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Makepeace KAT, Mohammed Y, Rudashevskaya EL, Petrotchenko EV, Vögtle FN, Meisinger C, Sickmann A, Borchers CH. Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker. Mol Cell Proteomics 2020; 19:624-639. [PMID: 32051233 PMCID: PMC7124466 DOI: 10.1074/mcp.ra119.001839] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/17/2020] [Indexed: 12/24/2022] Open
Abstract
An experimental and computational approach for identification of protein-protein interactions by ex vivo chemical crosslinking and mass spectrometry (CLMS) has been developed that takes advantage of the specific characteristics of cyanurbiotindipropionylsuccinimide (CBDPS), an affinity-tagged isotopically coded mass spectrometry (MS)-cleavable crosslinking reagent. Utilizing this reagent in combination with a crosslinker-specific data-dependent acquisition strategy based on MS2 scans, and a software pipeline designed for integrating crosslinker-specific mass spectral information led to demonstrated improvements in the application of the CLMS technique, in terms of the detection, acquisition, and identification of crosslinker-modified peptides. This approach was evaluated on intact yeast mitochondria, and the results showed that hundreds of unique protein-protein interactions could be identified on an organelle proteome-wide scale. Both known and previously unknown protein-protein interactions were identified. These interactions were assessed based on their known sub-compartmental localizations. Additionally, the identified crosslinking distance constraints are in good agreement with existing structural models of protein complexes involved in the mitochondrial electron transport chain.
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Affiliation(s)
- Karl A T Makepeace
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada; University of Victoria - Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Yassene Mohammed
- University of Victoria - Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada; Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | | | - Evgeniy V Petrotchenko
- University of Victoria - Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada; Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada
| | - F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Germany
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Germany
| | - Albert Sickmann
- Leibniz Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany.
| | - Christoph H Borchers
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada; University of Victoria - Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada; Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada; Department of Data Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Nobel St., Moscow 143026, Russia.
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2
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Enhanced anti-tumor efficiency of gemcitabine prodrug by FAPα-mediated activation. Int J Pharm 2019; 559:48-57. [DOI: 10.1016/j.ijpharm.2019.01.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/28/2018] [Accepted: 01/10/2019] [Indexed: 12/22/2022]
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3
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A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein–protein interactions. Nat Protoc 2018; 13:2864-2889. [DOI: 10.1038/s41596-018-0068-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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4
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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: 196] [Impact Index Per Article: 32.7] [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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5
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Barysz HM, Malmström J. Development of Large-scale Cross-linking Mass Spectrometry. Mol Cell Proteomics 2017; 17:1055-1066. [PMID: 28389583 DOI: 10.1074/mcp.r116.061663] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 03/26/2017] [Indexed: 11/06/2022] Open
Abstract
Cross-linking mass spectrometry (CLMS) provides distance constraints to study the structure of proteins, multiprotein complexes and protein-protein interactions which are critical for the understanding of protein function. CLMS is an attractive technology to bridge the gap between high-resolution structural biology techniques and proteomic-based interactome studies. However, as outlined in this review there are still several bottlenecks associated with CLMS which limit its application on a proteome-wide level. Specifically, there is an unmet need for comprehensive software that can reliably identify cross-linked peptides from large data sets. In this review we provide supporting information to reason that targeted proteomics of cross-links may provide the required sensitivity to reliably detect and quantify cross-linked peptides and that a reporter ion signature for cross-linked peptides may become a useful approach to increase confidence in the identification process of cross-linked peptides. In addition, the review summarizes the recent advances in CLMS workflows using the analysis of condensin complex in intact chromosomes as a model complex.
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Affiliation(s)
- Helena Maria Barysz
- From the ‡Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Johan Malmström
- From the ‡Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
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6
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Hage C, Ihling CH, Götze M, Schäfer M, Sinz A. Dissociation Behavior of a TEMPO-Active Ester Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS) in Negative ESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:56-68. [PMID: 27418170 DOI: 10.1007/s13361-016-1426-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/14/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
We have synthesized a homobifunctional amine-reactive cross-linking reagent, containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) and a benzyl group (Bz), termed TEMPO-Bz-linker, to derive three-dimensional structural information of proteins. The aim for designing this novel cross-linker was to facilitate the mass spectrometric analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). In an initial study, we had investigated the fragmentation behavior of TEMPO-Bz-derivatized peptides upon collision activation in (+)-electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS) experiments. In addition to the homolytic NO-C bond cleavage FRIPS pathway delivering the desired odd-electron product ions, an alternative heterolytic NO-C bond cleavage, resulting in even-electron product ions mechanism was found to be relevant. The latter fragmentation route clearly depends on the protonation of the TEMPO-Bz-moiety itself, which motivated us to conduct (-)-ESI-MS, CID-MS/MS, and MS3 experiments of TEMPO-Bz-cross-linked peptides to further clarify the fragmentation behavior of TEMPO-Bz-peptide molecular ions. We show that the TEMPO-Bz-linker is highly beneficial for conducting FRIPS in negative ionization mode as the desired homolytic cleavage of the NO-C bond is the major fragmentation pathway. Based on characteristic fragments, the isomeric amino acids leucine and isoleucine could be discriminated. Interestingly, we observed pronounced amino acid side chain losses in cross-linked peptides if the cross-linked peptides contain a high number of acidic amino acids. Graphical Abstract ᅟ.
