting in native MS. These strategies mainly focus on buffer exchange into volatile salts (offline and online approaches), addition of solution additives (e.g., anion, supercharging reagent, solution phase chelator and amino acid), use of submicron electrospray emitters (down to 60 nm), and other potential approaches (e.g., induced and electrophoretic nanoelectrospray ionization). The strategies of online buffer exchange and using nanoscale electrospray emitters are highlighted. This review would not only be a valuable addition to the field of sample preparation in MS, but would also serve as a beginner's guide to desalting in native MS.
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Affiliation(s)
- Yun Li
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Weijie Li
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Yajun Zheng
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China.
| | - Tong Wang
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Ruijin Pu
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China
| | - Zhiping Zhang
- School of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, China.
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5
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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] [MESH Headings] [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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6
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 PMCID: PMC11996003 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M. Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
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7
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Marie A, Georgescauld F, Johnson KR, Ray S, Engen JR, Ivanov AR. Native Capillary Electrophoresis-Mass Spectrometry of Near 1 MDa Non-Covalent GroEL/GroES/Substrate Protein Complexes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306824. [PMID: 38191978 PMCID: PMC10953559 DOI: 10.1002/advs.202306824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/21/2023] [Indexed: 01/10/2024]
Abstract
Protein complexes are essential for proteins' folding and biological function. Currently, native analysis of large multimeric protein complexes remains challenging. Structural biology techniques are time-consuming and often cannot monitor the proteins' dynamics in solution. Here, a capillary electrophoresis-mass spectrometry (CE-MS) method is reported to characterize, under near-physiological conditions, the conformational rearrangements of ∽1 MDa GroEL upon complexation with binding partners involved in a protein folding cycle. The developed CE-MS method is fast (30 min per run), highly sensitive (low-amol level), and requires ∽10 000-fold fewer samples compared to biochemical/biophysical techniques. The method successfully separates GroEL14 (∽800 kDa), GroEL7 (∽400 kDa), GroES7 (∽73 kDa), and NanA4 (∽130 kDa) oligomers. The non-covalent binding of natural substrate proteins with GroEL14 can be detected and quantified. The technique allows monitoring of GroEL14 conformational changes upon complexation with (ATPγS)4-14 and GroES7 (∽876 kDa). Native CE-pseudo-MS3 analyses of wild-type (WT) GroEL and two GroEL mutants result in up to 60% sequence coverage and highlight subtle structural differences between WT and mutated GroEL. The presented results demonstrate the superior CE-MS performance for multimeric complexes' characterization versus direct infusion ESI-MS. This study shows the CE-MS potential to provide information on binding stoichiometry and kinetics for various protein complexes.
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Affiliation(s)
- Anne‐Lise Marie
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Florian Georgescauld
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Kendall R. Johnson
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Somak Ray
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - John R. Engen
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Alexander R. Ivanov
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
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8
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Esser TK, Böhning J, Önür A, Chinthapalli DK, Eriksson L, Grabarics M, Fremdling P, Konijnenberg A, Makarov A, Botman A, Peter C, Benesch JLP, Robinson CV, Gault J, Baker L, Bharat TAM, Rauschenbach S. Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar. SCIENCE ADVANCES 2024; 10:eadl4628. [PMID: 38354247 PMCID: PMC10866560 DOI: 10.1126/sciadv.adl4628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
Native mass spectrometry (MS) has become widely accepted in structural biology, providing information on stoichiometry, interactions, homogeneity, and shape of protein complexes. Yet, the fundamental assumption that proteins inside the mass spectrometer retain a structure faithful to native proteins in solution remains a matter of intense debate. Here, we reveal the gas-phase structure of β-galactosidase using single-particle cryo-electron microscopy (cryo-EM) down to 2.6-Å resolution, enabled by soft landing of mass-selected protein complexes onto cold transmission electron microscopy (TEM) grids followed by in situ ice coating. We find that large parts of the secondary and tertiary structure are retained from the solution. Dehydration-driven subunit reorientation leads to consistent compaction in the gas phase. By providing a direct link between high-resolution imaging and the capability to handle and select protein complexes that behave problematically in conventional sample preparation, the approach has the potential to expand the scope of both native mass spectrometry and cryo-EM.
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Affiliation(s)
- Tim K. Esser
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Thermo Fisher Scientific, 1 Boundary Park, Hemel Hempstead, Hertfordshire HP2 7GE, UK
| | - Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alpcan Önür
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Dinesh K. Chinthapalli
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Lukas Eriksson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Marko Grabarics
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Aurelien Botman
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Justin L. P. Benesch
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lindsay Baker
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephan Rauschenbach
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
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9
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Gozzo TA, Bush MF. Quantitatively Differentiating Antibodies Using Charge-State Manipulation, Collisional Activation, and Ion Mobility-Mass Spectrometry. Anal Chem 2024; 96:505-513. [PMID: 38146701 DOI: 10.1021/acs.analchem.3c04638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Antibody-based therapeutics continue to expand both in the number of products and in their use in patients. These heterogeneous proteins challenge traditional drug characterization strategies, but ion mobility (IM) and mass spectrometry (MS) approaches have eased the challenge of higher-order structural characterization. Energy-dependent IM-MS, e.g., collision-induced unfolding (CIU), has been demonstrated to be sensitive to subtle differences in structure. In this study, we combine a charge-reduction method, cation-to-anion proton-transfer reactions (CAPTR), with energy-dependent IM-MS and varied solution conditions to probe their combined effects on the gas-phase structures of IgG1κ and IgG4κ from human myeloma. CAPTR paired with MS-only analysis improves the confidence of charge-state assignments and the resolution of the interfering protein species. Collision cross-section distributions were determined for each of the charge-reduced products. Similarity scoring was used to quantitatively compare distributions determined from matched experiments analyzing samples of the two antibodies. Relative to workflows using energy-dependent IM-MS without charge-state manipulation, combining CAPTR and energy-dependent IM-MS enhanced the differentiation of these antibodies. Combined, these results indicate that CAPTR can benefit many aspects of antibody characterization and differentiation.
