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Zhou S, Li Z, Li Y, Wang X, Deng K. Construction of a cleavable linker chemistry-based HBEXO-Chip to isolate circulating exosomes for breast cancer diagnosis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:6738-6749. [PMID: 38054244 DOI: 10.1039/d3ay01938a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Breast cancer is presently the most common form of malignant tumour globally, and its precise diagnosis is vital for enhancing patient survival rates and their quality of life. Exosomes, which are small extracellular vesicles containing proteins and nucleic acid molecules, have emerged as ideal cancer markers for liquid biopsy-based diagnostics. Nevertheless, the current methods for isolating exosomes present challenges for clinical implementation. Although immunoaffinity-based microfluidics hold potential for exosome-based cancer diagnostics, existing microfluidic chips struggle to capture and release intact, high-purity, and highly specific exosomes effectively. To surmount these obstacles, we developed the HBEXO-Chip, an innovative immunoaffinity microfluidic device that employs cleavable linker chemistry technology. This chip enables rapid isolation and detection of breast cancer-derived exosomes in peripheral blood. The fishbone-like microfluidic chip design of the HBEXO-Chip heightens the binding likelihood between specific exosomes and antibodies, significantly augmenting capture efficiency. Furthermore, the gentle reaction conditions of the cleavable linker chemistry retain the exosomes' membrane structure's integrity during the release process, which is advantageous for downstream experimental analysis. Our study demonstrated the effectiveness of the HBEXO-Chip in distinguishing breast cancer patients, patients with benign breast tumours, and healthy controls. By quantitatively analysing Epcam+ exosomes in clinical plasma samples, this technology platform provides a quick, user-friendly, highly sensitive, and specific assay for detecting tumour exosomes in peripheral blood, making it a valuable liquid biopsy tool for clinicians to diagnose breast cancer.
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Affiliation(s)
- Shanshan Zhou
- Department of Laboratory Medicine, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
| | - Zongxin Li
- Department of Laboratory Medicine, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
| | - Yan Li
- Department of Laboratory Medicine, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
| | - Xiaoyao Wang
- Department of Laboratory Medicine, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
| | - Kun Deng
- Department of Laboratory Medicine, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
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2
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Murvai N, Gellen G, Micsonai A, Schlosser G, Kardos J. Cross-Linked α-Synuclein as Inhibitor of Amyloid Formation. Int J Mol Sci 2023; 24:13403. [PMID: 37686208 PMCID: PMC10487470 DOI: 10.3390/ijms241713403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The aggregation and amyloid formation of α-synuclein is associated with Parkinson's disease and other synucleinopathies. In its native, monomeric form α-synuclein is an intrinsically disordered protein represented by highly dynamic conformational ensembles. Inhibition of α-synuclein aggregation using small molecules, peptides, or proteins has been at the center of interest in recent years. Our aim was to explore the effects of cross-linking on the structure and aggregation/amyloid formation properties of α-synuclein. Comparative analysis of available high-resolution amyloid structures and representative structural models and MD trajectory of monomeric α-synuclein revealed that potential cross-links in the monomeric protein are mostly incompatible with the amyloid forms and thus might inhibit fibrillation. Monomeric α-synuclein has been intramolecularly chemically cross-linked under various conditions using different cross-linkers. We determined the location of cross-links and their frequency using mass spectrometry and found that most of them cannot be realized in the amyloid structures. The inhibitory potential of cross-linked proteins has been experimentally investigated using various methods, including thioflavin-T fluorescence and transmission electron microscopy. We found that conformational constraints applied by cross-linking fully blocked α-synuclein amyloid formation. Moreover, DTSSP-cross-linked molecules exhibited an inhibitory effect on the aggregation of unmodified α-synuclein as well.
