1
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Nouchikian L, Fernandez-Martinez D, Renard PY, Sabot C, Duménil G, Rey M, Chamot-Rooke J. Do Not Waste Time─Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin. Anal Chem 2024; 96:2506-2513. [PMID: 38294351 PMCID: PMC10867798 DOI: 10.1021/acs.analchem.3c04682] [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: 10/17/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) has become a very useful tool for studying protein complexes and interactions in living systems. It enables the investigation of many large and dynamic assemblies in their native state, providing an unbiased view of their protein interactions and restraints for integrative modeling. More researchers are turning toward trying XL-MS to probe their complexes of interest, especially in their native environments. However, due to the presence of other potentially higher abundant proteins, sufficient cross-links on a system of interest may not be reached to achieve satisfactory structural and interaction information. There are currently no rules for predicting whether XL-MS experiments are likely to work or not; in other words, if a protein complex of interest will lead to useful XL-MS data. Here, we show that a simple iBAQ (intensity-based absolute quantification) analysis performed from trypsin digest data can provide a good understanding of whether proteins of interest are abundant enough to achieve successful cross-linking data. Comparing our findings to large-scale data on diverse systems from several other groups, we show that proteins of interest should be at least in the top 20% abundance range to expect more than one cross-link found per protein. We foresee that this guideline is a good starting point for researchers who would like to use XL-MS to study their protein of interest and help ensure a successful cross-linking experiment from the beginning. Data are available via ProteomeXchange with identifier PXD045792.
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Affiliation(s)
- Lucienne Nouchikian
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
| | - David Fernandez-Martinez
- Institut
Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis
of Vascular Infections Unit, Paris 75015, France
| | - Pierre-Yves Renard
- Univ
Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA
UMR 6014, INC3M FR 3038, Rouen F-76000, France
| | - Cyrille Sabot
- Univ
Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA
UMR 6014, INC3M FR 3038, Rouen F-76000, France
| | - Guillaume Duménil
- Institut
Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis
of Vascular Infections Unit, Paris 75015, France
| | - Martial Rey
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
| | - Julia Chamot-Rooke
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
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2
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Keller A, Tang X, Bruce JE. Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS. J Proteome Res 2023; 22:2900-2908. [PMID: 37552582 PMCID: PMC10866149 DOI: 10.1021/acs.jproteome.3c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Chemical cross-linking with mass spectrometry provides low-resolution structural information on proteins in cells and tissues. Combined with quantitation, it can identify changes in the interactome between samples, for example, control and drug-treated cells or young and old mice. A difference can originate from protein conformational changes that alter the solvent-accessible distance separating the cross-linked residues. Alternatively, a difference can result from conformational changes localized to the cross-linked residues, for example, altering the solvent exposure or reactivity of those residues or post-translational modifications of the cross-linked peptides. In this manner, cross-linking is sensitive to a variety of protein conformational features. Dead-end peptides are cross-links attached only at one end to a protein with the other terminus being hydrolyzed. As a result, changes in their abundance reflect only conformational changes localized to the attached residue. For this reason, analyzing both quantified cross-links and their corresponding dead-end peptides can help elucidate the likely conformational changes giving rise to observed differences in cross-link abundance. We describe analysis of dead-end peptides in the XLinkDB public cross-link database and, with quantified mitochondrial data isolated from failing heart versus healthy mice, show how a comparison of abundance ratios between cross-links and their corresponding dead-end peptides can be leveraged to reveal possible conformational explanations.
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Affiliation(s)
- Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105 ,United States
| | - Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105 ,United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105 ,United States
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3
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Keller A, Tang X, Bruce JE. Integrated Analysis of Cross-Links and Dead-End Peptides for Enhanced Interpretation of Quantitative XL-MS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542474. [PMID: 37398466 PMCID: PMC10312474 DOI: 10.1101/2023.05.26.542474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
XL-MS provides low-resolution structural information of proteins in cells and tissues. Combined with quantitation, it can identify changes in the interactome between samples, for example, control and drug-treated cells, or young and old mice. A difference can originate from protein conformational changes altering the solvent-accessible distance separating the cross-linked residues. Alternatively, a difference can result from conformational changes localized to the cross-linked residues, for example, altering the solvent exposure or reactivity of those residues or post-translational modifications on the cross-linked peptides. In this manner, cross-linking is sensitive to a variety of protein conformational features. Dead-end peptides are cross-links attached only at one end to a protein, the other terminus being hydrolyzed. As a result, changes in their abundance reflect only conformational changes localized to the attached residue. For this reason, analyzing both quantified cross-links and their corresponding dead-end peptides can help elucidate the likely conformational changes giving rise to observed differences of cross-link abundance. We describe analysis of dead-end peptides in the XLinkDB public cross-link database and, with quantified mitochondrial data isolated from failing heart versus healthy mice, show how a comparison of abundance ratios between cross-links and their corresponding dead-end peptides can be leveraged to reveal possible conformational explanations.