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Affiliation(s)
- Theresa A Gozzo
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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10
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Westphall MS, Lee KW, Salome AZ, Coon JJ, Grant T. Mass spectrometers as cryoEM grid preparation instruments. Curr Opin Struct Biol 2023; 83:102699. [PMID: 37703606 PMCID: PMC11019453 DOI: 10.1016/j.sbi.2023.102699] [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: 05/21/2023] [Revised: 07/18/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023]
Abstract
Structure determination by single-particle cryoEM has matured into a core structural biology technique. Despite many methodological advancements, most cryoEM grids are still prepared using the plunge-freezing method developed ∼40 years ago. Embedding samples in thin films and exposing them to the air-water interface often leads to sample damage and preferential orientation of the particles. Using native mass spectrometry to create cryoEM samples, potentially avoids these problems and allows the use of mass spectrometry sample isolation techniques during EM grid creation. We review the recent publications that have demonstrated protein complexes can be ionized, flown through the mass spectrometer, gently landed onto EM grids, imaged, and reconstructed in 3D. Although many uncertainties and challenges remain, the combination of cryoEM and MS has great potential.
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Affiliation(s)
- Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Kenneth W Lee
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Austin Z Salome
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Morgridge Institute for Research, 330 N Orchard Street, Madison, WI 53706, United States.
| | - Timothy Grant
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Morgridge Institute for Research, 330 N Orchard Street, Madison, WI 53706, United States.
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11
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Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
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Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
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12
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Westphall M, Lee KW, Hemme C, Salome AZ, Mertz K, Grant T, Coon JJ. Cryogenic Soft Landing Improves Structural Preservation of Protein Complexes. Anal Chem 2023; 95:15094-15101. [PMID: 37732836 PMCID: PMC10568529 DOI: 10.1021/acs.analchem.3c03228] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023]
Abstract
We describe an apparatus for the cryogenic landing of particles from the ion beam of a mass spectrometer onto transmission electron microscope grids for cryo-electron microscopy. This system also allows for the controlled formation of thin films of amorphous ice on the grid surface. We demonstrate that as compared to room temperature landings, the use of this cryogenic landing device greatly improves the structural preservation of deposited protein-protein complexes. Furthermore, landing under cryogenic conditions can increase the diversity of particle orientations, allowing for improved 3D structural interpretation. We conclude that this approach allows for the direct coupling of mass spectrometry with cryo-electron microscopy.
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Affiliation(s)
- Michael
S. Westphall
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kenneth W. Lee
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Colin Hemme
- Department
of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
| | - Austin Z. Salome
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Keaton Mertz
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Timothy Grant
- Department
of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
| | - Joshua J. Coon
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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13
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Campuzano IDG. A Research Journey: Over a Decade of Denaturing and Native-MS Analyses of Hydrophobic and Membrane Proteins in Amgen Therapeutic Discovery. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2413-2431. [PMID: 37643331 DOI: 10.1021/jasms.3c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Membrane proteins and associated complexes currently comprise the majority of therapeutic targets and remain among the most challenging classes of proteins for analytical characterization. Through long-term strategic collaborations forged between industrial and academic research groups, there has been tremendous progress in advancing membrane protein mass spectrometry (MS) analytical methods and their concomitant application to Amgen therapeutic project progression. Herein, I will describe a detailed and personal account of how electrospray ionization (ESI) native mass spectrometry (nMS), ion mobility-MS (IM-MS), reversed phase liquid chromatographic mass spectrometry (RPLC-MS), high-throughput solid phase extraction mass spectrometry, and matrix-assisted laser desorption ionization mass spectrometry methods were developed, optimized, and validated within Amgen Research, and importantly, how these analytical methods were applied for membrane and hydrophobic protein analyses and ultimately therapeutic project support and progression. Additionally, I will discuss all the highly important and productive collaborative efforts, both internal Amgen and external academic, which were key in generating the samples, methods, and associated data described herein. I will also describe some early and previously unpublished nano-ESI (nESI) native-MS data from Amgen Research and the highly productive University of California Los Angeles (UCLA) collaboration. I will also present previously unpublished examples of real-life Amgen biotherapeutic membrane protein projects that were supported by all the MS (and IM) analytical techniques described herein. I will start by describing the initial nESI nMS experiments performed at Amgen in 2011 on empty nanodisc molecules, using a quadrupole time-of-flight MS, and how these experiments progressed on to the 15 Tesla Fourier transform ion cyclotron resonance MS at UCLA. Then described are monomeric and multimeric membrane protein data acquired in both nESI nMS and tandem-MS modes, using multiple methods of ion activation, resulting in dramatic spectral simplification. Also described is how we investigated the far less established and less published subject, that is denaturing RPLC-MS analysis of membrane proteins, and how we developed a highly robust and reproducible RPLC-MS method capable of effective separation of membrane proteins differing in only the presence or absence of an N-terminal post translational modification. Also described is the evolution of the aforementioned RPLC-MS method into a high-throughput solid phase extraction MS method. Finally, I will give my opinion on key developments and how the area of nMS of membrane proteins needs to evolve to a state where it can be applied within the biopharmaceutical research environment for routine therapeutic project support.
