1
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Cross-linking mass spectrometry for mapping protein complex topologies in situ. Essays Biochem 2023; 67:215-228. [PMID: 36734207 PMCID: PMC10070479 DOI: 10.1042/ebc20220168] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/04/2023]
Abstract
Cross-linking mass spectrometry has become an established technology to provide structural information on the topology and dynamics of protein complexes. Readily accessible workflows can provide detailed data on simplified systems, such as purified complexes. However, using this technology to study the structure of protein complexes in situ, such as in organelles, cells, and even tissues, is still a technological frontier. The complexity of these systems remains a considerable challenge, but there have been dramatic improvements in sample handling, data acquisition, and data processing. Here, we summarise these developments and describe the paths towards comprehensive and comparative structural interactomes by cross-linking mass spectrometry.
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2
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Enzymatic Modification of Plant Proteins for Improved Functional and Bioactive Properties. FOOD BIOPROCESS TECH 2022. [DOI: 10.1007/s11947-022-02971-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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3
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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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4
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Piersimoni L, Kastritis PL, Arlt C, Sinz A. Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions─A Method for All Seasons. Chem Rev 2021; 122:7500-7531. [PMID: 34797068 DOI: 10.1021/acs.chemrev.1c00786] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this review, the contributions of chemical cross-linking combined with mass spectrometry (XL-MS) for studying three-dimensional structures of proteins and for investigating protein-protein interactions are outlined. We summarize the most important cross-linking reagents, software tools, and XL-MS workflows and highlight prominent examples for characterizing proteins, their assemblies, and interaction networks in vitro and in vivo. Computational modeling plays a crucial role in deriving 3D-structural information from XL-MS data. Integrating XL-MS with other techniques of structural biology, such as cryo-electron microscopy, has been successful in addressing biological questions that to date could not be answered. XL-MS is therefore expected to play an increasingly important role in structural biology in the future.
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Affiliation(s)
- Lolita Piersimoni
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Biozentrum, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
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5
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Abstract
A growing theme in chemistry is the joining of multiple organic molecular building blocks to create functional molecules. Diverse derivatizable structures—here termed “scaffolds” comprised of “hubs”—provide the foundation for systematic covalent organization of a rich variety of building blocks. This review encompasses 30 tri- or tetra-armed molecular hubs (e.g., triazine, lysine, arenes, dyes) that are used directly or in combination to give linear, cyclic, or branched scaffolds. Each scaffold is categorized by graph theory into one of 31 trees to express the molecular connectivity and overall architecture. Rational chemistry with exacting numbers of derivatizable sites is emphasized. The incorporation of water-solubilization motifs, robust or self-immolative linkers, enzymatically cleavable groups and functional appendages affords immense (and often late-stage) diversification of the scaffolds. Altogether, 107 target molecules are reviewed along with 19 syntheses to illustrate the distinctive chemistries for creating and derivatizing scaffolds. The review covers the history of the field up through 2020, briefly touching on statistically derivatized carriers employed in immunology as counterpoints to the rationally assembled and derivatized scaffolds here, although most citations are from the past two decades. The scaffolds are used widely in fields ranging from pure chemistry to artificial photosynthesis and biomedical sciences.
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6
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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: 6] [Impact Index Per Article: 2.0] [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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7
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Abstract
Cross-linking, in general, involves the covalent linkage of two amino acid residues of proteins or protein complexes in close proximity. Mass spectrometry and computational analysis are then applied to identify the formed linkage and deduce structural information such as distance restraints. Quantitative cross-linking coupled with mass spectrometry is well suited to study protein dynamics and conformations of protein complexes. The quantitative cross-linking workflow described here is based on the application of isotope labelled cross-linkers. Proteins or protein complexes present in different structural states are differentially cross-linked using a "light" and a "heavy" cross-linker. The intensity ratios of cross-links (i.e., light/heavy or heavy/light) indicate structural changes or interactions that are maintained in the different states. These structural insights lead to a better understanding of the function of the proteins or protein complexes investigated. The described workflow is applicable to a wide range of research questions including, for instance, protein dynamics or structural changes upon ligand binding.
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Affiliation(s)
- Marie Barth
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany.
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8
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Belsom A, Rappsilber J. Anatomy of a crosslinker. Curr Opin Chem Biol 2020; 60:39-46. [PMID: 32829152 DOI: 10.1016/j.cbpa.2020.07.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/17/2022]
Abstract
Crosslinking mass spectrometry has become a core technology in structural biology and is expanding its reach towards systems biology. Its appeal lies in a rapid workflow, high sensitivity and the ability to provide data on proteins in complex systems, even in whole cells. The technology depends heavily on crosslinking reagents. The anatomy of crosslinkers can be modular, sometimes comprising combinations of functional groups. These groups are defined by concepts including: reaction selectivity to increase information density, enrichability to improve detection, cleavability to enhance the identification process and isotope-labelling for quantification. Here, we argue that both concepts and functional groups need more thorough experimental evaluation, so that we can show exactly how and where they are useful when applied to crosslinkers. Crosslinker design should be driven by data, not only concepts. We focus on two crosslinker concepts with large consequences for the technology, namely reactive group reaction kinetics and enrichment groups.
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Affiliation(s)
- Adam Belsom
- 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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9
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Moschny J, Lorenzen W, Hilfer A, Eckenstaler R, Jahns S, Enke H, Enke D, Schneider P, Benndorf RA, Niedermeyer THJ. Precursor-Directed Biosynthesis and Fluorescence Labeling of Clickable Microcystins. JOURNAL OF NATURAL PRODUCTS 2020; 83:1960-1970. [PMID: 32464061 DOI: 10.1021/acs.jnatprod.0c00251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microcystins, cyclic nonribosomal heptapeptides, are the most well-known cyanobacterial toxins. They are exceptionally well studied, but open questions remain concerning their physiological role for the producing microorganism or their suitability as lead compounds for anticancer drug development. One means to study specialized metabolites in more detail is the introduction of functional groups that make a compound amenable for bioorthogonal, so-called click reactions. Although it was reported that microcystins cannot be derivatized by precursor-directed biosynthesis, we successfully used this approach to prepare clickable microcystins. Supplementing different azide- or terminal alkyne containing amino acid analogues into the cultivation medium of microcystin-producing cyanobacteria strains, we found that these strains differ strongly in their substrate acceptance. Exploiting this flexibility, we generated more than 40 different clickable microcystins. We conjugated one of these derivatives with a fluorogenic dye and showed that neither incorporation of the unnatural amino acid analogue nor attachment of the fluorescent label significantly affects the cytotoxicity against cell lines expressing the human organic anion transporting polypeptides 1B1 or 1B3. Using time-lapse microscopy, we observed that the fluorescent microcystin is rapidly taken up into eukaryotic cells expressing these transporters.