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4
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Chen ZA, Rappsilber J. Protein structure dynamics by crosslinking mass spectrometry. Curr Opin Struct Biol 2023; 80:102599. [PMID: 37104977 DOI: 10.1016/j.sbi.2023.102599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023]
Abstract
Crosslinking mass spectrometry captures protein structures in solution. The crosslinks reveal spatial proximities as distance restraints, but do not easily reveal which of these restraints derive from the same protein conformation. This superposition can be reduced by photo-crosslinking, and adding information from protein structure models, or quantitative crosslinking reveals conformation-specific crosslinks. As a consequence, crosslinking MS has proven useful already in the context of multiple dynamic protein systems. We foresee a breakthrough in the resolution and scale of studying protein dynamics when crosslinks are used to guide deep-learning-based protein modelling. Advances in crosslinking MS, such as photoactivatable crosslinking and in-situ crosslinking, will then reveal protein conformation dynamics in the cellular context, at a pseudo-atomic resolution, and plausibly in a time-resolved manner.
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Affiliation(s)
- Zhuo Angel Chen
- Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany
| | - Juri Rappsilber
- Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany; Si-M/"Der Simulierte Mensch", a Science Framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, 10623 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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5
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Caudal A, Tang X, Chavez JD, Keller A, Mohr JP, Bakhtina AA, Villet O, Chen H, Zhou B, Walker MA, Tian R, Bruce JE. Mitochondrial interactome quantitation reveals structural changes in metabolic machinery in the failing murine heart. NATURE CARDIOVASCULAR RESEARCH 2022; 1:855-866. [PMID: 36405497 PMCID: PMC9667921 DOI: 10.1038/s44161-022-00127-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/02/2022] [Indexed: 11/09/2022]
Abstract
Advancements in cross-linking mass spectrometry (XL-MS) bridge the gap between purified systems and native tissue environments, allowing the detection of protein structural interactions in their native state. Here we use isobaric quantitative protein interaction reporter technology (iqPIR) to compare the mitochondria protein interactomes in healthy and hypertrophic murine hearts, 4 weeks post-transaortic constriction. The failing heart interactome includes 588 statistically significant cross-linked peptide pairs altered in the disease condition. We observed an increase in the assembly of ketone oxidation oligomers corresponding to an increase in ketone metabolic utilization; remodeling of NDUA4 interaction in Complex IV, likely contributing to impaired mitochondria respiration; and conformational enrichment of ADP/ATP carrier ADT1, which is non-functional for ADP/ATP translocation but likely possesses non-selective conductivity. Our application of quantitative cross-linking technology in cardiac tissue provides molecular-level insights into the complex mitochondria remodeling in heart failure while bringing forth new hypotheses for pathological mechanisms.
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Affiliation(s)
- Arianne Caudal
- Department of Biochemistry, Department of Anesthesiology & Pain Medicine, University of Washington
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
- These authors contributed equally
| | - Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
- These authors contributed equally
| | - Juan D. Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Jared P. Mohr
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Anna A. Bakhtina
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Outi Villet
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
| | - Hongye Chen
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
| | - Bo Zhou
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
| | - Matthew A. Walker
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
| | - Rong Tian
- Department of Biochemistry, Department of Anesthesiology & Pain Medicine, University of Washington
- Mitochondria and Metabolism Center, Department of Anesthesiology & Pain Medicine, University of Washington
- These authors jointly supervised this work
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
- These authors jointly supervised this work
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6
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Yu C, Wang X, Huang L. Developing a Targeted Quantitative Strategy for Sulfoxide-Containing MS-Cleavable Cross-Linked Peptides to Probe Conformational Dynamics of Protein Complexes. Anal Chem 2022; 94:4390-4398. [PMID: 35193351 DOI: 10.1021/acs.analchem.1c05298] [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
In recent years, cross-linking mass spectrometry (XL-MS) has made enormous strides as a technology for probing protein-protein interactions (PPIs) and elucidating architectures of multisubunit assemblies. To define conformational and interaction dynamics of protein complexes under different physiological conditions, various quantitative cross-linking mass spectrometry (QXL-MS) strategies based on stable isotope labeling have been developed. These QXL-MS approaches have effectively allowed comparative analysis of cross-links to determine their relative abundance changes at global scales. Although successful, it remains challenging to consistently obtain quantitative measurements on low-abundant cross-links. Therefore, targeted QXL-MS is needed to enable MS "Western" analysis of cross-links to enhance sensitivity and reliability in quantitation. To this end, we have established a robust parallel reaction monitoring (PRM)-based targeted QXL-MS platform using sulfoxide-containing MS-cleavable cross-linker disuccinimidyl sulfoxide (DSSO), permitting label-free comparative analysis of selected cross-links across multiple samples. In addition, we have applied this methodology to study phosphorylation-dependent conformational dynamics of the human 26S proteasome. The PRM-based targeted QXL-MS analytical platform described here is applicable for all sulfoxide-containing MS-cleavable cross-linkers and can be directly adopted for comparative studies of protein-protein interactions in various cellular contexts.