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Affiliation(s)
- Iain D G Campuzano
- Amgen Research, Center for Research Acceleration by Digital Innovation, Molecular Analytics, Thousand Oaks, California 91320, United States
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15
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Han BG, Avila-Sakar A, Remis J, Glaeser RM. Challenges in making ideal cryo-EM samples. Curr Opin Struct Biol 2023; 81:102646. [PMID: 37392555 DOI: 10.1016/j.sbi.2023.102646] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 07/03/2023]
Abstract
Recognizing that interaction with the air-water interface (AWI) is a major challenge for cryo-EM, we first review current approaches designed to avoid it. Of these, immobilizing particles on affinity grids is arguably the most promising. In addition, we review efforts to gain more reliable control of the sample thicknesses, not the least important reason being to prevent immobilized particles from coming in contact with the AWI of the remaining buffer. It is emphasized that avoiding such a contact is as important for cryo-ET as for single-particle cryo-EM. Finally, looking to the future, it is proposed that immobilized samples might be used to perform time-resolved biochemical experiments directly on EM grids rather than just in test tubes or cuvettes.
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Affiliation(s)
- Bong-Gyoon Han
- Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
| | - Agustin Avila-Sakar
- Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
| | - Jonathan Remis
- Department of Physics, University of California, Berkeley, CA 94720, USA
| | - Robert M Glaeser
- Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.
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16
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Westphall MS, Lee KW, Hemme C, Salome AZ, Mertz K, Grant T, Coon JJ. Cryogenic Soft Landing Improves Structural Preservation of Protein Complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.550105. [PMID: 37502880 PMCID: PMC10370175 DOI: 10.1101/2023.07.21.550105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
We describe an apparatus for the cryogenic landing of particles from the ion beam of a mass spectrometer onto transmission electron microscope grids for cryo-electron microscopy. This system also allows for the controlled formation of thin films of amorphous ice on the grid surface. We demonstrate that as compared to room temperature landings, use of this cryogenic landing device greatly improves the structural preservation of deposited protein-protein complexes. Further, landing under cryogenic conditions can increase the diversity of particle orientations, allowing for improved 3D structural interpretation. Finally, we conclude that this approach allows for the direct coupling of mass spectrometry with cryo-electron microscopy.
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Zercher BP, Hong S, Roush AE, Feng Y, Bush MF. Are the Gas-Phase Structures of Molecular Elephants Enduring or Ephemeral? Results from Time-Dependent, Tandem Ion Mobility. Anal Chem 2023; 95:9589-9597. [PMID: 37294019 PMCID: PMC10549206 DOI: 10.1021/acs.analchem.3c01222] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The structural stability of biomolecules in the gas phase remains an important topic in mass spectrometry applications for structural biology. Here, we evaluate the kinetic stability of native-like protein ions using time-dependent, tandem ion mobility (IM). In these tandem IM experiments, ions of interest are mobility-selected after a first dimension of IM and trapped for up to ∼14 s. Time-dependent, collision cross section distributions are then determined from separations in a second dimension of IM. In these experiments, monomeric protein ions exhibited structural changes specific to both protein and charge state, whereas large protein complexes did not undergo resolvable structural changes on the timescales of these experiments. We also performed energy-dependent experiments, i.e., collision-induced unfolding, as a comparison for time-dependent experiments to understand the extent of unfolding. Collision cross section values observed in energy-dependent experiments using high collision energies were significantly larger than those observed in time-dependent experiments, indicating that the structures observed in time-dependent experiments remain kinetically trapped and retain some memory of their solution-phase structure. Although structural evolution should be considered for highly charged, monomeric protein ions, these experiments demonstrate that higher-mass protein ions can have remarkable kinetic stability in the gas phase.