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Affiliation(s)
- Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany
| | - Christian H Ihling
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany
| | - Michael Götze
- Institute of Biochemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120, Halle, Saale, Germany
| | - Mathias Schäfer
- Department of Chemistry, University Cologne, Greinstr. 4, D-50939, Köln, Germany.
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany.
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7
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Sinz A. Divide and conquer: cleavable cross-linkers to study protein conformation and protein–protein interactions. Anal Bioanal Chem 2016; 409:33-44. [DOI: 10.1007/s00216-016-9941-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/25/2016] [Accepted: 09/09/2016] [Indexed: 01/28/2023]
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8
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Arlt C, Götze M, Ihling CH, Hage C, Schäfer M, Sinz A. Integrated Workflow for Structural Proteomics Studies Based on Cross-Linking/Mass Spectrometry with an MS/MS Cleavable Cross-Linker. Anal Chem 2016; 88:7930-7. [DOI: 10.1021/acs.analchem.5b04853] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Christian Arlt
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
| | - Michael Götze
- Institute
of Biochemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str.
3, D-06120 Halle
(Saale), Germany
| | - Christian H. Ihling
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
| | - Christoph Hage
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
| | - Mathias Schäfer
- Institute
for Organic Chemistry, Department of Chemistry, University of Cologne, Greinstr. 4, D-50939 Cologne, Germany
| | - Andrea Sinz
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
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9
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Kandur WV, Kao A, Vellucci D, Huang L, Rychnovsky SD. Design of CID-cleavable protein cross-linkers: identical mass modifications for simpler sequence analysis. Org Biomol Chem 2016; 13:9793-807. [PMID: 26269432 DOI: 10.1039/c5ob01410g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cross-linking Mass Spectrometry (XL-MS) technique has enormous potential for studying the interactions between proteins, and it can provide detailed structural information about the interaction interfaces in large protein complexes. Such information has been difficult to obtain by conventional structural methods. One of the primary impediments to the wider use of the XL-MS technique is the extreme challenge in sequencing cross-linked peptides because of their complex fragmentation patterns in MS. A recent innovation is the development of MS-cleavable cross-linkers, which allows direct sequencing of component peptides for facile identification. Sulfoxides are an intriguing class of thermally-cleavable compounds that have been shown to fragment selectively during low-energy collisional induced dissociation (CID) analysis. Current CID-cleavable cross-linkers create fragmentation patterns in MS(2) of multiple peaks for each cross-linked peptide. Reducing the complexity of the fragmentation pattern in MS(2) facilitates subsequent MS(3) sequencing of the cross-linked peptides. The first authentic identical mass linker (IML) has now been designed, prepared, and evaluated. Multistage tandem mass spectrometry (MS(n)) analysis has demonstrated that the IML cross-linked peptides indeed yield one peak per peptide constituent in MS(2) as predicted, thus allowing effective and sensitive MS(3) analysis for unambiguous identification. Selective fragmentation for IML cross-linked peptides from the 19S proteasome complex was observed, providing a proof-of-concept demonstration for XL-MS studies on protein complexes.
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Affiliation(s)
- Wynne V Kandur
- Department of Chemistry, University of California, Irvine, CA 92697, USA.
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10
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Burke AM, Kandur W, Novitsky EJ, Kaake RM, Yu C, Kao A, Vellucci D, Huang L, Rychnovsky SD. Synthesis of two new enrichable and MS-cleavable cross-linkers to define protein-protein interactions by mass spectrometry. Org Biomol Chem 2015; 13:5030-7. [PMID: 25823605 DOI: 10.1039/c5ob00488h] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The cross-linking Mass Spectrometry (XL-MS) technique extracts structural information from protein complexes without requiring highly purified samples, crystallinity, or large amounts of material. However, there are challenges to applying the technique to protein complexes in vitro, and those challenges become more daunting with in vivo experiments. Issues include effective detection and identification of cross-linked peptides from complex mixtures. While MS-cleavable cross-linkers facilitate the sequencing and identification of cross-linked peptides, enrichable cross-linkers increase their detectability by allowing their separation from non-cross-linked peptides prior to MS analysis. Although a number of cross-linkers with single functionality have been developed in recent years, an ideal reagent would incorporate both capabilities for XL-MS studies. Therefore, two new cross-linkers have been designed and prepared that incorporate an azide (azide-A-DSBSO) or alkyne (alkyne-A-DSBSO) to enable affinity purification strategies based on click chemistry. The integration of an acid cleavage site next to the enrichment handle allows easy recovery of cross-linked products during affinity purification. In addition, these sulfoxide containing cross-linking reagents possess robust MS-cleavable bonds to facilitate fast and easy identification of cross-linked peptides using MS analysis. Optimized, gram-scale syntheses of these cross-linkers have been developed and the azide-A-DSBSO cross-linker has been evaluated with peptides and proteins to demonstrate its utility in XL-MS analysis.