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Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Medical Science I, D233, Irvine, California 92697-4560, United States
| | - Xiaorong Wang
- Department of Physiology & Biophysics, University of California, Irvine, Medical Science I, D233, Irvine, California 92697-4560, United States
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Medical Science I, D233, Irvine, California 92697-4560, United States
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7
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Wippel HH, Chavez JD, Tang X, Bruce JE. Quantitative interactome analysis with chemical cross-linking and mass spectrometry. Curr Opin Chem Biol 2022; 66:102076. [PMID: 34393043 PMCID: PMC8837725 DOI: 10.1016/j.cbpa.2021.06.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 01/03/2023]
Abstract
Structural plasticity and dynamic protein-protein interactions are critical determinants of protein function within living systems. Quantitative chemical cross-linking with mass spectrometry (qXL-MS) is an emerging technology able to provide information on changes in protein conformations and interactions. Importantly, qXL-MS is applicable to complex biological systems, including living cells and tissues, thereby providing insights into proteins within their native environments. Here, we present an overview of recent technological developments and applications involving qXL-MS, including design and synthesis of isotope-labeled cross-linkers, development of new liquid chromatography-MS methodologies, and computational developments enabling interpretation of the data.
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Affiliation(s)
- Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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8
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Graziadei A, Rappsilber J. Leveraging crosslinking mass spectrometry in structural and cell biology. Structure 2021; 30:37-54. [PMID: 34895473 DOI: 10.1016/j.str.2021.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/11/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022]
Abstract
Crosslinking mass spectrometry (crosslinking-MS) is a versatile tool providing structural insights into protein conformation and protein-protein interactions. Its medium-resolution residue-residue distance restraints have been used to validate protein structures proposed by other methods and have helped derive models of protein complexes by integrative structural biology approaches. The use of crosslinking-MS in integrative approaches is underpinned by progress in estimating error rates in crosslinking-MS data and in combining these data with other information. The flexible and high-throughput nature of crosslinking-MS has allowed it to complement the ongoing resolution revolution in electron microscopy by providing system-wide residue-residue distance restraints, especially for flexible regions or systems. Here, we review how crosslinking-MS information has been leveraged in structural model validation and integrative modeling. Crosslinking-MS has also been a key technology for cell biology studies and structural systems biology where, in conjunction with cryoelectron tomography, it can provide structural and mechanistic insights directly in situ.
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Affiliation(s)
- Andrea Graziadei
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK.
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9
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Chavez JD, Wippel HH, Tang X, Keller A, Bruce JE. In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology. Chem Rev 2021; 122:7647-7689. [PMID: 34232610 PMCID: PMC8966414 DOI: 10.1021/acs.chemrev.1c00223] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Biological systems have evolved to utilize proteins to accomplish nearly all functional roles needed to sustain life. A majority of biological functions occur within the crowded environment inside cells and subcellular compartments where proteins exist in a densely packed complex network of protein-protein interactions. The structural biology field has experienced a renaissance with recent advances in crystallography, NMR, and CryoEM that now produce stunning models of large and complex structures previously unimaginable. Nevertheless, measurements of such structural detail within cellular environments remain elusive. This review will highlight how advances in mass spectrometry, chemical labeling, and informatics capabilities are merging to provide structural insights on proteins, complexes, and networks that exist inside cells. Because of the molecular detection specificity provided by mass spectrometry and proteomics, these approaches provide systems-level information that not only benefits from conventional structural analysis, but also is highly complementary. Although far from comprehensive in their current form, these approaches are currently providing systems structural biology information that can uniquely reveal how conformations and interactions involving many proteins change inside cells with perturbations such as disease, drug treatment, or phenotypic differences. With continued advancements and more widespread adaptation, systems structural biology based on in-cell labeling and mass spectrometry will provide an even greater wealth of structural knowledge.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
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10
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Kalathiya U, Padariya M, Faktor J, Coyaud E, Alfaro JA, Fahraeus R, Hupp TR, Goodlett DR. Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS). Biomolecules 2021; 11:382. [PMID: 33806612 PMCID: PMC8001575 DOI: 10.3390/biom11030382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/28/2022] Open
Abstract
The fundamentals of how protein-protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein-protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.
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Affiliation(s)
- Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Etienne Coyaud
- Protéomique Réponse Inflammatoire Spectrométrie de Mass—PRISM, Inserm U1192, University Lille, CHU Lille, F-59000 Lille, France;
| | - Javier A. Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
| | - Ted R. Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
| | - David R. Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (M.P.); (J.F.); (J.A.A.); (R.F.); (T.R.H.)
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC V8Z 7X8, Canada
- Genome BC Proteome Centre, University of Victoria, Victoria, BC V8Z 5N3, Canada
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11
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Tang X, Wippel HH, Chavez JD, Bruce JE. Crosslinking mass spectrometry: A link between structural biology and systems biology. Protein Sci 2021; 30:773-784. [PMID: 33594738 DOI: 10.1002/pro.4045] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022]
Abstract
Protein structure underpins functional roles in all biological processes; therefore, improved understanding of protein structures is of fundamental importance in nearly all biological and biomedical research areas. Traditional techniques such as X-ray crystallography and more recently, cryo-EM, can reveal structural features on isolated proteins/protein complexes at atomic resolution level and have become indispensable tools for structural biology. Crosslinking mass spectrometry (XL-MS), on the other hand, is an emerging technique capable of capturing transient and dynamic information on protein interactions and assemblies in their native environment. The combination of XL-MS with traditional techniques holds potential for bridging the gap between structural biology and systems biology approaches. Such a combination will enable visualization of protein structures and interactions within the crowded macromolecular environment in living systems that can dramatically increase understanding of biological functions. In this review, we first discuss general strategies of XL-MS and then survey recent examples to show how qualitative and quantitative XL-MS studies can be integrated with available protein structural data to better understand biological function at systems level.