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Affiliation(s)
- Benjamin P. Zercher
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Seoyeon Hong
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Addison E. Roush
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Yuan Feng
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
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Cropley TC, Liu FC, Pedrete T, Hossain MA, Agar JN, Bleiholder C. Structure Relaxation Approximation (SRA) for Elucidation of Protein Structures from Ion Mobility Measurements (II). Protein Complexes. J Phys Chem B 2023. [PMID: 37311097 DOI: 10.1021/acs.jpcb.3c01024] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Characterizing structures of protein complexes and their disease-related aberrations is essential to understanding molecular mechanisms of many biological processes. Electrospray ionization coupled with hybrid ion mobility/mass spectrometry (ESI-IM/MS) methods offer sufficient sensitivity, sample throughput, and dynamic range to enable systematic structural characterization of proteomes. However, because ESI-IM/MS characterizes ionized protein systems in the gas phase, it generally remains unclear to what extent the protein ions characterized by IM/MS have retained their solution structures. Here, we discuss the first application of our computational structure relaxation approximation [Bleiholder, C.; et al. J. Phys. Chem. B 2019, 123 (13), 2756-2769] to assign structures of protein complexes in the range from ∼16 to ∼60 kDa from their "native" IM/MS spectra. Our analysis shows that the computed IM/MS spectra agree with the experimental spectra within the errors of the methods. The structure relaxation approximation (SRA) indicates that native backbone contacts appear largely retained in the absence of solvent for the investigated protein complexes and charge states. Native contacts between polypeptide chains of the protein complex appear to be retained to a comparable extent as contacts within a folded polypeptide chain. Our computations also indicate that the hallmark "compaction" often observed for protein systems in native IM/MS measurements appears to be a poor indicator of the extent to which native residue-residue interactions are lost in the absence of solvent. Further, the SRA indicates that structural reorganization of the protein systems in IM/MS measurements appears driven largely by remodeling of the protein surface that increases its hydrophobic content by approximately 10%. For the systems studied here, this remodeling of the protein surface appears to occur mainly by structural reorganization of surface-associated hydrophilic amino acid residues not associated with β-strand secondary structure elements. Properties related to the internal protein structure, as assessed by void volume or packing density, appear unaffected by remodeling of the surface. Taken together, the structural reorganization of the protein surface appears to be generic in nature and to sufficiently stabilize protein structures to render them metastable on the time scale of IM/MS measurements.
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Affiliation(s)
- Tyler C Cropley
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Fanny C Liu
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Thais Pedrete
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Md Amin Hossain
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
- Barnett Institute of Chemical and Biological Analysis, 140 The Fenway, Boston, Massachusetts 02115, United States
| | - Jeffrey N Agar
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
- Barnett Institute of Chemical and Biological Analysis, 140 The Fenway, Boston, Massachusetts 02115, United States
- Department of Pharmaceutical Sciences, Northeastern University, 10 Leon St, Boston, Massachusetts 02115, United States
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
- Institute of Molecular Biophysics, Florida State University, 91 Chieftain Way, Tallahassee, Florida 32306, United States
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19
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Moore CC, Staroverov VN, Konermann L. Using Density Functional Theory for Testing the Robustness of Mobile-Proton Molecular Dynamics Simulations on Electrosprayed Ions: Structural Implications for Gaseous Proteins. J Phys Chem B 2023; 127:4061-4071. [PMID: 37116098 DOI: 10.1021/acs.jpcb.3c01581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Current experiments only provide low-resolution information on gaseous protein ions generated by electrospray ionization (ESI). Molecular dynamics (MD) simulations can yield complementary insights. Unfortunately, conventional MD does not capture the mobile nature of protons in gaseous proteins. Mobile-proton MD (MPMD) overcomes this limitation. Earlier MPMD data at 300 K indicated that protein ions generated by "native" ESI retain solution-like structures with a hydrophobic core and zwitterionic exterior [Bakhtiari, M.; Konermann, L. J. Phys. Chem. B 2019, 123, 1784-1796]. MPMD redistributes protons using electrostatic and proton affinity calculations. The robustness of this approach has never been scrutinized. Here, we close this gap by benchmarking MPMD against density functional theory (DFT) at the B3LYP/6-31G* level, which is well suited for predicting proton affinities. The computational cost of DFT necessitated the use of small peptides. The MPMD energetic ranking of proton configurations was found to be consistent with DFT single-point energies, implying that MPMD can reliably identify favorable protonation sites. Peptide MPMD runs converged to DFT-optimized structures only when applying 300-500 K temperature cycling, which was necessary to prevent trapping in local minima. Temperature cycling MPMD was then applied to gaseous protein ions. Native ubiquitin converted to slightly expanded structures with a zwitterionic core and a nonpolar exterior. Our data suggest that such inside-out protein structures are intrinsically preferred in the gas phase, and that they form in ESI experiments after moderate collisional excitation. This is in contrast to native ESI (with minimal collisional excitation, simulated by MPMD at 300 K), where kinetic trapping promotes the survival of solution-like structures. In summary, this work validates the MPMD approach for simulations on gaseous peptides and proteins.
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Affiliation(s)
- Conrad C Moore
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Viktor N Staroverov
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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Brodmerkel MN, De Santis E, Caleman C, Marklund EG. Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration. Protein J 2023:10.1007/s10930-023-10110-y. [PMID: 37031302 DOI: 10.1007/s10930-023-10110-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
Proteins can be oriented in the gas phase using strong electric fields, which brings advantages for structure determination using X-ray free electron lasers. Both the vacuum conditions and the electric-field exposure risk damaging the protein structures. Here, we employ molecular dynamics simulations to rehydrate and relax vacuum and electric-field exposed proteins in aqueous solution, which simulates a refinement of structure models derived from oriented gas-phase proteins. We find that the impact of the strong electric fields on the protein structures is of minor importance after rehydration, compared to that of vacuum exposure and ionization in electrospraying. The structures did not fully relax back to their native structure in solution on the simulated timescales of 200 ns, but they recover several features, including native-like intra-protein contacts, which suggests that the structures remain in a state from which the fully native structure is accessible. Our findings imply that the electric fields used in native mass spectrometry are well below a destructive level, and suggest that structures inferred from X-ray diffraction from gas-phase proteins are relevant for solution and in vivo conditions, at least after in silico rehydration.