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Affiliation(s)
- Anthony M Burke
- Department of Chemistry, University of California, Irvine, CA 92697, USA.
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11
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Argo AS, Shi C, Liu F, Goshe MB. Performing protein crosslinking using gas-phase cleavable chemical crosslinkers and liquid chromatography-tandem mass spectrometry. Methods 2015; 89:64-73. [DOI: 10.1016/j.ymeth.2015.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/12/2015] [Accepted: 06/09/2015] [Indexed: 12/13/2022] Open
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12
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Wang R, Yang B, Wu RR, Rodgers MT, Schäfer M, Armentrout PB. Guided ion beam and computational studies of the decomposition of a model thiourea protein cross-linker. J Phys Chem B 2015; 119:3727-42. [PMID: 25660315 DOI: 10.1021/jp512997z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The dissociation of protonated methyl-d3 thiourea-4-butyric acid methyl amide (1), a model of thiourea-based protein cross-linking compounds, is examined both experimentally and computationally. Using a guided ion beam tandem mass spectrometer (GIBMS), the threshold collision-induced dissociation (TCID) of [1 + H](+) with Xe is examined as a function of collision energy. Analysis of the kinetic energy-dependent CID cross sections provides the 0 K barriers for four primary and four secondary dissociation pathways, after accounting for competition between channels, sequential dissociations, unimolecular decay rates, internal energy of reactant ions, and multiple ion-neutral collisions. Computations are used to explore the pathways for the various processes and elucidation of their rate-limiting transition states. These results indicate that dissociation is initiated by migration of the excess proton from sulfur to one of three nitrogen atoms in 1, similar to the "mobile proton" model of peptide fragmentation. The computational energies for the rate-limiting transition states are generally in good agreement with the experimentally derived threshold energies, with MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) results being particularly favorable. This good comparison validates the mechanisms explored theoretically and allows identification of the structures of the various product ions and neutrals.
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Affiliation(s)
- Ran Wang
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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13
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Ihling C, Falvo F, Kratochvil I, Sinz A, Schäfer M. Dissociation behavior of a bifunctional tempo-active ester reagent for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:396-406. [PMID: 25800022 DOI: 10.1002/jms.3543] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/28/2014] [Accepted: 11/12/2014] [Indexed: 06/04/2023]
Abstract
We have synthesized a homobifunctional active ester cross-linking reagent containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) moiety connected to a benzyl group (Bz), termed TEMPO-Bz-linker. The aim for designing this novel cross-linker was to facilitate MS analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). The TEMPO-Bz-linker was reacted with all 20 proteinogenic amino acids as well as with model peptides to gain detailed insights into its fragmentation mechanism upon collision activation. The final goal of this proof-of-principle study was to evaluate the potential of the TEMPO-Bz-linker for chemical cross-linking studies to derive 3D-structure information of proteins. Our studies were motivated by the well documented instability of the central NO-C bond of TEMPO-Bz reagents upon collision activation. The fragmentation of this specific bond was investigated in respect to charge states and amino acid composition of a large set of precursor ions resulting in the identification of two distinct fragmentation pathways. Molecular ions with highly basic residues are able to keep the charge carriers located, i.e. protons or sodium cations, and consequently decompose via a homolytic cleavage of the NO-C bond of the TEMPO-Bz-linker. This leads to the formation of complementary open-shell peptide radical cations, while precursor ions that are protonated at the TEMPO-Bz-linker itself exhibit a charge-driven formation of even-electron product ions upon collision activation. MS(3) product ion experiments provided amino acid sequence information and allowed determining the cross-linking site. Our study fully characterizes the CID behavior of the TEMPO-Bz-linker and demonstrates its potential, but also its limitations for chemical cross-linking applications utilizing the special features of open-shell peptide ions on the basis of selective tandem MS analysis.
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Affiliation(s)
- Christian Ihling
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany
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14
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Götze M, Pettelkau J, Fritzsche R, Ihling CH, Schäfer M, Sinz A. Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:83-97. [PMID: 25261217 DOI: 10.1007/s13361-014-1001-1] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 05/03/2023]
Abstract
CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .