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Affiliation(s)
- Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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12
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Swamy KBS, Schuyler SC, Leu JY. Protein Complexes Form a Basis for Complex Hybrid Incompatibility. Front Genet 2021; 12:609766. [PMID: 33633780 PMCID: PMC7900514 DOI: 10.3389/fgene.2021.609766] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/20/2021] [Indexed: 12/20/2022] Open
Abstract
Proteins are the workhorses of the cell and execute many of their functions by interacting with other proteins forming protein complexes. Multi-protein complexes are an admixture of subunits, change their interaction partners, and modulate their functions and cellular physiology in response to environmental changes. When two species mate, the hybrid offspring are usually inviable or sterile because of large-scale differences in the genetic makeup between the two parents causing incompatible genetic interactions. Such reciprocal-sign epistasis between inter-specific alleles is not limited to incompatible interactions between just one gene pair; and, usually involves multiple genes. Many of these multi-locus incompatibilities show visible defects, only in the presence of all the interactions, making it hard to characterize. Understanding the dynamics of protein-protein interactions (PPIs) leading to multi-protein complexes is better suited to characterize multi-locus incompatibilities, compared to studying them with traditional approaches of genetics and molecular biology. The advances in omics technologies, which includes genomics, transcriptomics, and proteomics can help achieve this end. This is especially relevant when studying non-model organisms. Here, we discuss the recent progress in the understanding of hybrid genetic incompatibility; omics technologies, and how together they have helped in characterizing protein complexes and in turn multi-locus incompatibilities. We also review advances in bioinformatic techniques suitable for this purpose and propose directions for leveraging the knowledge gained from model-organisms to identify genetic incompatibilities in non-model organisms.
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Affiliation(s)
- Krishna B. S. Swamy
- Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Scott C. Schuyler
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Head and Neck Surgery, Department of Otolaryngology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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13
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Mendes ML, Fischer L, Chen ZA, Barbon M, O'Reilly FJ, Giese SH, Bohlke-Schneider M, Belsom A, Dau T, Combe CW, Graham M, Eisele MR, Baumeister W, Speck C, Rappsilber J. An integrated workflow for crosslinking mass spectrometry. Mol Syst Biol 2020; 15:e8994. [PMID: 31556486 PMCID: PMC6753376 DOI: 10.15252/msb.20198994] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 11/09/2022] Open
Abstract
We present a concise workflow to enhance the mass spectrometric detection of crosslinked peptides by introducing sequential digestion and the crosslink identification software xiSEARCH. Sequential digestion enhances peptide detection by selective shortening of long tryptic peptides. We demonstrate our simple 12‐fraction protocol for crosslinked multi‐protein complexes and cell lysates, quantitative analysis, and high‐density crosslinking, without requiring specific crosslinker features. This overall approach reveals dynamic protein–protein interaction sites, which are accessible, have fundamental functional relevance and are therefore ideally suited for the development of small molecule inhibitors.
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Affiliation(s)
- Marta L Mendes
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Lutz Fischer
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Zhuo A Chen
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Marta Barbon
- MRC London Institute of Medical Sciences (LMS), London, UK.,DNA Replication Group, Faculty of Medicine, Institute of Clinical Sciences (ICS), Imperial College London, London, UK
| | - Francis J O'Reilly
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Sven H Giese
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | | | - Adam Belsom
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Therese Dau
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Colin W Combe
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Martin Graham
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Markus R Eisele
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christian Speck
- MRC London Institute of Medical Sciences (LMS), London, UK.,DNA Replication Group, Faculty of Medicine, Institute of Clinical Sciences (ICS), Imperial College London, London, UK
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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14
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Müller F, Rappsilber J. A protocol for studying structural dynamics of proteins by quantitative crosslinking mass spectrometry and data-independent acquisition. J Proteomics 2020; 218:103721. [PMID: 32109607 DOI: 10.1016/j.jprot.2020.103721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/13/2019] [Accepted: 02/24/2020] [Indexed: 10/24/2022]
Abstract
Quantitative crosslinking mass spectrometry (QCLMS) reveals structural details of protein conformations in solution. QCLMS can benefit from data-independent acquisition (DIA), which maximises accuracy, reproducibility and throughput of the approach. This DIA-QCLMS protocol comprises of three main sections: sample preparation, spectral library generation and quantitation. The DIA-QCLMS workflow supports isotope-labelling as well as label-free quantitation strategies, uses xiSEARCH for crosslink identification, and xiDIA-Library to create a spectral library for a peptide-centric quantitative approach. We integrated Spectronaut, a leading quantitation software, to analyse DIA data. Spectronaut supports DIA-QCLMS data to quantify crosslinks. It can be used to reveal the structural dynamics of proteins and protein complexes, even against a complex background. In combination with photoactivatable crosslinkers (photo-DIA-QCLMS), the workflow can increase data density and better capture protein dynamics due to short reaction times. Additionally, this can reveal conformational changes caused by environmental influences that would otherwise affect crosslinking itself, such as changing pH conditions. SIGNIFICANCE: This protocol is an detailed step-by-step description on how to implement our previously published DIA-QCLMS workflow (Müller et al. Mol Cell Proteomics. 2019 Apr;18(4):786-795). It includes sample preparation for QCLMS, Optimization of DIA strategies, implementation of the Spectronaut software and required python scripts and guideline on how to analyse quantitative crosslinking data. The DIA-QCLMS workflow widen the scope for a range of new crosslinking applications and this step-by-step protocol enhances the accessibility to a broad scientific user base.