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Affiliation(s)
- Nikoletta Murvai
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
- ELTE—Functional Nucleic Acid Motifs Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Gabriella Gellen
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - András Micsonai
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
- ELTE—Functional Nucleic Acid Motifs Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
| | - József Kardos
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
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3
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Chen YF, Hsu MW, Su YC, Chang HM, Chang CH, Jan JS. Naturally derived DNA nanogels as pH- and glutathione-triggered anticancer drug carriers. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 114:111025. [PMID: 32994007 DOI: 10.1016/j.msec.2020.111025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/08/2020] [Accepted: 04/27/2020] [Indexed: 12/25/2022]
Abstract
Conventional chemotherapeutic drugs are nonselective and harmful toward normal tissues, causing severe side effects. Therefore, the development of chemotherapeutics that can target cancer cells and improve therapeutic efficacy is of high priority. Biomolecules isolated from nature serve as green solutions for biomedical use, solving biocompatibility and cytotoxicity issues in human bodies. Herein, we use kiwifruit-derived DNA to encapsulate doxorubicin (DOX) using crosslinkers, eventually forming DNA-DOX nanogels (NGs). Drug releasing assays, cell viability and anticancer effects were analyzed to evaluate the DNA NGs' applications. The amount of DOX released by the DOX-loaded DNA (DNA-DOX) NGs at acidic pH was higher than that of neutral pH, and high glutathione (GSH) concentration also triggered more DOX to release in cancer cells, demonstrating pH- and GSH-triggered drug release characteristics of the DNA NGs. The IC50 of DNA-DOX NGs in cancer cells was lower than that of free DOX. Moreover, DOX uptake of cancer cells and apoptotic death were enhanced by the DNA-DOX NGs compared to free DOX. The results suggest that the DNA NGs cross-linked via nitrogen bases of the nucleotides in DNA and presenting pH- and GSH-dependent drug releasing behavior can be alternative biocompatible drug delivery systems for anticancer strategies and other biomedical applications.
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Affiliation(s)
- Yu-Fon Chen
- Department of Chemical Engineering, National Cheng Kung University, No. 1 University Rd., Tainan 70101, Taiwan
| | - Ming-Wei Hsu
- Department of Chemical Engineering, National Cheng Kung University, No. 1 University Rd., Tainan 70101, Taiwan
| | - Yu-Chu Su
- Department of Otolaryngology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No. 1 University Rd., Tainan 70101, Taiwan
| | - Ho-Min Chang
- Department of Chemical Engineering, National Cheng Kung University, No. 1 University Rd., Tainan 70101, Taiwan
| | - Chien-Hsiang Chang
- Department of Chemical Engineering, National Cheng Kung University, No. 1 University Rd., Tainan 70101, Taiwan.
| | - Jeng-Shiung Jan
- Department of Chemical Engineering, National Cheng Kung University, No. 1 University Rd., Tainan 70101, Taiwan.
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4
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Zhan L, Liu Y, Xie X, Xiong C, Nie Z. Heat-Induced Rearrangement of the Disulfide Bond of Lactoglobulin Characterized by Multiply Charged MALDI-TOF/TOF Mass Spectrometry. Anal Chem 2018; 90:10670-10675. [DOI: 10.1021/acs.analchem.8b02563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Lingpeng Zhan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Liu
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaobo Xie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- National Center for Mass Spectrometry in Beijing, Beijing 100190, China
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5
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Kang YT, Kim YJ, Bu J, Cho YH, Han SW, Moon BI. High-purity capture and release of circulating exosomes using an exosome-specific dual-patterned immunofiltration (ExoDIF) device. NANOSCALE 2017; 9:13495-13505. [PMID: 28862274 DOI: 10.1039/c7nr04557c] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We present a microfluidic device for the capture and release of circulating exosomes from human blood. The exosome-specific dual-patterned immunofiltration (ExoDIF) device is composed of two distinct immuno-patterned layers, and is capable of enhancing the chance of binding between the antibody and exosomes by generating mechanical whirling, thus achieving high-throughput exosome isolation with high specificity. Moreover, follow-up recovery after the immuno-affinity based isolation, via cleavage of a linker, enables further downstream analysis. We verified the performance of the present device using MCF-7 secreted exosomes and found that both the concentration and proportion of exosome-sized vesicles were higher than in the samples obtained from the conventional exosome isolation kit. We then isolated exosomes from the human blood samples with our device to compare the exosome level between cancer patients and healthy donors. Cancer patients show a significantly higher exosome level with higher selectivity when validating the exosome-sized vesicles using both electron microscopy and nanoparticle tracking analysis. The captured exosomes from cancer patients also express abundant cancer-associated antigens, the epithelial cell adhesion molecule (EpCAM) on their surface. Our simple and rapid exosome recovery technique has huge potential to elucidate the function of exosomes in cancer patients and can thus be applied for various exosome-based cancer research studies.