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Affiliation(s)
- Julia Moschny
- Department of Pharmaceutical Biology/Pharmacognosy, Institute of Pharmacy, University of Halle-Wittenberg, 06120 Halle (Saale), Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | | | | | - Robert Eckenstaler
- Department of Clinical Pharmacy and Pharmacotherapy, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | | | - Heike Enke
- Cyano Biotech GmbH, 12489 Berlin, Germany
| | - Dan Enke
- Cyano Biotech GmbH, 12489 Berlin, Germany
| | - Philipp Schneider
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Ralf A Benndorf
- Department of Clinical Pharmacy and Pharmacotherapy, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Timo H J Niedermeyer
- Department of Pharmaceutical Biology/Pharmacognosy, Institute of Pharmacy, University of Halle-Wittenberg, 06120 Halle (Saale), Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
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10
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Ihling CH, Springorum P, Iacobucci C, Hage C, Götze M, Schäfer M, Sinz A. The Isotope-Labeled, MS-Cleavable Cross-Linker Disuccinimidyl Dibutyric Urea for Improved Cross-Linking/Mass Spectrometry Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:183-189. [PMID: 32031397 DOI: 10.1021/jasms.9b00008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Previous studies have shown the benefits of the amine-reactive, CID-MS/MS-cleavable cross-linker disuccinimidyl dibutyric urea (DSBU) for structural proteomics studies via cross-linking/MS (XL-MS). To further facilitate the automation of XL-MS experiments, we synthesized a deuterated (D12) version of the DSBU cross-linker combining the advantages of MS-cleavable linkers and isotope labeling. The rationale of conducting XL-MS with a mixture of unlabeled and stable isotope-labeled DSBU is to obtain characteristic mass differences at the MS level indicating cross-linked species. These cross-linked species can then be selected for fragmentation by collisional activation. At the MS/MS level, the characteristic 26-u doublets arising from cleavage of the central urea group in DSBU confirm the amino acid sequences of cross-linked peptides as well as the exact cross-linking sites. D12-labeled DSBU was tested on three systems with increasing complexity: (i) bovine serum albumin as purified protein, (ii) Escherichia coli ribosome as large, multimeric protein assembly, and (iii) Drosophila embryo extract as complete proteome. We demonstrate the benefits arising from the use of isotope-labeled DSBU for an automated assignment of cross-linked products. Combining isotope labeling and MS cleavability in one cross-linker resulted in higher cross-link identification numbers especially for highly complex protein mixtures.
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Affiliation(s)
- Christian H Ihling
- Institute of Pharmacy , Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , D-06120 Halle/Saale , Germany
| | - Patrizia Springorum
- Institute of Pharmacy , Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , D-06120 Halle/Saale , Germany
| | - Claudio Iacobucci
- Institute of Pharmacy , Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , D-06120 Halle/Saale , Germany
| | - Christoph Hage
- Institute of Pharmacy , Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , D-06120 Halle/Saale , Germany
| | - Michael Götze
- Institute of Biochemistry , Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , 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, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , D-06120 Halle/Saale , Germany
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11
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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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12
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Xiang Y, Shen Z, Shi Y. Chemical Cross-Linking and Mass Spectrometric Analysis of the Endogenous Yeast Exosome Complexes. Methods Mol Biol 2020; 2062:383-400. [PMID: 31768986 DOI: 10.1007/978-1-4939-9822-7_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chemical cross-linking and mass spectrometric readout (CX-MS) has become a useful toolkit for structural analysis of protein complexes. CX-MS enables rapid detection of a larger number of cross-link peptides from the chemically cross-linked protein assembly, providing invaluable cross-link spatial restraints to understand the architecture of the complex. Since CX-MS is complementary with other structural and computational modeling tools, it can be used for integrative structural determination of large native protein assemblies. However, due to technical limitations, current CX-MS applications have still been predominantly confined to complexes reconstituted from recombinant proteins where large amount of purified materials are available. Cross-linking and hybrid structural proteomic analysis of endogenous protein complexes remains a challenge. In this chapter, we present a protocol that efficiently couples affinity capture of endogenous complexes with sensitive CX-MS analysis, with particular application to the yeast RNA processing exosome complexes.
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Affiliation(s)
- Yufei Xiang
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zhuolun Shen
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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13
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James JMB, Cryar A, Thalassinos K. Optimization Workflow for the Analysis of Cross-Linked Peptides Using a Quadrupole Time-of-Flight Mass Spectrometer. Anal Chem 2019; 91:1808-1814. [PMID: 30620560 PMCID: PMC6383985 DOI: 10.1021/acs.analchem.8b02319] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Cross-linking
mass spectrometry is an emerging structural biology
technique. Almost exclusively, the analyzer of choice for such an
experiment has been the Orbitrap. We present an optimized protocol
for the use of a Synapt G2-Si for the analysis of cross-linked peptides.
We first tested six different energy ramps and analyzed the fragmentation
behavior of cross-linked peptides identified by xQuest. By combining
the most successful energy ramps, cross-link yield can be increased
by up to 40%. When compared to previously published Orbitrap data,
the Synapt G2-Si also offers improved fragmentation of the β
peptide. In order to improve cross-link quality control we have also
developed ValidateXL, a programmatic solution that works with existing
cross-linking software to improve cross-link quality control.
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Affiliation(s)
- Juliette M B James
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology , University College London , Gower Street , London , WC1E 6BT , United Kingdom
| | - Adam Cryar
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology , University College London , Gower Street , London , WC1E 6BT , United Kingdom.,LGC Group , Queen's Road , Teddington , TW11 0LY , United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Department of Structural and Molecular Biology , University College London , Gower Street , London , WC1E 6BT , United Kingdom.,Institute of Structural and Molecular Biology, Department of Biological Sciences , Birkbeck, University of London , London , WC1E 7HX , United Kingdom
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14
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Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:1435934. [PMID: 30533169 PMCID: PMC6250043 DOI: 10.1155/2018/1435934] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
Mitochondria are highly dynamic and regulated organelles that historically have been defined based on their crucial role in cell metabolism. However, they are implicated in a variety of other important functions, making mitochondrial dysfunction an important axis in several pathological contexts. Despite that conventional biochemical and molecular biology approaches have provided significant insight into mitochondrial functionality, innovative techniques that provide a global view of the mitochondrion are still necessary. Proteomics fulfils this need by enabling accurate, systems-wide quantitative analysis of protein abundance. More importantly, redox proteomics approaches offer unique opportunities to tackle oxidative stress, a phenomenon that is intimately linked to aging, cardiovascular disease, and cancer. In addition, cutting-edge proteomics approaches reveal how proteins exert their functions in complex interaction networks where even subtle alterations stemming from early pathological states can be monitored. Here, we describe the proteomics approaches that will help to deepen the role of mitochondria in health and disease by assessing not only changes to mitochondrial protein composition but also alterations to their redox state and how protein interaction networks regulate mitochondrial function and dynamics. This review is aimed at showing the reader how the application of proteomics approaches during the last 20 years has revealed crucial mitochondrial roles in the context of aging, neurodegenerative disorders, metabolic disease, and cancer.