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Affiliation(s)
- Fränze Müller
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom.
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15
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Mintseris J, Gygi SP. High-density chemical cross-linking for modeling protein interactions. Proc Natl Acad Sci U S A 2020; 117:93-102. [PMID: 31848235 PMCID: PMC6955236 DOI: 10.1073/pnas.1902931116] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Detailed mechanistic understanding of protein complex function is greatly enhanced by insights from its 3-dimensional structure. Traditional methods of protein structure elucidation remain expensive and labor-intensive and require highly purified starting material. Chemical cross-linking coupled with mass spectrometry offers an alternative that has seen increased use, especially in combination with other experimental approaches like cryo-electron microscopy. Here we report advances in method development, combining several orthogonal cross-linking chemistries as well as improvements in search algorithms, statistical analysis, and computational cost to achieve coverage of 1 unique cross-linked position pair for every 7 amino acids at a 1% false discovery rate. This is accomplished without any peptide-level fractionation or enrichment. We apply our methods to model the complex between a carbonic anhydrase (CA) and its protein inhibitor, showing that the cross-links are self-consistent and define the interaction interface at high resolution. The resulting model suggests a scaffold for development of a class of protein-based inhibitors of the CA family of enzymes. We next cross-link the yeast proteasome, identifying 3,893 unique cross-linked peptides in 3 mass spectrometry runs. The dataset includes 1,704 unique cross-linked position pairs for the proteasome subunits, more than half of them intersubunit. Using multiple recently solved cryo-EM structures, we show that observed cross-links reflect the conformational dynamics and disorder of some proteasome subunits. We further demonstrate that this level of cross-linking density is sufficient to model the architecture of the 19-subunit regulatory particle de novo.
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Affiliation(s)
- Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
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16
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Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review. Comput Struct Biotechnol J 2019; 17:805-811. [PMID: 31316724 PMCID: PMC6611912 DOI: 10.1016/j.csbj.2019.05.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 01/06/2023] Open
Abstract
Studying protein-protein interaction networks provide key evidence for the underlying molecular mechanisms. Mass spectrometry-based proteomic approaches have been playing a pivotal role in deciphering these interaction networks, along with precise quantification for individual interactions. In this mini-review we discuss the available techniques and methods for qualitative and quantitative elucidation of protein-protein interaction networks. We then summarize the down-stream computational strategies for identification and quantification of interactions from those techniques. Finally, we highlight the challenges and limitations of current computational pipelines in eliminating false positive interactors, followed by a summary of the innovative algorithms to address these issues, along with the scope for future improvements.
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17
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Chen ZA, Rappsilber J. Quantitative cross-linking/mass spectrometry to elucidate structural changes in proteins and their complexes. Nat Protoc 2019; 14:171-201. [PMID: 30559374 DOI: 10.1038/s41596-018-0089-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantitative cross-linking/mass spectrometry (QCLMS/QXL-MS) probes structural changes of proteins in solution. This method has revealed induced conformational changes, composition shifts in conformational ensembles and changes in protein interactions. It illuminates different structural states of proteins or protein complexes by comparing which residue pairs can be cross-linked in these states. Cross-links provide information about structural changes that may be inaccessible by alternative technologies. Small local conformational changes affect relative abundances of nearby cross-links, whereas larger conformational changes cause new cross-links to be formed. Distinguishing between minor and major changes requires a robust analysis based on carefully selected replicates and, when using isotope-labeled cross-linkers, replicated analysis with a permutated isotope-labeling scheme. A label-free workflow allows for application of a wide range of cross-linking chemistries and enables parallel comparison of multiple conformations. In this protocol, we demonstrate both label-free and isotope-labeled cross-linker-based workflows using the cross-linker bis(sulfosuccinimidyl)suberate (BS3). The software XiSearch, developed by our group, is used to identify cross-linked residue pairs, although the workflow is not limited to this search software. The open-access software Skyline is used for automated quantitation. Note that additional manual correction greatly enhances quantitation accuracy. The protocol has been applied to purified multi-protein complexes but is not necessarily limited to that level of sample complexity. Optimizing the cross-linker/protein ratio and fractionating peptides increase the data density of quantified cross-links, and thus the resolution of QCLMS. The entire procedure takes ~1-3 weeks.