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Affiliation(s)
- Yoon-Tae Kang
- Cell Bench Research Center, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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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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7
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Liu L, Mayo DJ, Sahu ID, Zhou A, Zhang R, McCarrick RM, Lorigan GA. Determining the Secondary Structure of Membrane Proteins and Peptides Via Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. Methods Enzymol 2015; 564:289-313. [PMID: 26477255 DOI: 10.1016/bs.mie.2015.06.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Revealing detailed structural and dynamic information of membrane embedded or associated proteins is challenging due to their hydrophobic nature which makes NMR and X-ray crystallographic studies challenging or impossible. Electron paramagnetic resonance (EPR) has emerged as a powerful technique to provide essential structural and dynamic information for membrane proteins with no size limitations in membrane systems which mimic their natural lipid bilayer environment. Therefore, tremendous efforts have been devoted toward the development and application of EPR spectroscopic techniques to study the structure of biological systems such as membrane proteins and peptides. This chapter introduces a novel approach established and developed in the Lorigan lab to investigate membrane protein and peptide local secondary structures utilizing the pulsed EPR technique electron spin echo envelope modulation (ESEEM) spectroscopy. Detailed sample preparation strategies in model membrane protein systems and the experimental setup are described. Also, the ability of this approach to identify local secondary structure of membrane proteins and peptides with unprecedented efficiency is demonstrated in model systems. Finally, applications and further developments of this ESEEM approach for probing larger size membrane proteins produced by overexpression systems are discussed.
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Affiliation(s)
- Lishan Liu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA.
| | - Daniel J Mayo
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Andy Zhou
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Rongfu Zhang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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8
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Premkumar L, Kurth F, Duprez W, Grøftehauge MK, King GJ, Halili MA, Heras B, Martin JL. Structure of the Acinetobacter baumannii dithiol oxidase DsbA bound to elongation factor EF-Tu reveals a novel protein interaction site. J Biol Chem 2014; 289:19869-80. [PMID: 24860094 DOI: 10.1074/jbc.m114.571737] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The multidrug resistant bacterium Acinetobacter baumannii is a significant cause of nosocomial infection. Biofilm formation, that requires both disulfide bond forming and chaperone-usher pathways, is a major virulence trait in this bacterium. Our biochemical characterizations show that the periplasmic A. baumannii DsbA (AbDsbA) enzyme has an oxidizing redox potential and dithiol oxidase activity. We found an unexpected non-covalent interaction between AbDsbA and the highly conserved prokaryotic elongation factor, EF-Tu. EF-Tu is a cytoplasmic protein but has been localized extracellularly in many bacterial pathogens. The crystal structure of this complex revealed that the EF-Tu switch I region binds to the non-catalytic surface of AbDsbA. Although the physiological and pathological significance of a DsbA/EF-Tu association is unknown, peptides derived from the EF-Tu switch I region bound to AbDsbA with submicromolar affinity. We also identified a seven-residue DsbB-derived peptide that bound to AbDsbA with low micromolar affinity. Further characterization confirmed that the EF-Tu- and DsbB-derived peptides bind at two distinct sites. These data point to the possibility that the non-catalytic surface of DsbA is a potential substrate or regulatory protein interaction site. The two peptides identified in this work together with the newly characterized interaction site provide a novel starting point for inhibitor design targeting AbDsbA.