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Affiliation(s)
- Maxim N Brodmerkel
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
- Department of Physics and Astronomy, Uppsala University, 75120, Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, 75120, Uppsala, Sweden
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden.
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21
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Reid DJ, Thibert S, Zhou M. Dissecting the structural heterogeneity of proteins by native mass spectrometry. Protein Sci 2023; 32:e4612. [PMID: 36851867 PMCID: PMC10031758 DOI: 10.1002/pro.4612] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher-order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the "bottom-up" approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher-order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the "top-down" approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in-depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero-complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near-native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins.
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Affiliation(s)
- Deseree J. Reid
- Chemical and Biological Signature SciencesPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Stephanie Thibert
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Mowei Zhou
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWashingtonUSA
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22
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Lee KW, Salome AZ, Westphall MS, Grant T, Coon JJ. Onto Grid Purification and 3D Reconstruction of Protein Complexes Using Matrix-Landing Native Mass Spectrometry. J Proteome Res 2023; 22:851-856. [PMID: 36608276 PMCID: PMC10002473 DOI: 10.1021/acs.jproteome.2c00595] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Addressing mixtures and heterogeneity in structural biology requires approaches that can differentiate and separate structures based on mass and conformation. Mass spectrometry (MS) provides tools for measuring and isolating gas-phase ions. The development of native MS including electrospray ionization allowed for manipulation and analysis of intact noncovalent biomolecules as ions in the gas phase, leading to detailed measurements of structural heterogeneity. Conversely, transmission electron microscopy (TEM) generates detailed images of biomolecular complexes that show an overall structure. Our matrix-landing approach uses native MS to probe and select biomolecular ions of interest for subsequent TEM imaging, thus unifying information on mass, stoichiometry, heterogeneity, etc., available via native MS with TEM images. Here, we prepare TEM grids of protein complexes purified via quadrupolar isolation and matrix-landing and generate 3D reconstructions of the isolated complexes. Our results show that these complexes maintain their structure through gas-phase isolation.
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Affiliation(s)
- Kenneth W. Lee
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Austin Z. Salome
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | | | - Timothy Grant
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706
- Morgridge Institute for Research, 330 N Orchard Street, Madison, WI, 53706
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
- Morgridge Institute for Research, 330 N Orchard Street, Madison, WI, 53706
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23
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Mass spectrometry in materials synthesis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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Anggara K, Ochner H, Szilagyi S, Malavolti L, Rauschenbach S, Kern K. Landing Proteins on Graphene Trampoline Preserves Their Gas-Phase Folding on the Surface. ACS CENTRAL SCIENCE 2023; 9:151-158. [PMID: 36844500 PMCID: PMC9951278 DOI: 10.1021/acscentsci.2c00815] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Indexed: 06/18/2023]
Abstract
Molecule-surface collisions are known to initiate dynamics that lead to products inaccessible by thermal chemistry. These collision dynamics, however, have mostly been examined on bulk surfaces, leaving vast opportunities unexplored for molecular collisions on nanostructures, especially on those that exhibit mechanical properties radically different from those of their bulk counterparts. Probing energy-dependent dynamics on nanostructures, particularly for large molecules, has been challenging due to their fast time scales and high structural complexity. Here, by examining the dynamics of a protein impinging on a freestanding, single-atom-thick membrane, we discover molecule-on-trampoline dynamics that disperse the collision impact away from the incident protein within a few picoseconds. As a result, our experiments and ab initio calculations show that cytochrome c retains its gas-phase folded structure when it collides onto freestanding single-layer graphene at low energies (∼20 meV/atom). The molecule-on-trampoline dynamics, expected to be operative on many freestanding atomic membranes, enable reliable means to transfer gas-phase macromolecular structures onto freestanding surfaces for their single-molecule imaging, complementing many bioanalytical techniques.
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Affiliation(s)
- Kelvin Anggara
- Max-Planck
Institute for Solid-State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
| | - Hannah Ochner
- Max-Planck
Institute for Solid-State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
| | - Sven Szilagyi
- Max-Planck
Institute for Solid-State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
| | - Luigi Malavolti
- Max-Planck
Institute for Solid-State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
| | - Stephan Rauschenbach
- Max-Planck
Institute for Solid-State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Klaus Kern
- Max-Planck
Institute for Solid-State Research, Heisenbergstrasse 1, Stuttgart DE-70569, Germany
- Institut
de Physique, École Polytechnique
Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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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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26
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Mass spectrometry of intact membrane proteins: shifting towards a more native-like context. Essays Biochem 2023; 67:201-213. [PMID: 36807530 PMCID: PMC10070488 DOI: 10.1042/ebc20220169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/23/2023]
Abstract
Integral membrane proteins are involved in a plethora of biological processes including cellular signalling, molecular transport, and catalysis. Many of these functions are mediated by non-covalent interactions with other proteins, substrates, metabolites, and surrounding lipids. Uncovering such interactions and deciphering their effect on protein activity is essential for understanding the regulatory mechanisms underlying integral membrane protein function. However, the detection of such dynamic complexes has proven to be challenging using traditional approaches in structural biology. Native mass spectrometry has emerged as a powerful technique for the structural characterisation of membrane proteins and their complexes, enabling the detection and identification of protein-binding partners. In this review, we discuss recent native mass spectrometry-based studies that have characterised non-covalent interactions of membrane proteins in the presence of detergents or membrane mimetics. We additionally highlight recent progress towards the study of membrane proteins within native membranes and provide our perspective on how these could be combined with recent developments in instrumentation to investigate increasingly complex biomolecular systems.