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Affiliation(s)
- Zhuo A Chen
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany. .,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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18
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McDonald AJ, Leon DR, Markham KA, Wu B, Heckendorf CF, Schilling K, Showalter HD, Andrews PC, McComb ME, Pushie MJ, Costello CE, Millhauser GL, Harris DA. Altered Domain Structure of the Prion Protein Caused by Cu 2+ Binding and Functionally Relevant Mutations: Analysis by Cross-Linking, MS/MS, and NMR. Structure 2019; 27:907-922.e5. [PMID: 30956132 DOI: 10.1016/j.str.2019.03.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/17/2019] [Accepted: 03/14/2019] [Indexed: 12/24/2022]
Abstract
The cellular isoform of the prion protein (PrPC) serves as precursor to the infectious isoform (PrPSc), and as a cell-surface receptor, which binds misfolded protein oligomers as well as physiological ligands such as Cu2+ ions. PrPC consists of two domains: a flexible N-terminal domain and a structured C-terminal domain. Both the physiological and pathological functions of PrP depend on intramolecular interactions between these two domains, but the specific amino acid residues involved have proven challenging to define. Here, we employ a combination of chemical cross-linking, mass spectrometry, NMR, molecular dynamics simulations, and functional assays to identify residue-level contacts between the N- and C-terminal domains of PrPC. We also determine how these interdomain contacts are altered by binding of Cu2+ ions and by functionally relevant mutations. Our results provide a structural basis for interpreting both the normal and toxic activities of PrP.
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Affiliation(s)
- Alex J McDonald
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Deborah R Leon
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kathleen A Markham
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bei Wu
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Christian F Heckendorf
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kevin Schilling
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hollis D Showalter
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Philip C Andrews
- Department of Biological Chemistry, Department of Chemistry, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark E McComb
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, USA
| | - M Jake Pushie
- Department of Surgery, Division of Neurosurgery, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Catherine E Costello
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
| | - David A Harris
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA.
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19
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Müller F, Kolbowski L, Bernhardt OM, Reiter L, Rappsilber J. Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry. Mol Cell Proteomics 2019; 18:786-795. [PMID: 30651306 PMCID: PMC6442367 DOI: 10.1074/mcp.tir118.001276] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Indexed: 11/24/2022] Open
Abstract
Quantitative cross-linking mass spectrometry (QCLMS) reveals structural detail on altered protein states in solution. On its way to becoming a routine technology, QCLMS could benefit from data-independent acquisition (DIA), which generally enables greater reproducibility than data-dependent acquisition (DDA) and increased throughput over targeted methods. Therefore, here we introduce DIA to QCLMS by extending a widely used DIA software, Spectronaut, to also accommodate cross-link data. A mixture of seven proteins cross-linked with bis[sulfosuccinimidyl] suberate (BS3) was used to evaluate this workflow. Out of the 414 identified unique residue pairs, 292 (70%) were quantifiable across triplicates with a coefficient of variation (CV) of 10%, with manual correction of peak selection and boundaries for PSMs in the lower quartile of individual CV values. This compares favorably to DDA where we quantified cross-links across triplicates with a CV of 66%, for a single protein. We found DIA-QCLMS to be capable of detecting changing abundances of cross-linked peptides in complex mixtures, despite the ratio compression encountered when increasing sample complexity through the addition of E. coli cell lysate as matrix. In conclusion, the DIA software Spectronaut can now be used in cross-linking and DIA is indeed able to improve QCLMS.
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Affiliation(s)
- Fränze Müller
- From the ‡Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Lars Kolbowski
- From the ‡Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany;; §Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom
| | | | | | - Juri Rappsilber
- From the ‡Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany;; §Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom;.
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20
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Giese SH, Belsom A, Sinn L, Fischer L, Rappsilber J. Noncovalently Associated Peptides Observed during Liquid Chromatography-Mass Spectrometry and Their Effect on Cross-Link Analyses. Anal Chem 2019; 91:2678-2685. [PMID: 30649854 PMCID: PMC6396951 DOI: 10.1021/acs.analchem.8b04037] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/16/2019] [Indexed: 12/14/2022]
Abstract
Cross-linking mass spectrometry draws structural information from covalently linked peptide pairs. When these links do not match to previous structural models, they may indicate changes in protein conformation. Unfortunately, such links can also be the result of experimental error or artifacts. Here, we describe the observation of noncovalently associated peptides during liquid chromatography-mass spectrometry analysis, which can easily be misidentified as cross-linked. Strikingly, they often mismatch to the protein structure. Noncovalently associated peptides presumably form during ionization and can be distinguished from cross-linked peptides by observing coelution of the corresponding linear peptides in MS1 spectra, as well as the presence of the individual (intact) peptide fragments in MS2 spectra. To suppress noncovalent peptide formations, increasingly disruptive ionization settings can be used, such as in-source fragmentation.