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Affiliation(s)
- Michael Götze
- Institute for Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany,
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15
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Simon ES, Papoulias PG, Andrews PC. Selective collision-induced fragmentation of ortho-hydroxybenzyl-aminated lysyl-containing tryptic peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1619-1630. [PMID: 23765610 DOI: 10.1002/rcm.6611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/16/2013] [Accepted: 04/24/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE In protein studies that employ tandem mass spectrometry the manipulation of protonated peptide fragmentation through exclusive dissociation pathways may be preferred in some applications over the comprehensive amide backbone fragmentation that is typically observed. In this study, we characterized the selective cleavage of the side-chain Cζ-Nε bond of peptides with ortho-hydroxybenzyl-aminated lysine residues. METHODS Internal lysyl residues of representative peptides were derivatized via reductive amination with ortho-hydroxybenzaldehyde. The modified peptides were analyzed using collision-induced dissociation (CID) on an Orbitrap tandem mass spectrometer. Theoretical calculations using computational methods (density functional theory) were performed to investigate the potential dissociation mechanisms for the Cζ-Nε bond of the derivatized lysyl residue resulting in the formation of the observed product ions. RESULTS Tandem mass spectra of the derivatized peptide ions exhibit product peaks corresponding to selective cleavage of the side-chain Cζ-Nε bond that links the derivative to lysine. The ortho-hydroxybenzyl derivative is released either as a neutral moiety [C7H6O1] or as a carbocation [C7H7O1](+) through competing pathways (retro-Michael versus Carbocation Elimination (CCE), respectively). The calculated transition state activation barriers indicate that the retro-Michael pathway is kinetically favored over CCE and both are favored over amide cleavage. CONCLUSIONS The application of ortho-hydroxybenzyl amination is a promising peptide derivatization scheme for promoting selective dissociation pathways in the tandem mass spectrometry of protonated peptides. This can be implemented in the rational development of peptide reactive reagents for applications that may benefit from selective fragmentation paths (including crosslinking or MRM reagents).
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Affiliation(s)
- E S Simon
- Departments of Biological Chemistry, Bioinformatics, and Chemistry, University of Michigan, Ann Arbor, Michigan 48103, USA.
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16
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O'Brien JP, Pruet JM, Brodbelt JS. Chromogenic chemical probe for protein structural characterization via ultraviolet photodissociation mass spectrometry. Anal Chem 2013; 85:7391-7. [PMID: 23855605 DOI: 10.1021/ac401305f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A chemical probe/ultraviolet photodissociation (UVPD) mass spectrometry strategy for evaluating structures of proteins and protein complexes is reported, as demonstrated for lysozyme and beta-lactoglobulin with and without bound ligands. The chemical probe, NN, incorporates a UV chromophore that endows peptides with high cross sections at 351 nm, a wavelength not absorbed by unmodified peptides. Thus, NN-modified peptides can readily be differentiated from nonmodified peptides in complex tryptic digests created upon proteolysis of proteins after their exposure to the NN chemical probe. The NN chemical probe also affords two diagnostic reporter ions detected upon UVPD of the NN-modified peptide that provides a facile method for the identification of NN peptides within complex mixtures. Quantitation of the modified and unmodified peptides allows estimation of the surface accessibilities of lysine residues based on their relative reactivities with the NN chemical probe.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, United States
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17
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Paramelle D, Miralles G, Subra G, Martinez J. Chemical cross-linkers for protein structure studies by mass spectrometry. Proteomics 2013; 13:438-56. [PMID: 23255214 DOI: 10.1002/pmic.201200305] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 10/12/2012] [Accepted: 10/22/2012] [Indexed: 12/24/2022]
Abstract
The cross-linking approach combined with MS for protein structure determination is one of the most striking examples of multidisciplinary success. Indeed, it has become clear that the bottleneck of the method was the detection and the identification of low-abundance cross-linked peptides in complex mixtures. Sample treatment or chromatography separation partially addresses these issues. However, the main problem comes from over-represented unmodified peptides, which do not yield any structural information. A real breakthrough was provided by high mass accuracy measurement, because of the outstanding technical developments in MS. This improvement greatly simplified the identification of cross-linked peptides, reducing the possible combinations matching with an observed m/z value. In addition, the huge amount of data collected has to be processed with dedicated software whose role is to propose distance constraints or ideally a structural model of the protein. In addition to instrumentation and algorithms efficiency, significant efforts have been made to design new cross-linkers matching all the requirements in terms of reactivity and selectivity but also displaying probes or reactive systems facilitating the isolation, the detection of cross-links, or the interpretation of MS data. These chemical features are reviewed and commented on in the light of the more recent strategies.