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15
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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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16
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Tokmina-Lukaszewska M, Patterson A, Berry L, Scott L, Balasubramanian N, Bothner B. The Role of Mass Spectrometry in Structural Studies of Flavin-Based Electron Bifurcating Enzymes. Front Microbiol 2018; 9:1397. [PMID: 30026733 PMCID: PMC6041385 DOI: 10.3389/fmicb.2018.01397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/07/2018] [Indexed: 12/01/2022] Open
Abstract
For decades, biologists and biochemists have taken advantage of atomic resolution structural models of proteins from X-ray crystallography, nuclear magnetic resonance spectroscopy, and more recently cryo-electron microscopy. However, not all proteins relent to structural analyses using these approaches, and as the depth of knowledge increases, additional data elucidating a mechanistic understanding of protein function is desired. Flavin-based electron bifurcating enzymes, which are responsible for producing high energy compounds through the simultaneous endergonic and exergonic reduction of two intercellular electron carriers (i.e., NAD+ and ferredoxin) are one class of proteins that have challenged structural biologists and in which there is great interest to understand the mechanism behind electron gating. A limited number of X-ray crystallography projects have been successful; however, it is clear that to understand how these enzymes function, techniques that can reveal detailed in solution information about protein structure, dynamics, and interactions involved in the bifurcating reaction are needed. In this review, we cover a general set of mass spectrometry-based techniques that, combined with protein modeling, are capable of providing information on both protein structure and dynamics. Techniques discussed include surface labeling, covalent cross-linking, native mass spectrometry, and hydrogen/deuterium exchange. We cover how biophysical data can be used to validate computationally generated protein models and develop mechanistic explanations for regulation and performance of enzymes and protein complexes. Our focus will be on flavin-based electron bifurcating enzymes, but the broad applicability of the techniques will be showcased.
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Affiliation(s)
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Luke Berry
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Liam Scott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
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17
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Chu F, Thornton DT, Nguyen HT. Chemical cross-linking in the structural analysis of protein assemblies. Methods 2018; 144:53-63. [PMID: 29857191 DOI: 10.1016/j.ymeth.2018.05.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
For decades, chemical cross-linking of proteins has been an established method to study protein interaction partners. The chemical cross-linking approach has recently been revived by mass spectrometric analysis of the cross-linking reaction products. Chemical cross-linking and mass spectrometric analysis (CXMS) enables the identification of residues that are close in three-dimensional (3D) space but not necessarily close in primary sequence. Therefore, this approach provides medium resolution information to guide de novo structure prediction, protein interface mapping and protein complex model building. The robustness and compatibility of the CXMS approach with multiple biochemical methods have made it especially appealing for challenging systems with multiple biochemical compositions and conformation states. This review provides an overview of the CXMS approach, describing general procedures in sample processing, data acquisition and analysis. Selection of proper chemical cross-linking reagents, strategies for cross-linked peptide identification, and successful application of CXMS in structural characterization of proteins and protein complexes are discussed.
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Affiliation(s)
- Feixia Chu
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, United States.
| | - Daniel T Thornton
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
| | - Hieu T Nguyen
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
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18
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Bifunctional cross-linking approaches for mass spectrometry-based investigation of nucleic acids and protein-nucleic acid assemblies. Methods 2018; 144:64-78. [PMID: 29753003 DOI: 10.1016/j.ymeth.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/30/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022] Open
Abstract
With the goal of expanding the very limited toolkit of cross-linking agents available for nucleic acids and their protein complexes, we evaluated the merits of a wide range of bifunctional agents that may be capable of reacting with the functional groups characteristic of these types of biopolymers. The survey specifically focused on the ability of test reagents to produce desirable inter-molecular conjugates, which could reveal the identity of interacting components and the position of mutual contacts, while also considering a series of practical criteria for their utilization as viable nucleic acid probes. The survey employed models consisting of DNA, RNA, and corresponding protein complexes to mimic as close as possible typical applications. Denaturing polyacrylamide gel electrophoresis (PAGE) and mass spectrometric (MS) analyses were implemented in concert to monitor the formation of the desired conjugates. In particular, the former was used as a rapid and inexpensive tool for the efficient evaluation of cross-linker activity under a broad range of experimental conditions. The latter was applied after preliminary rounds of reaction optimization to enable full-fledged product characterization and, more significantly, differentiation between mono-functional and intra- versus inter-molecular conjugates. This information provided the feedback necessary to further optimize reaction conditions and explain possible outcomes. Among the reagents tested in the study, platinum complexes and nitrogen mustards manifested the most favorable characteristics for practical cross-linking applications, whereas other compounds provided inferior yields, or produced rather unstable conjugates that did not survive the selected analytical conditions. The observed outcomes will help guide the selection of the most appropriate cross-linking reagent for a specific task, whereas the experimental conditions described here will provide an excellent starting point for approaching these types of applications. As a whole, the results of the survey clearly emphasize that finding a universal reagent, which may afford excellent performance with all types of nucleic acid substrates, will require extending the exploration beyond the traditional chemistries employed to modify the constitutive functional groups of these vital biopolymers.
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19
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Yu C, Huang L. Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology. Anal Chem 2018; 90:144-165. [PMID: 29160693 PMCID: PMC6022837 DOI: 10.1021/acs.analchem.7b04431] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
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20
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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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21
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Dong W, Lin G, Wang H, Lu W. New Dendritic Polydiacetylene Sensor with Good Reversible Thermochromic Ability in Aqueous Solution and Solid Film. ACS APPLIED MATERIALS & INTERFACES 2017; 9:11918-11923. [PMID: 28293942 DOI: 10.1021/acsami.7b02846] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Thermal responsive polydiacetylene derived from PAMAM dendrimer (PDA-G0) was synthesized. Unlike the ethylenediamine substituted PDA (PDA-NH2) solution, the prepared PDA-G0 vesicle solution showed reversible thermochromism property when temperature varied from 20 to 90 °C, which is due to the formation of an internal hydrogen bond in amide groups. Furthermore, PDA-G0/PMMA film with excellent stability was obtained by a mixed-drying method, which could be stored for a long time without denaturation. After polymerization by UV irradiation, it displayed much better reversible thermochromic ability and the responded temperature range became wider, from 20 to 110 °C.
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Affiliation(s)
- Wenjie Dong
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Surface Science, Institute of Chemistry, Chinese Academy of Science , Beijing 100190, P. R. China
| | - Guanhua Lin
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Surface Science, Institute of Chemistry, Chinese Academy of Science , Beijing 100190, P. R. China
| | - Haifei Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Surface Science, Institute of Chemistry, Chinese Academy of Science , Beijing 100190, P. R. China
| | - Wensheng Lu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Surface Science, Institute of Chemistry, Chinese Academy of Science , Beijing 100190, P. R. China
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22
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Yu J, Grant OC, Pett C, Strahl S, Stahl S, Woods RJ, Westerlind U. Induction of Antibodies Directed Against Branched Core O-Mannosyl Glycopeptides-Selectivity Complimentary to the ConA Lectin. Chemistry 2017; 23:3466-3473. [PMID: 28079948 PMCID: PMC5548291 DOI: 10.1002/chem.201605627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Indexed: 01/31/2023]
Abstract
Mammalian protein O-mannosylation, initiated by attachment of α-mannopyranose to Ser or Thr residues, comprise a group of post-translational modifications (PTMs) involved in muscle and brain development. Recent advances in glycoproteomics methodology and the "SimpleCell" strategy have enabled rapid identification of glycoproteins and specific glycosylation sites. Despite the enormous progress made, the biological impact of the mammalian O-mannosyl glycoproteome remains largely unknown to date. Tools are still needed to investigate the structure, role, and abundance of O-mannosyl glycans. Although O-mannosyl branching has been shown to be of relevance in integrin-dependent cell migration, and also plays a role in demyelinating diseases, such as multiple sclerosis, a broader understanding of the biological roles of branched O-mannosyl glycans is lacking in part due to the paucity of detection tools. In this work, a glycopeptide vaccine construct was synthesized and used to generate antibodies against branched O-mannosyl glycans. Glycopeptide microarray screening revealed high selectivity of the induced antibodies for branched glycan core structures presented on different peptide backbones, with no cross-reactivity observed with related linear glycans. For comparison, microarray screening of the mannose-binding lectin concanavalin A (ConA), which is commonly used in glycoproteomics workflows to enrich tryptic O-mannosyl peptides, showed that the ConA lectin did not recognize branched O-mannosyl glycans. The binding preference of ConA for short linear O-mannosyl glycans was rationalized in terms of molecular structure using crystallographic data augmented by molecular modeling. The contrast between the ConA binding specificity and that of the new antibodies indicates a novel role for the antibodies in studies of protein O-mannosylation.