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Affiliation(s)
- Sven H. Giese
- Bioanalytics,
Institute of Biotechnology, Technische Universität
Berlin, 13355 Berlin, Germany
| | - Adam Belsom
- Bioanalytics,
Institute of Biotechnology, Technische Universität
Berlin, 13355 Berlin, Germany
- Wellcome
Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH93BF, United Kingdom
| | - Ludwig Sinn
- Bioanalytics,
Institute of Biotechnology, Technische Universität
Berlin, 13355 Berlin, Germany
| | - Lutz Fischer
- Bioanalytics,
Institute of Biotechnology, Technische Universität
Berlin, 13355 Berlin, Germany
- Wellcome
Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH93BF, United Kingdom
| | - Juri Rappsilber
- Bioanalytics,
Institute of Biotechnology, Technische Universität
Berlin, 13355 Berlin, Germany
- Wellcome
Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH93BF, United Kingdom
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21
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Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology. Nat Struct Mol Biol 2018; 25:1000-1008. [PMID: 30374081 DOI: 10.1038/s41594-018-0147-0] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/19/2018] [Indexed: 01/11/2023]
Abstract
Over the past decade, cross-linking mass spectrometry (CLMS) has developed into a robust and flexible tool that provides medium-resolution structural information. CLMS data provide a measure of the proximity of amino acid residues and thus offer information on the folds of proteins and the topology of their complexes. Here, we highlight notable successes of this technique as well as common pipelines. Novel CLMS applications, such as in-cell cross-linking, probing conformational changes and tertiary-structure determination, are now beginning to make contributions to molecular biology and the emerging fields of structural systems biology and interactomics.
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22
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Chen ZA, Rappsilber J. Protein Dynamics in Solution by Quantitative Crosslinking/Mass Spectrometry. Trends Biochem Sci 2018; 43:908-920. [PMID: 30318267 PMCID: PMC6240160 DOI: 10.1016/j.tibs.2018.09.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/20/2018] [Accepted: 09/12/2018] [Indexed: 01/09/2023]
Abstract
The dynamics of protein structures and their interactions are responsible for many cellular processes. The rearrangements and interactions of proteins, which are often transient, occur in solution and may require a biological environment that is difficult to maintain in traditional structural biological approaches. Quantitative crosslinking/mass spectrometry (QCLMS) has emerged as an excellent method to fill this gap. Numerous recent applications of the technique have demonstrated that protein dynamics can now be studied in solution at sufficient resolution to gain valuable biological insights, suggesting that extending these investigations to native environments is possible. These breakthroughs have been based on the maturation of CLMS at large, and its recent fusion with quantitative proteomics. We provide here an overview of the current state of the technique, the available workflows and their applications, and remaining challenges. In-solution dynamics of protein structures and their interactions can be studied by QCLMS. Successful applications of QCLMS provide insights into multiple different biological processes. Recent advances in QCLMS allow analyses in the context of native cellular environments, including living cells. Alternative workflows allow researchers to tailor the analysis to their biological question. Progress in data processing now offers this technique to researchers with limited initial expertise in crosslinking and quantitative proteomics.
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Affiliation(s)
- Zhuo A Chen
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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23
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Chavez JD, Bruce JE. Chemical cross-linking with mass spectrometry: a tool for systems structural biology. Curr Opin Chem Biol 2018; 48:8-18. [PMID: 30172868 DOI: 10.1016/j.cbpa.2018.08.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 01/14/2023]
Abstract
Biological processes supporting life are orchestrated by a highly dynamic array of protein structures and interactions comprising the interactome. Defining the interactome, visualizing how structures and interactions change and function to support life is essential to improved understanding of fundamental molecular processes, but represents a challenge unmet by any single analytical technique. Chemical cross-linking with mass spectrometry provides identification of proximal amino acid residues within proteins and protein complexes, yielding low resolution structural information. This approach has predominantly been employed to provide structural insight on isolated protein complexes, and has been particularly useful for molecules that are recalcitrant to conventional structural biology studies. Here we discuss recent developments in cross-linking and mass spectrometry technologies that are providing large-scale or systems-level interactome data with successful applications to isolated organelles, cell lysates, virus particles, intact bacterial and mammalian cultured cells and tissue samples.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
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24
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Politis A, Schmidt C. Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling. J Proteomics 2018; 175:34-41. [DOI: 10.1016/j.jprot.2017.04.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 01/14/2023]
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25
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Müller F, Fischer L, Chen ZA, Auchynnikava T, Rappsilber J. On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:405-412. [PMID: 29256016 PMCID: PMC5814520 DOI: 10.1007/s13361-017-1837-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/14/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between multiple cross-linking reactions using bis[sulfosuccinimidyl] suberate (BS3)-cross-linked human serum albumin (HSA) and evaluated how reproducible cross-linked peptides can be identified and quantified by LC-MS analysis. To make QCLMS accessible to a broader research community, we developed a workflow that integrates the established software tools MaxQuant for spectra preprocessing, Xi for cross-linked peptide identification, and finally Skyline for quantification (MS1 filtering). Out of the 221 unique residue pairs identified in our sample, 124 were subsequently quantified across 10 analyses with coefficient of variation (CV) values of 14% (injection replica) and 32% (reaction replica). Thus our results demonstrate that the reproducibility of QCLMS is in line with the reproducibility of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Fränze Müller
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355, Berlin, Germany
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, EH9 3BF, UK
| | - Lutz Fischer
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, EH9 3BF, UK
| | - Zhuo Angel Chen
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355, Berlin, Germany
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, EH9 3BF, UK
| | - Tania Auchynnikava
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, EH9 3BF, UK
| | - Juri Rappsilber
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355, Berlin, Germany.
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, EH9 3BF, UK.