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27
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Schramm HM, Tamadate T, Hogan CJ, Clowers BH. Ion-neutral clustering alters gas-phase hydrogen-deuterium exchange rates. Phys Chem Chem Phys 2023; 25:4959-4968. [PMID: 36722872 DOI: 10.1039/d2cp04388b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The rates and mechanisms of chemical reactions that occur at a phase boundary often differ considerably from chemical behavior in bulk solution, but remain difficult to quantify. Ion-neutral interactions are one such class of chemical reactions whose behavior during the nascent stages of solvation differs from bulk solution while occupying critical roles in aerosol formation, atmospheric chemistry, and gas-phase ion separations. Through a gas-phase ion separation technique utilizing a counter-current flow of deuterated vapor, we quantify the degree of hydrogen-deuterium exchange (HDX) and ion-neutral clustering on a series of model chemical systems (i.e. amino acids). By simultaneously quantifying the degree of vapor association and HDX, the effects of cluster formation on reaction kinetics are realized. These results imply that cluster formation cannot be ignored when modeling complex nucleation processes and biopolymer structural dynamics.
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Affiliation(s)
- Haley M Schramm
- Department of Chemistry, Washington State University, Pullman, WA 99163, USA.
| | - Tomoya Tamadate
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher J Hogan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, WA 99163, USA.
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28
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Salome AZ, Lee KW, Grant T, Westphall MS, Coon JJ. Matrix-Landing Mass Spectrometry for Electron Microscopy Imaging of Native Protein Complexes. Anal Chem 2022; 94:17616-17624. [PMID: 36475605 PMCID: PMC9951558 DOI: 10.1021/acs.analchem.2c04263] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, we described the use of a chemical matrix for landing and preserving the cations of protein-protein complexes within a mass spectrometer (MS) instrument. By use of a glycerol-landing matrix, we used negative stain transmission electron microscopy (TEM) to obtain a three-dimensional (3D) reconstruction of landed GroEL complexes. Here, we investigate the utilities of other chemical matrices for their abilities to land, preserve, and allow for direct imaging of these cationic particles using TEM. We report here that poly(propylene) glycol (PPG) offers superior performance over glycerol for matrix landing. We demonstrated the utility of the PPG matrix landing using three protein-protein complexes─GroEL, the 20S proteasome core particle, and β-galactosidase─and obtained a 3D reconstruction of each complex from matrix-landed particles. These structures have no detectable differences from the structures obtained using conventional preparation methods, suggesting the structures are well preserved at least to the resolution limit of the reconstructions (∼20 Å). We conclude that matrix landing offers a direct approach to couple native MS with TEM for protein structure determination.
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Affiliation(s)
- Austin Z. Salome
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI
| | - Kenneth W. Lee
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI
| | - Timothy Grant
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI
- Morgridge Institute for Research, Madison, WI
| | - Michael S. Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI
- Morgridge Institute for Research, Madison, WI
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29
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Esser TK, Böhning J, Fremdling P, Bharat T, Gault J, Rauschenbach S. Cryo-EM samples of gas-phase purified protein assemblies using native electrospray ion-beam deposition. Faraday Discuss 2022; 240:67-80. [PMID: 36065984 PMCID: PMC9641999 DOI: 10.1039/d2fd00065b] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
An increasing number of studies on biomolecular function indirectly combine mass spectrometry (MS) with imaging techniques such as cryo electron microscopy (cryo-EM). This approach allows information on the homogeneity, stoichiometry, shape, and interactions of native protein complexes to be obtained, complementary to high-resolution protein structures. We have recently demonstrated TEM sample preparation via native electrospray ion-beam deposition (ES-IBD) as a direct link between native MS and cryo-EM. This workflow forms a potential new route to the reliable preparation of homogeneous cryo-EM samples and a better understanding of the relation between native solution-phase and native-like gas-phase structures. However, many aspects of the workflow need to be understood and optimized to obtain performance comparable to that of state-of-the-art cryo-EM. Here, we expand on the previous discussion of key factors by probing the effects of substrate type and deposition energy. We present and discuss micrographs from native ES-IBD samples with amorphous carbon, graphene, and graphene oxide, as well as landing energies in the range between 2 and 150 eV per charge.