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Affiliation(s)
- Jin Yu
- Gesellschaft zur Förderung der Analytischen Wissenschaften e.V., ISAS-Leibniz Institute for Analytical Sciences, Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Christian Pett
- Gesellschaft zur Förderung der Analytischen Wissenschaften e.V., ISAS-Leibniz Institute for Analytical Sciences, Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
| | | | - Sabine Stahl
- Centre for Organismal Studies (COS), Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Ulrika Westerlind
- Gesellschaft zur Förderung der Analytischen Wissenschaften e.V., ISAS-Leibniz Institute for Analytical Sciences, Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
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23
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Lössl P, van de Waterbeemd M, Heck AJ. The diverse and expanding role of mass spectrometry in structural and molecular biology. EMBO J 2016; 35:2634-2657. [PMID: 27797822 PMCID: PMC5167345 DOI: 10.15252/embj.201694818] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/25/2016] [Accepted: 10/07/2016] [Indexed: 12/20/2022] Open
Abstract
The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes.
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Affiliation(s)
- Philip Lössl
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
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24
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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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25
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Bastien E, Schneider R, Hackbarth S, Dumas D, Jasniewski J, Röder B, Bezdetnaya L, Lassalle HP. PAMAM G4.5-chlorin e6 dendrimeric nanoparticles for enhanced photodynamic effects. Photochem Photobiol Sci 2016; 14:2203-12. [PMID: 26496965 DOI: 10.1039/c5pp00274e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
There is currently great interest in the development of efficient and specific carrier delivery platforms for systemic photodynamic therapy. Therefore, we aimed to develop covalent conjugates between the photosensitizer chlorin e6 (Ce6) and PAMAM G4.5 dendrimers. Singlet oxygen generation (SOG) efficiency and fluorescence emission were moderately affected by the covalent binding of the Ce6 to the dendrimer. Compared to free Ce6, PAMAM anchored Ce6 displays a much higher photodynamic effect, which is ascribable to better internalization in a tumor cell model. Intracellular fate and internalization pathway of our different compounds were investigated using specific inhibition conditions and confocal fluorescence microscopy. Free Ce6 was shown to enter the cells by a simple diffusion mechanism, while G4.5-Ce6-PEG internalization was dependent on the caveolae pathway, whereas G4.5-Ce6 was subjected to the clathrin-mediated endocytosis pathway. Subcellular localization of PAMAM anchored Ce6, PEGylated or not, was very similar suggesting that the nanoparticles behave similarly in the cells. As a conclusion, we have demonstrated that PEGylated G4.5 PAMAM-Ce6 dendrimers may offer effective biocompatible nanoparticles for improved photodynamic treatment in a preclinical tumor model.
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Affiliation(s)
- Estelle Bastien
- Université de Lorraine, Centre de Recherche en Automatique de Nancy, Campus Sciences, Vandœuvre-lès-Nancy, France. and Centre National de la Recherche Scientifique, Centre de Recherche en Automatique de Nancy, France
| | - Raphaël Schneider
- Université de Lorraine, Laboratoire Réactions et Génie des Procédés (LRGP), UMR 7274, CNRS, 1 rue Grandville, BP 20451, 54001 Nancy Cedex, France
| | - Steffen Hackbarth
- Institut für Physik, Humboldt, Universität zu Berlin, Newtonstrasse, Berlin, Germany
| | - Dominique Dumas
- Université de Lorraine, Plateforme IBISA d'Imagerie et de Biophysique Cellulaire de Nancy, IMOPA7365, FR3209 BMCT, Centre National de la Recherche Scientifique, Vandœuvre-lès-Nancy, France
| | - Jordane Jasniewski
- Université de Lorraine, Laboratoire d'ingénierie des biomolécues (LIBio), 2 avenue de la Forêt de Haye, Vandœuvre-lès-Nancy, France
| | - Beate Röder
- Institut für Physik, Humboldt, Universität zu Berlin, Newtonstrasse, Berlin, Germany
| | - Lina Bezdetnaya
- Université de Lorraine, Centre de Recherche en Automatique de Nancy, Campus Sciences, Vandœuvre-lès-Nancy, France. and Centre National de la Recherche Scientifique, Centre de Recherche en Automatique de Nancy, France
| | - Henri-Pierre Lassalle
- Université de Lorraine, Centre de Recherche en Automatique de Nancy, Campus Sciences, Vandœuvre-lès-Nancy, France. and Centre National de la Recherche Scientifique, Centre de Recherche en Automatique de Nancy, France
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26
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Leitner A. Cross-linking and other structural proteomics techniques: how chemistry is enabling mass spectrometry applications in structural biology. Chem Sci 2016; 7:4792-4803. [PMID: 30155128 PMCID: PMC6016523 DOI: 10.1039/c5sc04196a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 04/25/2016] [Indexed: 01/05/2023] Open
Abstract
The biological function of proteins is heavily influenced by their structures and their organization into assemblies such as protein complexes and regulatory networks. Mass spectrometry (MS) has been a key enabling technology for high-throughput and comprehensive protein identification and quantification on a proteome-wide scale. Besides these essential contributions, MS can also be used to study higher-order structures of biomacromolecules in a variety of ways. In one approach, intact proteins or protein complexes may be directly probed in the mass spectrometer. Alternatively, various forms of solution-phase chemistry are used to introduce modifications in intact proteins and localizing these modifications by MS analysis at the peptide level is used to derive structural information. Here, I will put a spotlight on the central role of chemistry in such mass spectrometry-based methods that bridge proteomics and structural biology, with a particular emphasis on chemical cross-linking of protein complexes.
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Affiliation(s)
- Alexander Leitner
- Department of Biology , Institute of Molecular Systems Biology , ETH Zurich , Auguste-Piccard-Hof 1 , 8093 Zurich , Switzerland .
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27
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Chait BT, Cadene M, Olinares PD, Rout MP, Shi Y. Revealing Higher Order Protein Structure Using Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:952-65. [PMID: 27080007 PMCID: PMC5125627 DOI: 10.1007/s13361-016-1385-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 05/24/2023]
Abstract
The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope. Graphical Abstract ᅟ.