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Affiliation(s)
- David Paramelle
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 3 Research Link, Singapore
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18
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Calabrese AN, Pukala TL. Chemical Cross-linking and Mass Spectrometry for the Structural Analysis of Protein Assemblies. Aust J Chem 2013. [DOI: 10.1071/ch13164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cellular functions are performed and regulated at a molecular level by the coordinated action of intricate protein assemblies, and hence the study of protein folding, structure, and interactions is vital to the appreciation and understanding of complex biological problems. In the past decade, continued development of chemical cross-linking methodologies combined with mass spectrometry has seen this approach develop to enable detailed structural information to be elucidated for protein assemblies often intractable by traditional structural biology methods. In this review article, we describe recent advances in reagent design, cross-linking protocols, mass spectrometric analysis, and incorporation of cross-linking constraints into structural models, which are contributing to overcoming the intrinsic challenges of the cross-linking method. We also highlight pioneering applications of chemical cross-linking mass spectrometry approaches to the study of structure and function of protein assemblies.
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19
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Hyung SJ, Ruotolo BT. Integrating mass spectrometry of intact protein complexes into structural proteomics. Proteomics 2012; 12:1547-64. [PMID: 22611037 DOI: 10.1002/pmic.201100520] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MS analysis of intact protein complexes has emerged as an established technology for assessing the composition and connectivity within dynamic, heterogeneous multiprotein complexes at low concentrations and in the context of mixtures. As this technology continues to move forward, one of the main challenges is to integrate the information content of such intact protein complex measurements with other MS approaches in structural biology. Methods such as H/D exchange, oxidative foot-printing, chemical cross-linking, affinity purification, and ion mobility separation add complementary information that allows access to every level of protein structure and organization. Here, we survey the structural information that can be retrieved by such experiments, demonstrate the applicability of integrative MS approaches in structural proteomics, and look to the future to explore upcoming innovations in this rapidly advancing area.
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Affiliation(s)
- Suk-Joon Hyung
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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20
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He Y, Lauber MA, Reilly JP. Unique fragmentation of singly charged DEST cross-linked peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1046-1052. [PMID: 22460622 DOI: 10.1007/s13361-012-0372-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 03/03/2012] [Accepted: 03/08/2012] [Indexed: 05/31/2023]
Abstract
It has previously been shown that when cross-linking reagent diethyl suberthioimidate (DEST) reacts with primary amines of proteins to yield amidinated residues, the primary amines retain their high basicity, and cross-linked species can be enriched by strong cation exchange. It is now demonstrated that collisional activation of singly-charged DEST cross-linked peptide ions leads to preferential cleavage at the cross-linked sites. The resulting product ions facilitate the detection and identification of cross-linked peptides.
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Affiliation(s)
- Yi He
- Indiana University, Bloomington, IN, USA
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21
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Simon ES, Papoulias PG, Andrews PC. Substituent effects on the gas-phase fragmentation reactions of protonated peptides containing benzylamine-derivatized lysyl residues. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:631-638. [PMID: 22328216 DOI: 10.1002/rcm.6141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Motivated by the need for chemical strategies designed to tune peptide fragmentation to selective cleavage reactions, benzyl ring substituent influence on the relative formation of carbocation elimination (CCE) products from peptides with benzylamine-derivatized lysyl residues has been examined using collision-induced dissociation (CID) tandem mass spectrometry. Unsubstituted benzylamine-derivatized peptides yield a mixture of products derived from amide backbone cleavage and CCE. The latter involves side-chain cleavage of the derivatized lysyl residue to form a benzylic carbocation [C(7)H(7)](+) and an intact peptide product ion [(MH(n))(n+) - (C(7)H(7))(+)]((n-1)+). The CCE pathway is contingent upon protonation of the secondary ε-amino group (N(ε)) of the derivatized lysyl residue. Using the Hammett methodology to evaluate the electronic contributions of benzyl ring substituents on chemical reactivity, a direct correlation was observed between changes in the CCE product ion intensity ratios (relative to backbone fragmentation) and the Hammett substituent constants, σ, of the corresponding substituents. There was no correlation between the substituent-influenced gas-phase proton affinity of N(ε) and the relative ratios of CCE product ions. However, a strong correlation was observed between the π orbital interaction energies (ΔE(int)) of the eliminated benzylic carbocation and the logarithm of the relative ratios, indicating the predominant factor in the CCE pathway is the substituent effect on the level of hyperconjugation and resonance stability of the eliminated benzylic carbocation. This work effectively demonstrates the applicability of σ (and ΔE(int)) as substituent selection parameters for the design of benzyl-based peptide-reactive reagents which tune CCE product formation as desired for specific applications.
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Affiliation(s)
- E S Simon
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48103, USA.