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Affiliation(s)
- Tim K. Esser
- Department of Chemistry, University of OxfordOxfordOX1 3TFUK
| | - Jan Böhning
- Sir William Dunn School of Pathology, University of OxfordSouth Parks RoadOxfordOX1 3REUK
| | - Paul Fremdling
- Department of Chemistry, University of OxfordOxfordOX1 3TFUK
| | - Tanmay Bharat
- Sir William Dunn School of Pathology, University of OxfordSouth Parks RoadOxfordOX1 3REUK,Structural Studies Division, MRC Laboratory of Molecular BiologyFrancis Crick AvenueCambridgeCB2 0QHUK
| | - Joseph Gault
- Department of Chemistry, University of OxfordOxfordOX1 3TFUK
| | - Stephan Rauschenbach
- Department of Chemistry, University of OxfordOxfordOX1 3TFUK,Max Planck Institute for Solid State ResearchHeisenbergstrasse 1StuttgartDE-70569Germany
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30
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Brodmerkel MN, De Santis E, Uetrecht C, Caleman C, Marklund EG. Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins. Curr Res Struct Biol 2022; 4:338-348. [PMID: 36440379 PMCID: PMC9685359 DOI: 10.1016/j.crstbi.2022.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/23/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Proteins are innately dynamic, which is important for their functions, but which also poses significant challenges when studying their structures. Gas-phase techniques can utilise separation and a range of sample manipulations to transcend some of the limitations of conventional techniques for structural biology in crystalline or solution phase, and isolate different states for separate interrogation. However, the transfer from solution to the gas phase risks affecting the structures, and it is unclear to what extent different conformations remain distinct in the gas phase, and if resolution in silico can recover the native conformations and their differences. Here, we use extensive molecular dynamics simulations to study the two distinct conformations of dimeric capsid protein of the MS2 bacteriophage. The protein undergoes notable restructuring of its peripheral parts in the gas phase, but subsequent simulation in solvent largely recovers the native structure. Our results suggest that despite some structural loss due to the experimental conditions, gas-phase structural biology techniques provide meaningful data that inform not only about the structures but also conformational dynamics of proteins.
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Affiliation(s)
- Maxim N. Brodmerkel
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, 75123, Sweden
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, 75123, Sweden
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala, 75120, Sweden
| | - Charlotte Uetrecht
- Leibniz Institute of Virology (LIV), Hamburg, 20251, Germany
- Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron, DESY, Notkestrasse 85, Hamburg, 22607, Germany
- School of Life Sciences, University of Siegen, Siegen, Germany
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala, 75120, Sweden
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Erik G. Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, 75123, Sweden
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31
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Borotto NB, Richards TK. Rapid Online Oxidation of Proteins and Peptides via Electrospray-Accelerated Ozonation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2078-2086. [PMID: 36194498 DOI: 10.1021/jasms.2c00182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Mass spectrometry-based analyses of protein conformation continue to grow in utilization due their speed, low sample requirements, and applicability to most protein systems. These techniques typically rely on chemical derivatization of proteins and as with all label-based analyses must ensure the integrity of the protein conformation throughout the duration of the labeling reaction. Hydroxyl radical footprinting of proteins and the recently developed fast fluoroalkylation of proteins attempt to bypass this consideration via rapid reactions that occur on time scales faster than protein folding, but they often require microfluidic setups or electromagnetic radiation sources. In this work, we demonstrate that ozonation of proteins and peptides, which normally occurs in the second to minute time scales, can be accelerated to the submillisecond to millisecond time scale with an electrospray ionization source. This rapid ozonation results in selective labeling of tryptophan and methionine residues. When applied to cytochrome C and carbonic anhydrase, this labeling technique is sensitive to solution conditions and correlates with solution-phase analyses of conformation. While significant work is still needed to characterize this fast chemical labeling strategy, it requires no complicated sample handling, electromagnetic radiation sources, or microfluidic systems outside of the electrospray source and may represent a facile alternative to other rapid labeling technologies that are utilized today.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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32
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Fremdling P, Esser TK, Saha B, Makarov AA, Fort KL, Reinhardt-Szyba M, Gault J, Rauschenbach S. A Preparative Mass Spectrometer to Deposit Intact Large Native Protein Complexes. ACS NANO 2022; 16:14443-14455. [PMID: 36037396 PMCID: PMC9527803 DOI: 10.1021/acsnano.2c04831] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Electrospray ion-beam deposition (ES-IBD) is a versatile tool to study the structure and reactivity of molecules from small metal clusters to large protein assemblies. It brings molecules gently into the gas phase, where they can be accurately manipulated and purified, followed by controlled deposition onto various substrates. In combination with imaging techniques, direct structural information on well-defined molecules can be obtained, which is essential to test and interpret results from indirect mass spectrometry techniques. To date, ion-beam deposition experiments are limited to a small number of custom instruments worldwide, and there are no commercial alternatives. Here we present a module that adds ion-beam deposition capabilities to a popular commercial MS platform (Thermo Scientific Q Exactive UHMR mass spectrometer). This combination significantly reduces the overhead associated with custom instruments, while benefiting from established high performance and reliability. We present current performance characteristics including beam intensity, landing-energy control, and deposition spot size for a broad range of molecules. In combination with atomic force microscopy (AFM) and transmission electron microscopy (TEM), we distinguish near-native from unfolded proteins and show retention of the native shape of protein assemblies after dehydration and deposition. Further, we use an enzymatic assay to quantify the activity of a noncovalent protein complex after deposition on a dry surface. Together, these results not only indicate a great potential of ES-IBD for applications in structural biology, but also outline the challenges that need to be solved for it to reach its full potential.