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Affiliation(s)
- Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA.
| | - Martine Cadene
- CBM, CNRS UPR4301, Rue Charles Sadron, CS 80054, 45071, Orleans Cedex 2, France
| | - Paul Dominic Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA
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28
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Tan D, Li Q, Zhang MJ, Liu C, Ma C, Zhang P, Ding YH, Fan SB, Tao L, Yang B, Li X, Ma S, Liu J, Feng B, Liu X, Wang HW, He SM, Gao N, Ye K, Dong MQ, Lei X. Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states. eLife 2016; 5. [PMID: 26952210 PMCID: PMC4811778 DOI: 10.7554/elife.12509] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/26/2016] [Indexed: 12/20/2022] Open
Abstract
To improve chemical cross-linking of proteins coupled with mass spectrometry (CXMS), we developed a lysine-targeted enrichable cross-linker containing a biotin tag for affinity purification, a chemical cleavage site to separate cross-linked peptides away from biotin after enrichment, and a spacer arm that can be labeled with stable isotopes for quantitation. By locating the flexible proteins on the surface of 70S ribosome, we show that this trifunctional cross-linker is effective at attaining structural information not easily attainable by crystallography and electron microscopy. From a crude Rrp46 immunoprecipitate, it helped identify two direct binding partners of Rrp46 and 15 protein-protein interactions (PPIs) among the co-immunoprecipitated exosome subunits. Applying it to E. coli and C. elegans lysates, we identified 3130 and 893 inter-linked lysine pairs, representing 677 and 121 PPIs. Using a quantitative CXMS workflow we demonstrate that it can reveal changes in the reactivity of lysine residues due to protein-nucleic acid interaction. DOI:http://dx.doi.org/10.7554/eLife.12509.001 Proteins fold into structures that are determined by the order of the amino acids that they are built from. These structures enable the protein to carry out its role, which often involves interacting with other proteins. Chemical cross-linking coupled with mass spectrometry (CXMS) is a powerful method used to study protein structure and how proteins interact, with a benefit of stabilizing and capturing brief interactions. CXMS uses a chemical compound called a linker that has two arms, each of which can bind specific amino acids in a protein or in multiple proteins. Only when the regions are close to each other can they be “cross-linked” in this way. After cross-linking, the proteins are cut into small pieces known as peptides. The cross-linked peptides are then separated from the non cross-linked ones and characterized. Although CXMS is a popular method, there are aspects about it that limit its use. It does not work well on complex samples that contain lots of different proteins, as it is difficult to separate the cross-linked peptides from the overwhelming amounts of non cross-linked peptides. Also, although it can be used to detect changes in the shape of a protein, which are often crucial to the protein's role, the method has not been smoothed out. Tan, Li et al. have now developed a new cross-linker called Leiker that addresses these limitations. Leiker cross-links the amino acid lysine to another lysine, and contains a molecular tag that allows cross-linked peptides to be efficiently purified away from non cross-linked peptides. As part of a streamlined workflow to detect changes in the shape of a protein, Leiker also contains a region that can be labeled. Analysing a bacterial ribosome, which contains more than 50 proteins, showed that Leiker-based CXMS could detect many more protein interactions than previous studies had. These included interactions that changed too rapidly to be studied by other structural methods. Tan, Li et al. then applied Leiker-based CXMS to the entire contents of bacterial cells at different stages of growth, and identified a protein interaction that is only found in growing cells. In future, Leiker will be useful for analyzing the structure of large protein complexes, probing changes in protein structure, and mapping the interactions between proteins in complex mixtures. DOI:http://dx.doi.org/10.7554/eLife.12509.002
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Affiliation(s)
- Dan Tan
- Graduate Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Qiang Li
- National Institute of Biological Sciences, Beijing, China.,Synthetic and Functional Biomolecules Center, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Mei-Jun Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Chao Liu
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Chengying Ma
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Pan Zhang
- Graduate Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Yue-He Ding
- Graduate Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Sheng-Bo Fan
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Li Tao
- Graduate Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Bing Yang
- National Institute of Biological Sciences, Beijing, China
| | - Xiangke Li
- National Institute of Biological Sciences, Beijing, China
| | - Shoucai Ma
- National Institute of Biological Sciences, Beijing, China
| | - Junjie Liu
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Boya Feng
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohui Liu
- National Institute of Biological Sciences, Beijing, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Si-Min He
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Keqiong Ye
- National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- Graduate Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Xiaoguang Lei
- National Institute of Biological Sciences, Beijing, China.,Synthetic and Functional Biomolecules Center, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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Goetz J, Nonat A, Diallo A, Sy M, Sera I, Lecointre A, Lefevre C, Chan CF, Wong KL, Charbonnière LJ. Ultrabright Lanthanide Nanoparticles. Chempluschem 2016; 81:526-534. [DOI: 10.1002/cplu.201600007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 01/27/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Joan Goetz
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse; Institut Pluridisciplinaire Hubert Curien; École Européenne de Chimie, Polymères et Matériaux; IPHC, UMR 7178, CNRS/Université de Strasbourg; 25 rue Becquerel 67087 Strasbourg Cedex France
| | - Aline Nonat
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse; Institut Pluridisciplinaire Hubert Curien; École Européenne de Chimie, Polymères et Matériaux; IPHC, UMR 7178, CNRS/Université de Strasbourg; 25 rue Becquerel 67087 Strasbourg Cedex France
| | - Abdoulaye Diallo
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse; Institut Pluridisciplinaire Hubert Curien; École Européenne de Chimie, Polymères et Matériaux; IPHC, UMR 7178, CNRS/Université de Strasbourg; 25 rue Becquerel 67087 Strasbourg Cedex France
| | - Mohamadou Sy
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse; Institut Pluridisciplinaire Hubert Curien; École Européenne de Chimie, Polymères et Matériaux; IPHC, UMR 7178, CNRS/Université de Strasbourg; 25 rue Becquerel 67087 Strasbourg Cedex France
| | - Ildan Sera
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse; Institut Pluridisciplinaire Hubert Curien; École Européenne de Chimie, Polymères et Matériaux; IPHC, UMR 7178, CNRS/Université de Strasbourg; 25 rue Becquerel 67087 Strasbourg Cedex France
| | - Alexandre Lecointre
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse; Institut Pluridisciplinaire Hubert Curien; École Européenne de Chimie, Polymères et Matériaux; IPHC, UMR 7178, CNRS/Université de Strasbourg; 25 rue Becquerel 67087 Strasbourg Cedex France
| | - Christophe Lefevre
- Institut de Physique et Chimie des Matériaux de Strasbourg (UMR 7504 CNRS); and Laboratory of Nanostructures in Interactions with Their Environment (NIE); Université de Strasbourg; 23 rue du Loess, BP 43 67034 Strasbourg Cedex 2 France
| | - Chi Fai Chan
- Department of Chemistry; Hong Kong Baptist University; Hong Kong SAR Hong Kong
| | - Ka-Leung Wong
- Department of Chemistry; Hong Kong Baptist University; Hong Kong SAR Hong Kong
| | - Loïc J. Charbonnière
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse; Institut Pluridisciplinaire Hubert Curien; École Européenne de Chimie, Polymères et Matériaux; IPHC, UMR 7178, CNRS/Université de Strasbourg; 25 rue Becquerel 67087 Strasbourg Cedex France
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Leitner A, Faini M, Stengel F, Aebersold R. Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines. Trends Biochem Sci 2016; 41:20-32. [DOI: 10.1016/j.tibs.2015.10.008] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/18/2015] [Accepted: 10/29/2015] [Indexed: 01/30/2023]
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Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an “Elephant and Blind Men” Situation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:215-60. [DOI: 10.1007/978-3-319-20164-1_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Koniev O, Wagner A. Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation. Chem Soc Rev 2015; 44:5495-551. [PMID: 26000775 DOI: 10.1039/c5cs00048c] [Citation(s) in RCA: 391] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.