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22
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Clifford-Nunn B, Showalter HDH, Andrews PC. Quaternary diamines as mass spectrometry cleavable crosslinkers for protein interactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:201-12. [PMID: 22131227 PMCID: PMC3573217 DOI: 10.1007/s13361-011-0288-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 10/20/2011] [Accepted: 10/22/2011] [Indexed: 05/11/2023]
Abstract
Mapping protein interactions and their dynamics is crucial to defining physiologic states, building effective models for understanding cell function, and to allow more effective targeting of new drugs. Crosslinking studies can estimate the proximity of proteins, determine sites of protein-protein interactions, and have the potential to provide a snapshot of dynamic interactions by covalently locking them in place for analysis. Several major challenges are associated with the use of crosslinkers in mass spectrometry, particularly in complex mixtures. We describe the synthesis and characterization of a MS-cleavable crosslinker containing cyclic amines, which address some of these challenges. The DC4 crosslinker contains two intrinsic positive charges, which allow crosslinked peptides to fragment into their component peptides by collision-induced dissociation (CID) or in-source decay. Initial fragmentation events result in cleavage on either side of the positive charges so crosslinked peptides are identified as pairs of ions separated by defined masses. The structures of the component peptides can then be robustly determined by MS(3) because their fragmentation products rearrange to generate a mobile proton. The DC4 crosslinking reagent is stable to storage, highly reactive, highly soluble (1 M solutions), quite labile to CID, and MS(3) results in productive backbone fragmentation.
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Affiliation(s)
- Billy Clifford-Nunn
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, USA
| | - H. D. Hollis Showalter
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan Vahlteich Medicinal Chemistry Core, Ann Arbor, MI, USA
| | - Philip C. Andrews
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Room 1198, 300 North Ingalls Building, 300 North Ingalls St., Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
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23
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Liu F, Wu C, Sweedler JV, Goshe MB. An enhanced protein crosslink identification strategy using CID-cleavable chemical crosslinkers and LC/MS(n) analysis. Proteomics 2012; 12:401-5. [PMID: 22213719 DOI: 10.1002/pmic.201100352] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 11/03/2011] [Accepted: 11/22/2011] [Indexed: 11/09/2022]
Abstract
We describe a novel two-step LC/MS(n) strategy to effectively and confidently identify numerous crosslinked peptides from complex mixtures. This method incorporates the use of our gas-phase cleavable crosslinking reagent, disuccinimidyl-succinamyl-aspartyl-proline (SuDP), and a new data-processing algorithm CXLinkS (Cleavable Crosslink Selection), which enables unequivocal crosslink peptide selection and identification on the basis of mass measurement accuracy, high resolving power, and the unique fragmentation pattern of each crosslinked peptide. We demonstrate our approach with well-characterized monomeric and multimeric protein systems with and without database searching restrictions where inter-peptide crosslink identification is increased 8-fold over our previously published data-dependent LC/MS³ method and discuss its applicability to other CID-cleavable crosslinkers and more complex protein systems.
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Affiliation(s)
- Fan Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
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24
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Serpa JJ, Parker CE, Petrotchenko EV, Han J, Pan J, Borchers CH. Mass spectrometry-based structural proteomics. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2012; 18:251-267. [PMID: 22641729 DOI: 10.1255/ejms.1178] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Structural proteomics is the application of protein chemistry and modern mass spectrometric techniques to problems such as the characterization of protein structures and assemblies and the detailed determination of protein-protein interactions. The techniques used in structural proteomics include crosslinking, photoaffinity labeling, limited proteolysis, chemical protein modification and hydrogen/deuterium exchange, all followed by mass spectrometric analysis. None of these methods alone can provide complete structural information, but a "combination" of these complementary approaches can be used to provide enough information for answering important biological questions. Structural proteomics can help to determine, for example, the detailed structure of the interfaces between proteins that may be important drug targets and the interactions between proteins and ligands. In this review, we have tried to provide a brief overview of structural proteomics methodologies, illustrated with examples from our laboratory and from the literature.
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Affiliation(s)
- Jason J Serpa
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC V8Z 7X8, Canada
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25
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Götze M, Pettelkau J, Schaks S, Bosse K, Ihling CH, Krauth F, Fritzsche R, Kühn U, Sinz A. StavroX--a software for analyzing crosslinked products in protein interaction studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:76-87. [PMID: 22038510 DOI: 10.1007/s13361-011-0261-2] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 09/19/2011] [Accepted: 09/20/2011] [Indexed: 05/03/2023]
Abstract
Chemical crosslinking in combination with mass spectrometry has matured into an alternative approach to derive low-resolution structural information of proteins and protein complexes. Yet, one of the major drawbacks of this strategy remains the lack of software that is able to handle the large MS datasets that are created after chemical crosslinking and enzymatic digestion of the crosslinking reaction mixtures. Here, we describe a software, termed StavroX, which has been specifically designed for analyzing highly complex crosslinking datasets. The StavroX software was evaluated for three diverse biological systems: (1) the complex between calmodulin and a peptide derived from Munc13, (2) an N-terminal ß-laminin fragment, and (3) the complex between guanylyl cyclase activating protein-2 and a peptide derived from retinal guanylyl cyclase. We show that the StavroX software is advantageous for analyzing crosslinked products due to its easy-to-use graphical user interface and the highly automated analysis of mass spectrometry (MS) and tandem mass spectrometry (MS/MS) data resulting in short times for analysis. StavroX is expected to give a further push to the chemical crosslinking approach as a routine technique for protein interaction studies.