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Affiliation(s)
- Paul Fremdling
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tim K. Esser
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Bodhisattwa Saha
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Alexander A. 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, Padualaan 8, 3584
CH Utrecht, The Netherlands
| | | | | | - Joseph Gault
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Stephan Rauschenbach
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart 70569, Germany
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33
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Esser TK, Böhning J, Fremdling P, Agasid MT, Costin A, Fort K, Konijnenberg A, Gilbert JD, Bahm A, Makarov A, Robinson CV, Benesch JLP, Baker L, Bharat TAM, Gault J, Rauschenbach S. Mass-selective and ice-free electron cryomicroscopy protein sample preparation via native electrospray ion-beam deposition. PNAS NEXUS 2022; 1:pgac153. [PMID: 36714824 PMCID: PMC9802471 DOI: 10.1093/pnasnexus/pgac153] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/03/2022] [Indexed: 02/01/2023]
Abstract
Despite tremendous advances in sample preparation and classification algorithms for electron cryomicroscopy (cryo-EM) and single-particle analysis (SPA), sample heterogeneity remains a major challenge and can prevent access to high-resolution structures. In addition, optimization of preparation conditions for a given sample can be time-consuming. In the current work, it is demonstrated that native electrospray ion-beam deposition (native ES-IBD) is an alternative, reliable approach for the preparation of extremely high-purity samples, based on mass selection in vacuum. Folded protein ions are generated by native electrospray ionization, separated from other proteins, contaminants, aggregates, and fragments, gently deposited on cryo-EM grids, frozen in liquid nitrogen, and subsequently imaged by cryo-EM. We demonstrate homogeneous coverage of ice-free cryo-EM grids with mass-selected protein complexes. SPA reveals that the complexes remain folded and assembled, but variations in secondary and tertiary structures are currently limiting information in 2D classes and 3D EM density maps. We identify and discuss challenges that need to be addressed to obtain a resolution comparable to that of the established cryo-EM workflow. Our results show the potential of native ES-IBD to increase the scope and throughput of cryo-EM for protein structure determination and provide an essential link between gas-phase and solution-phase protein structures.
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Affiliation(s)
- Tim K Esser
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Mark T Agasid
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Adam Costin
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Kyle Fort
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany
| | - Albert Konijnenberg
- Thermo Fisher Scientific, Zwaanstraat 31G/H, 5651 CA Eindhoven, The Netherlands
| | - Joshua D Gilbert
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alan Bahm
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alexander Makarov
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Lindsay Baker
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Stephan Rauschenbach
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, DE-70569 Stuttgart, Germany
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34
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Jooß K, McGee JP, Kelleher NL. Native Mass Spectrometry at the Convergence of Structural Biology and Compositional Proteomics. Acc Chem Res 2022; 55:1928-1937. [PMID: 35749283 DOI: 10.1021/acs.accounts.2c00216] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ConspectusBiology is driven by a vast set of molecular interactions that evolved over billions of years. Just as covalent modifications like acetylations and phosphorylations can change a protein's function, so too can noncovalent interactions with metals, small molecules, and other proteins. However, much of the language of protein-level biology is left either undiscovered or inferred, as traditional methods used in the field of proteomics use conditions that dissociate noncovalent interactions and denature proteins.Just in the past few years, mass spectrometry (MS) has evolved the capacity to preserve and subsequently characterize the complete composition of endogenous protein complexes. Using this "native" type of mass spectrometry, a complex can be activated to liberate some or all of its subunits, typically via collisions with neutral gas or solid surfaces and isolated before further characterization ("Native Top-Down MS," or nTDMS). The subunit mass, the parent ion mass, and the fragment ions of the activated subunits can be used to piece together the precise molecular composition of the parent complex. When performed en masse in discovery mode (i.e., "native proteomics"), the interactions of life─including protein modifications─will eventually be clarified and linked to dysfunction in human disease states.In this Account, we describe the current and future components of the native MS toolkit, covering the challenges the field faces to characterize ever larger bioassemblies. Each of the three pillars of native proteomics are addressed: (i) separations, (ii) top-down mass spectrometry, and (iii) integration with structural biology. Complexes such as endogenous nucleosomes can be targeted now using nTDMS, whereas virus particles, exosomes, and high-density lipoprotein particles will be tackled in the coming few years. The future work to adequately address the size and complexity of mega- to gigadalton complexes will include native separations, single ion mass spectrometry, and new data types. The use of nTDMS in discovery mode will incorporate native-compatible separation techniques to maximize the number of proteoforms in complexes identified. With a new wave of innovations, both targeted and discovery mode nTDMS will expand to include extremely scarce and exceedingly heterogeneous bioassemblies. Understanding the proteinaceous interactions of life and how they go wrong (e.g., misfolding, forming complexes in dysfunctional stoichiometries and configurations) will not only inform the development of life-restoring therapeutics but also deepen our understanding of life at the molecular level.
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Affiliation(s)
- Kevin Jooß
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - John P McGee
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States.,Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
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