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Affiliation(s)
- Oleksandr Koniev
- Laboratory of Functional Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg, 74 Route du Rhin, 67401 Illkirch-Graffenstaden, France.
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Ishiwata A, Taguchi Y, Lee YJ, Watanabe T, Kohda D, Ito Y. N-Glycosylation with synthetic undecaprenyl pyrophosphate-linked oligosaccharide to oligopeptides by PglB oligosaccharyltransferase from Campylobacter jejuni. Chembiochem 2015; 16:731-7. [PMID: 25688550 DOI: 10.1002/cbic.201402658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 11/11/2022]
Abstract
The oligosaccharyltransferase PglB from Campylobacter jejuni catalyses the N-glycosylation reaction with undecaprenyl-pyrophosphate-linked Glc1 GalNAc5 Bac1 (Und-PP-Glc1 GalNAc5 Bac1 ). Experiments using chemically synthesized donors coupled to fluorescently tagged peptides confirmed that biosynthetic intermediate Und-PP-Bac1 and Und-PP-GalNAc2 Bac1 are transferred efficiently to the Asn residue in the consensus sequence (D/E-X'-N-X-T/S, X',X≠P). The products were analyzed in detail by tandem MS to confirm their chemical structures.
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Lepvrier E, Doigneaux C, Moullintraffort L, Nazabal A, Garnier C. Optimized Protocol for Protein Macrocomplexes Stabilization Using the EDC, 1-Ethyl-3-(3-(dimethylamino)propyl)carbodiimide, Zero-Length Cross-Linker. Anal Chem 2014; 86:10524-30. [DOI: 10.1021/ac502561e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Eléonore Lepvrier
- Translation
and Folding, UMR-CNRS 6290, Université de Rennes 1, 35042 Rennes Cedex, France
| | - Cyrielle Doigneaux
- Translation
and Folding, UMR-CNRS 6290, Université de Rennes 1, 35042 Rennes Cedex, France
| | - Laura Moullintraffort
- Translation
and Folding, UMR-CNRS 6290, Université de Rennes 1, 35042 Rennes Cedex, France
| | | | - Cyrille Garnier
- Translation
and Folding, UMR-CNRS 6290, Université de Rennes 1, 35042 Rennes Cedex, France
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Sinz A. The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks. Expert Rev Proteomics 2014; 11:733-43. [DOI: 10.1586/14789450.2014.960852] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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da Costa JP, Oliveira-Silva R, Daniel-da-Silva AL, Vitorino R. Bionanoconjugation for Proteomics applications — An overview. Biotechnol Adv 2014; 32:952-70. [DOI: 10.1016/j.biotechadv.2014.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/15/2014] [Accepted: 04/26/2014] [Indexed: 12/29/2022]
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A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database. J Proteomics 2014; 108:65-77. [DOI: 10.1016/j.jprot.2014.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/23/2014] [Accepted: 05/08/2014] [Indexed: 11/23/2022]
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van Ingen H, Bonvin AMJJ. Information-driven modeling of large macromolecular assemblies using NMR data. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:103-114. [PMID: 24656083 DOI: 10.1016/j.jmr.2013.10.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 10/25/2013] [Indexed: 06/03/2023]
Abstract
Availability of high-resolution atomic structures is one of the prerequisites for a mechanistic understanding of biomolecular function. This atomic information can, however, be difficult to acquire for interesting systems such as high molecular weight and multi-subunit complexes. For these, low-resolution and/or sparse data from a variety of sources including NMR are often available to define the interaction between the subunits. To make best use of all the available information and shed light on these challenging systems, integrative computational tools are required that can judiciously combine and accurately translate the sparse experimental data into structural information. In this Perspective we discuss NMR techniques and data sources available for the modeling of large and multi-subunit complexes. Recent developments are illustrated by particularly challenging application examples taken from the literature. Within this context, we also position our data-driven docking approach, HADDOCK, which can integrate a variety of information sources to drive the modeling of biomolecular complexes. It is the synergy between experimentation and computational modeling that will provides us with detailed views on the machinery of life and lead to a mechanistic understanding of biomolecular function.
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Affiliation(s)
- Hugo van Ingen
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Faculty of Science - Chemistry, Padulaan 8, 3854 CH Utrecht, The Netherlands.
| | - Alexandre M J J Bonvin
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Faculty of Science - Chemistry, Padulaan 8, 3854 CH Utrecht, The Netherlands.
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Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A. Modeling of proteins and their assemblies with the Integrative Modeling Platform. Methods Mol Biol 2014; 1091:277-95. [PMID: 24203340 DOI: 10.1007/978-1-62703-691-7_20] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To understand the workings of the living cell, we need to characterize protein assemblies that constitute the cell (for example, the ribosome, 26S proteasome, and the nuclear pore complex). A reliable high-resolution structural characterization of these assemblies is frequently beyond the reach of current experimental methods, such as X-ray crystallography, NMR spectroscopy, electron microscopy, footprinting, chemical cross-linking, FRET spectroscopy, small angle X-ray scattering, and proteomics. However, the information garnered from different methods can be combined and used to build models of the assembly structures that are consistent with all of the available datasets, and therefore more accurate, precise, and complete. Here, we describe a protocol for this integration, whereby the information is converted to a set of spatial restraints and a variety of optimization procedures can be used to generate models that satisfy the restraints as well as possible. These generated models can then potentially inform about the precision and accuracy of structure determination, the accuracy of the input datasets, and further data generation. We also demonstrate the Integrative Modeling Platform (IMP) software, which provides the necessary computational framework to implement this protocol, and several applications for specific use cases.
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Affiliation(s)
- Benjamin Webb
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quanstitative Biosciences (QB3), University of California San Francisco, San Francisco, CA, USA
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Tinnefeld V, Sickmann A, Ahrends R. Catch me if you can: challenges and applications of cross-linking approaches. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2014; 20:99-116. [PMID: 24881459 DOI: 10.1255/ejms.1259] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Biomolecular complexes are the groundwork of life and the basis for cell signaling, energy transfer, motion, stability and cellular metabolism. Understanding the underlying complex interactions on the molecular level is an essential step to obtain a comprehensive insight into cellular and systems biology. For the investigation of molecular interactions, various methods, including Förster resonance energy transfer, nuclear magnetic resonance spectroscopy, X-ray crystallography and yeast two-hybrid screening, can be utilized. Nevertheless, the most reliable approach for structural proteomics and the identification of novel protein-binding partners is chemical cross-linking. The rationale is that upon forming a covalent bond between a protein and its interaction partner (protein, lipid, RNA/DNA, carbohydrate) the native complex state is "frozen" and accessible for detailed mass spectrometric analysis. In this review we provide a synopsis on crosslinker design, chemistry, pitfalls, limitations and novel applications in the field, and feature an overview of current software applications.