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Affiliation(s)
- Michael Götze
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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26
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Du X, Chowdhury SM, Manes NP, Wu S, Mayer MU, Adkins JN, Anderson GA, Smith RD. Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry. J Proteome Res 2011; 10:923-31. [PMID: 21175198 DOI: 10.1021/pr100848a] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chemical cross-linking combined with mass spectrometry provides a powerful method for identifying protein-protein interactions and probing the structure of protein complexes. A number of strategies have been reported that take advantage of the high sensitivity and high resolution of modern mass spectrometers. Approaches typically include synthesis of novel cross-linking compounds, and/or isotopic labeling of the cross-linking reagent and/or protein, and label-free methods. We report Xlink-Identifier, a comprehensive data analysis platform that has been developed to support label-free analyses. It can identify interpeptide, intrapeptide, and deadend cross-links as well as underivatized peptides. The software streamlines data preprocessing, peptide scoring, and visualization and provides an overall data analysis strategy for studying protein-protein interactions and protein structure using mass spectrometry. The software has been evaluated using a custom synthesized cross-linking reagent that features an enrichment tag. Xlink-Identifier offers the potential to perform large-scale identifications of protein-protein interactions using tandem mass spectrometry.
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Affiliation(s)
- Xiuxia Du
- Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina 28023, USA.
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27
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Müller MQ, Zeiser JJ, Dreiocker F, Pich A, Schäfer M, Sinz A. A universal matrix-assisted laser desorption/ionization cleavable cross-linker for protein structure analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:155-161. [PMID: 21157862 DOI: 10.1002/rcm.4812] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The concept of protein cross-linking in combination with mass spectrometry holds great promise to derive structural information on protein conformation and protein-protein interactions. We recently presented a dissociative amine-reactive cross-linker (NHS-BuUrBu-NHS) that is shown herein to be universally applicable to protein structure analysis under matrix-assisted laser desorption/ionization tandem mass spectrometric (MALDI-MS/MS) conditions, based on the examples of the peptides substance P, luteinizing hormone releasing hormone (LHRH), and the 32-kDa ligand-binding domain of peroxisome proliferator-activated receptor alpha (PPARα). The characteristic fragment ion patterns and constant neutral losses of the cross-linker greatly simplify the identification of different cross-linked species from complex mixtures and drastically reduce the potential of identifying false-positive cross-links. Therefore, this cross-linker holds an enormous potential for deriving structural information of proteins and protein complexes in a highly automated fashion.
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Affiliation(s)
- Mathias Q Müller
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany
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28
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Liu F, Goshe MB. Combinatorial electrostatic collision-induced dissociative chemical cross-linking reagents for probing protein surface topology. Anal Chem 2010; 82:6215-23. [PMID: 20560670 DOI: 10.1021/ac101030w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To ascertain more information on protein domain orientation and complex structure associations using chemical cross-linking, we have developed a combination of electrostatic collision-induced dissociative cross-linking reagents that differentially react with protein surfaces which are effectively analyzed by liquid chromatography-tandem mass spectrometry using ion trap multistage collision-induced dissociation. Implementing our original design and methodology based on disuccinimidyl-succinamyl-aspartyl-proline (SuDP) (Soderblom, E. J.; Goshe, M. B. Anal. Chem 2006, 78, 8059-8068. Soderblom, E. J.; Bobay, B. G.; Cavanagh, J.; Goshe, M. B. Rapid Commun Mass Spectrom 2007, 21, 3395-3408.), disuccinimidyl-succinamyl-valyl-proline (SuVP) was synthesized. The SuDP and SuVP reagents are the same except for the valyl and aspartyl groups which provide a distinctive chemical feature to each reagent. When performing labeling reactions using various protein-to-cross-linker ratios at pH 7.5, the negatively charged SuDP and neutral SuVP were used to label bovine serum albumin and hemoglobin. After protein digestion, the resulting peptides were analyzed using four different ion trap LC/MS(3) acquisition methods incorporating multistage CID. The more polar BSA surface resulted in a number of unique interpeptide and intrapeptide cross-links for each reagent whereas the less polarized surface of hemoglobin produced similar results for both reagents. Based on the identification of dead-end products (i.e., a cross-link modification containing a hydrolyzed end) for each protein, the aminolysis reactivity of each modified lysyl side chain revealed a preference for reacting with each reagent according to its local electrostatic surface environment. Overall, combinatorial application of SuDP and SuVP chemical labeling produces a set of unique interpeptide, intrapeptide, and dead-end cross-linked products that provides protein structural information according to its electrostatic surface topology which has the potential to be used to more comprehensively probe protein structure and dynamics.