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26
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Protein Tertiary Structure by Crosslinking/Mass Spectrometry. Trends Biochem Sci 2018; 43:157-169. [PMID: 29395654 PMCID: PMC5854373 DOI: 10.1016/j.tibs.2017.12.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/21/2022]
Abstract
Observing the structures of proteins within the cell and tracking structural changes under different cellular conditions are the ultimate challenges for structural biology. This, however, requires an experimental technique that can generate sufficient data for structure determination and is applicable in the native environment of proteins. Crosslinking/mass spectrometry (CLMS) and protein structure determination have recently advanced to meet these requirements and crosslinking-driven de novo structure determination in native environments is now possible. In this opinion article, we highlight recent successes in the field of CLMS with protein structure modeling and challenges it still holds. The earliest structural studies on proteins using crosslinking/mass spectrometry aimed to elucidate their tertiary three-dimensional structure. Tertiary structure modeling using crosslinking fell out of favor for almost two decades because crosslink data were not informative to aid structure modeling. Two game-changing trends emerged: using short-range crosslinkers that capture relevant modeling information and high-density crosslinking. High-density crosslinking uses unspecific crosslinkers to dramatically increase crosslink numbers. In addition, computational structure modeling methods made significant progress in exploiting CLMS data. The combination of high-density crosslinking and computational structure modeling enables the elucidation of tertiary protein structure in native environments. This sidesteps the key limitation of today’s structure determination methods, which are unable (except for a few, specialized methods) to probe the structure of proteins in cell lysates or even intact cells.
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27
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Chen ZA, Fischer L, Cox J, Rappsilber J. Quantitative Cross-linking/Mass Spectrometry Using Isotope-labeled Cross-linkers and MaxQuant. Mol Cell Proteomics 2016; 15:2769-78. [PMID: 27302889 PMCID: PMC4974350 DOI: 10.1074/mcp.m115.056481] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 12/20/2022] Open
Abstract
The conceptually simple step from cross-linking/mass spectrometry (CLMS) to quantitative cross-linking/mass spectrometry (QCLMS) is compounded by technical challenges. Currently, quantitative proteomics software is tightly integrated with the protein identification workflow. This prevents automatically quantifying other m/z features in a targeted manner including those associated with cross-linked peptides. Here we present a new release of MaxQuant that permits starting the quantification process from an m/z feature list. Comparing the automated quantification to a carefully manually curated test set of cross-linked peptides obtained by cross-linking C3 and C3b with BS3 and isotope-labeled BS3-d4 revealed a number of observations: (1) Fully automated process using MaxQuant can quantify cross-links in our reference data set with 68% recall rate and 88% accuracy. (2) Hidden quantification errors can be converted into exposed failures by label-swap replica, which makes label-swap replica an essential part of QCLMS. (3) Cross-links that failed during automated quantification can be recovered by semi-automated re-quantification. The integrated workflow of MaxQuant and semi-automated assessment provides the maximum of quantified cross-links. In contrast, work on larger data sets or by less experienced users will benefit from full automation in MaxQuant.
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Affiliation(s)
- Zhuo A Chen
- From the ‡Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Lutz Fischer
- From the ‡Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jürgen Cox
- §Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Juri Rappsilber
- From the ‡Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; ¶Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
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Chen ZA, Pellarin R, Fischer L, Sali A, Nilges M, Barlow PN, Rappsilber J. Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling. Mol Cell Proteomics 2016; 15:2730-43. [PMID: 27250206 PMCID: PMC4974347 DOI: 10.1074/mcp.m115.056473] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 11/30/2022] Open
Abstract
The slow but spontaneous and ubiquitous formation of C3(H2O), the hydrolytic and conformationally rearranged product of C3, initiates antibody-independent activation of the complement system that is a key first line of antimicrobial defense. The structure of C3(H2O) has not been determined. Here we subjected C3(H2O) to quantitative cross-linking/mass spectrometry (QCLMS). This revealed details of the structural differences and similarities between C3(H2O) and C3, as well as between C3(H2O) and its pivotal proteolytic cleavage product, C3b, which shares functionally similarity with C3(H2O). Considered in combination with the crystal structures of C3 and C3b, the QCMLS data suggest that C3(H2O) generation is accompanied by the migration of the thioester-containing domain of C3 from one end of the molecule to the other. This creates a stable C3b-like platform able to bind the zymogen, factor B, or the regulator, factor H. Integration of available crystallographic and QCLMS data allowed the determination of a 3D model of the C3(H2O) domain architecture. The unique arrangement of domains thus observed in C3(H2O), which retains the anaphylatoxin domain (that is excised when C3 is enzymatically activated to C3b), can be used to rationalize observed differences between C3(H2O) and C3b in terms of complement activation and regulation.
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Affiliation(s)
- Zhuo A Chen
- From the ‡Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Riccardo Pellarin
- §Unité de Bioinformatique Structurale, CNRS UMR 3528, Institut Pasteur, 75015 Paris, France; ¶Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, California 94158, United States
| | - Lutz Fischer
- From the ‡Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Andrej Sali
- ¶Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, California 94158, United States
| | - Michael Nilges
- §Unité de Bioinformatique Structurale, CNRS UMR 3528, Institut Pasteur, 75015 Paris, France
| | - Paul N Barlow
- ‖Schools of Chemistry and Biological Sciences, University of Edinburgh, Edinburgh EH9 3JJ, UK;
| | - Juri Rappsilber
- From the ‡Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; **Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
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