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Connell TU, Hayne DJ, Ackermann U, Tochon-Danguy HJ, White JM, Donnelly PS. Rhenium and technetium tricarbonyl complexes of 1,4-Substituted pyridyl-1,2,3-triazole bidentate ‘click’ ligands conjugated to a targeting RGD peptide. J Labelled Comp Radiopharm 2013; 57:262-9. [DOI: 10.1002/jlcr.3169] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/29/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Timothy U. Connell
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Melbourne 3010 Australia
| | - David J. Hayne
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Melbourne 3010 Australia
| | - Uwe Ackermann
- Centre for PET; Austin Health; Melbourne 3084 Australia
| | | | - Jonathan M. White
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Melbourne 3010 Australia
| | - Paul S. Donnelly
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Melbourne 3010 Australia
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42
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Karaca E, Bonvin AM. Advances in integrative modeling of biomolecular complexes. Methods 2013; 59:372-81. [DOI: 10.1016/j.ymeth.2012.12.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/30/2012] [Accepted: 12/14/2012] [Indexed: 11/25/2022] Open
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Loo JA, Darie CC. Investigation of stable and transient protein-protein interactions: Past, present, and future. Proteomics 2013. [PMID: 23193082 DOI: 10.1002/pmic.201200328] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (PPIs) with a focus on their function within cells, organs, and organisms. The significance of PTMs within the PPIs is also discussed. We focus on methods to study PPIs and methods of detecting PPIs, with particular emphasis on electrophoresis-based and MS-based investigation of PPIs, including specific examples. The validation of PPIs is emphasized and the limitations of the current methods for studying stable and transient PPIs are discussed. Perspectives regarding PPIs, with focus on bioinformatics and transient PPIs are also provided.
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Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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Dong W, Luo J, He H, Jiang L. A reinforced composite structure composed of polydiacetylene assemblies deposited on polystyrene microspheres and its application to H5N1 virus detection. Int J Nanomedicine 2013; 8:221-32. [PMID: 23403826 PMCID: PMC3565586 DOI: 10.2147/ijn.s39676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In this study, we immobilized polydiacetylene vesicles (PDAVs) onto the surface of polystyrene (PS) microspheres (1 μm in diameter) by using both electrical charge and conjugated forces to form a reinforced composite structure. These reinforced complexes could be easily washed, separated by centrifugation, and resuspended by gentle agitation. After passing through a narrow 200 μm-diameter channel, the composite structures maintained their original shape, demonstrating their resilience and potential for use in microfluidic technologies. The number of PDAVs in the composite structure could be mediated by changing the extent of layer deposition, which affected the sensitivity of detection. It showed that PDAVs did not change their blue color after addition of detecting probes such as anti-H5N1, which was of great importance in the fabrication and modification of stable color-changeable biosensors based on PDAVs. By conjugating anti-H5N1 antibodies to the PS@PDAV via N -hydroxysuccinimide and 1-ethyl3-(3-dimethylaminopropyl) carbodiimide chemistry, a stable blue complex, anti-H5N1 microsphere (PS@PDAV-anti-H5N1) was formed. A target antigen of H5N1 (HAQ [H5N1 strain A/ environment/Qinghai/1/2008{H5N1} in clade 0]) was detected by PS@PDAV-anti-H5N1. At an optimal PDAV deposition level of three layers, the limit of detection was determined to be approximately 3 0 ng/mL of HAQ by using optical spectrum measurement and visual inspection, meeting the needs of fast and simple color-changeable detection. However, a much lower limitation of detection (1 ng/mL) was able to be obtained using laser-scanning confocal microscopy, which could be compared with the results obtained with other sophisticated equipment.
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Affiliation(s)
- Wenjie Dong
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, People's Republic of China
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Calabrese AN, Wang T, Bowie JH, Pukala TL. Negative ion fragmentations of disulfide-containing cross-linking reagents are competitive with aspartic acid side-chain-induced cleavages. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:238-248. [PMID: 23239338 DOI: 10.1002/rcm.6445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/14/2012] [Accepted: 10/18/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE It has been shown that the disulfide moiety in the chemical cross-linking reagent dithiobis(succinimidyl)propionate (DSP), which is similar in structure to the natural cystine disulfide, cleaves preferentially to the peptide backbone in the negative ion mode. However, the tandem mass (MS/MS) spectra of peptides in the negative ion mode are often dominated by products arising from low-energy, side-chain-induced processes, which may compete with any facile cross-linker fragmentations and complicate identification of chemical cross-links in a complex mixture. METHODS Two disulfide-containing crosslinking reagents similar to DSP, but with varying spacer arm lengths, were synthesized and the MS/MS spectra of several model peptides cross-linked with these reagents were investigated. Theoretical calculations were used to describe the energetics of the cross-linker fragmentations as well as several low-energy side-chain-induced fragmentations which compete with disulfide cleavages. RESULTS Altering the spacer arm length of the cross-linker, such that there is one methylene group less than in DSP, results in a more facile cleavage process, whilst the opposite is true when a methylene group is added. Of the low-energy side-chain-induced fragmentations studied, only those from aspartic acid compete significantly with those of the cross-linker disulfide. CONCLUSIONS Low-energy cleavage processes from aspartic acid that compete with cross-linker fragmentations occur in the negative ion MS/MS spectra of the cross-linked peptides, irrespective of the spacer arm length. Other fragmentation pathways do not significantly interfere with low-energy disulfide cleavage, making the presence of additional product ions in the MS/MS spectrum diagnostic for the presence of aspartic acid.
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Affiliation(s)
- Antonio N Calabrese
- School of Chemistry and Physics, The University of Adelaide, Adelaide, SA, Australia, 5005
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46
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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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Mitchell N, Kalber TL, Cooper MS, Sunassee K, Chalker SL, Shaw KP, Ordidge KL, Badar A, Janes SM, Blower PJ, Lythgoe MF, Hailes HC, Tabor AB. Incorporation of paramagnetic, fluorescent and PET/SPECT contrast agents into liposomes for multimodal imaging. Biomaterials 2013; 34:1179-92. [PMID: 23131536 PMCID: PMC3520009 DOI: 10.1016/j.biomaterials.2012.09.070] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 09/28/2012] [Indexed: 12/20/2022]
Abstract
A series of metal-chelating lipid conjugates has been designed and synthesized. Each member of the series bears a 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) macrocycle attached to the lipid head group, using short n-ethylene glycol (n-EG) spacers of varying length. Liposomes incorporating these lipids, chelated to Gd(3+), (64)Cu(2+), or (111)In(3+), and also incorporating fluorescent lipids, have been prepared, and their application in optical, magnetic resonance (MR) and single-photon emission tomography (SPECT) imaging of cellular uptake and distribution investigated in vitro and in vivo. We have shown that these multimodal liposomes can be used as functional MR contrast agents as well as radionuclide tracers for SPECT, and that they can be optimized for each application. When shielded liposomes were formulated incorporating 50% of a lipid with a short n-EG spacer, to give nanoparticles with a shallow but even coverage of n-EG, they showed good cellular internalization in a range of tumour cells, compared to the limited cellular uptake of conventional shielded liposomes formulated with 7% 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[carboxy(polyethyleneglycol)(2000)] (DSPE-PEG2000). Moreover, by matching the depth of n-EG coverage to the length of the n-EG spacers of the DOTA lipids, we have shown that similar distributions and blood half lives to DSPE-PEG2000-stabilized liposomes can be achieved. The ability to tune the imaging properties and distribution of these liposomes allows for the future development of a flexible tri-modal imaging agent.