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Affiliation(s)
- Fan Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622, USA
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29
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Rappsilber J. The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J Struct Biol 2010; 173:530-40. [PMID: 21029779 PMCID: PMC3043253 DOI: 10.1016/j.jsb.2010.10.014] [Citation(s) in RCA: 319] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 10/21/2010] [Accepted: 10/21/2010] [Indexed: 11/17/2022]
Abstract
After more than a decade of method development, cross-linking in combination with mass spectrometry and bioinformatics is finally coming of age. This technology now provides improved opportunities for modelling by mapping structural details of functional complexes in solution. The structure of proteins or protein complexes is ascertained by identifying amino acid pairs that are positioned in close proximity to each other. The validity of this technique has recently been benchmarked for large multi-protein complexes, by comparing cross-link data with that from a crystal structure of RNA polymerase II. Here, the specific nature of this cross-linking data will be discussed to assess the technical challenges and opportunities for model building. We believe that once remaining technological challenges of cross-linking/mass spectrometry have been addressed and cross-linking/mass spectrometry data has been incorporated into modelling algorithms it will quickly become an indispensable companion of protein and protein complex modelling and a corner-stone of integrated structural biology.
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Affiliation(s)
- Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh, EH9 3JR Scotland, UK.
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30
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Müller MQ, Dreiocker F, Ihling CH, Schäfer M, Sinz A. Fragmentation behavior of a thiourea-based reagent for protein structure analysis by collision-induced dissociative chemical cross-linking. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:880-891. [PMID: 20607845 DOI: 10.1002/jms.1775] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The fragmentation behavior of a novel thiourea-based cross-linker molecule specifically designed for collision-induced dissociation (CID) MS/MS experiments is described. The development of this cross-linker is part of our ongoing efforts to synthesize novel reagents, which create either characteristic fragment ions or indicative constant neutral losses (CNLs) during tandem mass spectrometry allowing a selective and sensitive analysis of cross-linked products. The new derivatizing reagent for chemical cross-linking solely contains a thiourea moiety that is flanked by two amine-reactive N-hydroxy succinimide (NHS) ester moieties for reaction with lysines or free N-termini in proteins. The new reagent offers simple synthetic access and easy structural variation of either length or functionalities at both ends. The thiourea moiety exhibits specifically tailored CID fragmentation capabilities--a characteristic CNL of 85 u--ensuring a reliable detection of derivatized peptides by both electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry and as such possesses a versatile applicability for chemical cross-linking studies. A detailed examination of the CID behavior of the presented thiourea-based reagent reveals that slight structural variations of the reagent will be necessary to ensure its comprehensive and efficient application for chemical cross-linking of proteins.
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Affiliation(s)
- Mathias Q Müller
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
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31
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Müller MQ, Dreiocker F, Ihling CH, Schäfer M, Sinz A. Cleavable Cross-Linker for Protein Structure Analysis: Reliable Identification of Cross-Linking Products by Tandem MS. Anal Chem 2010; 82:6958-68. [DOI: 10.1021/ac101241t] [Citation(s) in RCA: 178] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mathias Q. Müller
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), and Institute for Organic Chemistry, Department of Chemistry, Universität zu Köln, Greinstrasse 4, D-50939 Cologne, Germany
| | - Frank Dreiocker
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), and Institute for Organic Chemistry, Department of Chemistry, Universität zu Köln, Greinstrasse 4, D-50939 Cologne, Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), and Institute for Organic Chemistry, Department of Chemistry, Universität zu Köln, Greinstrasse 4, D-50939 Cologne, Germany
| | - Mathias Schäfer
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), and Institute for Organic Chemistry, Department of Chemistry, Universität zu Köln, Greinstrasse 4, D-50939 Cologne, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), and Institute for Organic Chemistry, Department of Chemistry, Universität zu Köln, Greinstrasse 4, D-50939 Cologne, Germany
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32
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Gardner MW, Brodbelt JS. Preferential Cleavage of N−N Hydrazone Bonds for Sequencing Bis-arylhydrazone Conjugated Peptides by Electron Transfer Dissociation. Anal Chem 2010; 82:5751-9. [DOI: 10.1021/ac100788a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Myles W. Gardner
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712
| | - Jennifer S. Brodbelt
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712
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33
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Investigation of protein-protein interactions in living cells by chemical crosslinking and mass spectrometry. Anal Bioanal Chem 2010; 397:3433-40. [PMID: 20076950 DOI: 10.1007/s00216-009-3405-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2009] [Revised: 12/12/2009] [Accepted: 12/14/2009] [Indexed: 01/26/2023]
Abstract
The identification of protein-protein interactions within their physiological environment is the key to understanding biological processes at the molecular level. However, the artificial nature of in vitro experiments, with their lack of other cellular components, may obstruct observations of specific cellular processes. In vivo analyses can provide information on the processes within a cell that might not be observed in vitro. Chemical crosslinking combined with mass spectrometric analysis of the covalently connected binding partners allows us to identify interacting proteins and to map their interface regions directly in the cell. In this paper, different in vivo crosslinking strategies for deriving information on protein-protein interactions in their physiological environment are described.
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