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Key Words
- dota-lipid
- liposome
- mri (magnetic resonance imaging)
- peg (poly(ethylene)glycol)
- spect (single-photon emission tomography)
- dcc, n,n-dicyclohexylcarbodiimide
- deg1sl, dioleylethyleneglycol-1-succidimidyl linker
- deg3sl, dioleylethyleneglycol-3-succidimidyl linker
- deg6sl, dioleylethyleneglycol-6-succidimidyl linker
- dodeg4, dioleyldimethyl ethylene glycol 4
- dope, 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
- dota, 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid
- dotma, n-[1-(2,3-dioleyloxy)propyl]-n,n,n-trimethylammonium chloride
- dspe-peg2000, 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-n-[carboxy(polyethyleneglycol)2000]
- dtpa, diethylenetriamine pentacetic acid
- n-eg, n-ethylene glycol
- epr, enhanced permeability and retention effect
- fl-dhpe, n-(fluorescein-5-thiocarbamoyl)-1,2-dihexa-decanoyl-sn-glycero-3-phosphoethanolamine
- hbtu, o-(benzotriazol-1-yl)-n,n,n′,n′-tetramethyluronium hexafluorophosphate
- itlc, instant thin layer chromatography
- mr, magnetic resonance
- peg, polyethylene glycol
- pet, positron emission tomography
- res, reticuloendothelial system
- spect, single-photon emission tomography
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Affiliation(s)
- Nick Mitchell
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon St, London WC1H 0AJ, UK
| | - Tammy L. Kalber
- Centre of Advanced Biomedical Imaging, Division of Medicine and Institute of Child Health, University College London, 72 Huntley Street, WC1E 6DD, UK
- Centre for Respiratory Research, University College London, Rayne Building, 5 University Street, WC1E 6JJ, UK
| | - Margaret S. Cooper
- King's College London, St. Thomas' Hospital, Division of Imaging Sciences and Biomedical Engineering, 4th Floor, Lambeth Wing, St Thomas' Hospital, London SE1 7EH, UK
| | - Kavitha Sunassee
- King's College London, St. Thomas' Hospital, Division of Imaging Sciences and Biomedical Engineering, 4th Floor, Lambeth Wing, St Thomas' Hospital, London SE1 7EH, UK
| | - Samantha L. Chalker
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon St, London WC1H 0AJ, UK
- Royal Institution of Great Britain, Davy Faraday Research Laboratories, 21 Albemarle Street, London W1S 4BS, UK
| | - Karen P. Shaw
- Centre for Respiratory Research, University College London, Rayne Building, 5 University Street, WC1E 6JJ, UK
| | - Katherine L. Ordidge
- Centre of Advanced Biomedical Imaging, Division of Medicine and Institute of Child Health, University College London, 72 Huntley Street, WC1E 6DD, UK
- Centre for Respiratory Research, University College London, Rayne Building, 5 University Street, WC1E 6JJ, UK
| | - Adam Badar
- Centre of Advanced Biomedical Imaging, Division of Medicine and Institute of Child Health, University College London, 72 Huntley Street, WC1E 6DD, UK
| | - Samuel M. Janes
- Centre for Respiratory Research, University College London, Rayne Building, 5 University Street, WC1E 6JJ, UK
| | - Philip J. Blower
- King's College London, St. Thomas' Hospital, Division of Imaging Sciences and Biomedical Engineering, 4th Floor, Lambeth Wing, St Thomas' Hospital, London SE1 7EH, UK
- King's College London, Division of Chemistry, Hodgkin Building, Guy's Campus, London SE1 1UL, UK
| | - Mark F. Lythgoe
- Centre of Advanced Biomedical Imaging, Division of Medicine and Institute of Child Health, University College London, 72 Huntley Street, WC1E 6DD, UK
| | - Helen C. Hailes
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon St, London WC1H 0AJ, UK
| | - Alethea B. Tabor
- Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon St, London WC1H 0AJ, UK
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48
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Affiliation(s)
- David L Tabb
- Departments of Biomedical Informatics and Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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49
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Calabrese AN, Good NJ, Wang T, He J, Bowie JH, Pukala TL. A negative ion mass spectrometry approach to identify cross-linked peptides utilizing characteristic disulfide fragmentations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1364-1375. [PMID: 22644737 DOI: 10.1007/s13361-012-0407-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/29/2012] [Accepted: 04/30/2012] [Indexed: 06/01/2023]
Abstract
Chemical cross-linking combined with mass spectrometry (MS) is an analytical tool used to elucidate the topologies of proteins and protein complexes. However, identification of the low abundance cross-linked peptides and modification sites amongst a large quantity of proteolytic fragments remains challenging. In this work, we present a strategy to identify cross-linked peptides by negative ion MS for the first time. This approach is based around the facile cleavages of disulfide bonds in the negative mode, and allows identification of cross-linked products based on their characteristic fragmentations. MS(3) analysis of the cross-linked peptides allows for their sequencing and identification, with residue specific location of cross-linking sites. We demonstrate the applicability of the commercially available cystine based cross-linking reagent dithiobis(succinimidyl) propionate (DSP) and identify cross-linked peptides from ubiquitin. In each instance, the characteristic fragmentation behavior of the cross-linked species is described. The data presented here indicate that this negative ion approach may be a useful tool to characterize the structures of proteins and protein complexes, and provides the basis for the development of high throughput negative ion MS chemical cross-linking strategies.
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Affiliation(s)
- Antonio N Calabrese
- School of Chemistry and Physics, The University of Adelaide, Adelaide, SA, 5005, Australia
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50
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Auclair JR, Somasundaran M, Green KM, Evans JE, Schiffer CA, Ringe D, Petsko GA, Agar JN. Mass spectrometry tools for analysis of intermolecular interactions. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 896:387-98. [PMID: 22821539 DOI: 10.1007/978-1-4614-3704-8_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The small quantities of protein required for mass spectrometry (MS) make it a powerful tool to detect binding (protein-protein, protein-small molecule, etc.) of proteins that are difficult to express in large quantities, as is the case for many intrinsically disordered proteins. Chemical cross-linking, proteolysis, and MS analysis, combined, are a powerful tool for the identification of binding domains. Here, we present a traditional approach to determine protein-protein interaction binding sites using heavy water ((18)O) as a label. This technique is relatively inexpensive and can be performed on any mass spectrometer without specialized software.
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Affiliation(s)
- Jared R Auclair
- Department of Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA.
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