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Affiliation(s)
- Lakshmanane Premkumar
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Fabian Kurth
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Wilko Duprez
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Morten K Grøftehauge
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Gordon J King
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Maria A Halili
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Begoña Heras
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Jennifer L Martin
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
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9
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Rudashevskaya EL, Breitwieser FP, Huber ML, Colinge J, Müller AC, Bennett KL. Multiple and Sequential Data Acquisition Method: An Improved Method for Fragmentation and Detection of Cross-Linked Peptides on a Hybrid Linear Trap Quadrupole Orbitrap Velos Mass Spectrometer. Anal Chem 2013; 85:1454-61. [DOI: 10.1021/ac302251f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Elena L. Rudashevskaya
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Florian P. Breitwieser
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marie L. Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department
of Dermatology, Division
of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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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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11
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Stamenović MM, Espeel P, Baba E, Yamamoto T, Tezuka Y, Du Prez FE. Straightforward synthesis of functionalized cyclic polymers in high yield via RAFT and thiolactone–disulfide chemistry. Polym Chem 2013. [DOI: 10.1039/c2py20751f] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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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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13
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Clifford-Nunn B, Showalter HDH, Andrews PC. Quaternary diamines as mass spectrometry cleavable crosslinkers for protein interactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:201-12. [PMID: 22131227 PMCID: PMC3573217 DOI: 10.1007/s13361-011-0288-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 10/20/2011] [Accepted: 10/22/2011] [Indexed: 05/11/2023]
Abstract
Mapping protein interactions and their dynamics is crucial to defining physiologic states, building effective models for understanding cell function, and to allow more effective targeting of new drugs. Crosslinking studies can estimate the proximity of proteins, determine sites of protein-protein interactions, and have the potential to provide a snapshot of dynamic interactions by covalently locking them in place for analysis. Several major challenges are associated with the use of crosslinkers in mass spectrometry, particularly in complex mixtures. We describe the synthesis and characterization of a MS-cleavable crosslinker containing cyclic amines, which address some of these challenges. The DC4 crosslinker contains two intrinsic positive charges, which allow crosslinked peptides to fragment into their component peptides by collision-induced dissociation (CID) or in-source decay. Initial fragmentation events result in cleavage on either side of the positive charges so crosslinked peptides are identified as pairs of ions separated by defined masses. The structures of the component peptides can then be robustly determined by MS(3) because their fragmentation products rearrange to generate a mobile proton. The DC4 crosslinking reagent is stable to storage, highly reactive, highly soluble (1 M solutions), quite labile to CID, and MS(3) results in productive backbone fragmentation.
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Affiliation(s)
- Billy Clifford-Nunn
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, USA
| | - H. D. Hollis Showalter
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan Vahlteich Medicinal Chemistry Core, Ann Arbor, MI, USA
| | - Philip C. Andrews
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Room 1198, 300 North Ingalls Building, 300 North Ingalls St., Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
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14
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Serpa JJ, Parker CE, Petrotchenko EV, Han J, Pan J, Borchers CH. Mass spectrometry-based structural proteomics. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2012; 18:251-267. [PMID: 22641729 DOI: 10.1255/ejms.1178] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Structural proteomics is the application of protein chemistry and modern mass spectrometric techniques to problems such as the characterization of protein structures and assemblies and the detailed determination of protein-protein interactions. The techniques used in structural proteomics include crosslinking, photoaffinity labeling, limited proteolysis, chemical protein modification and hydrogen/deuterium exchange, all followed by mass spectrometric analysis. None of these methods alone can provide complete structural information, but a "combination" of these complementary approaches can be used to provide enough information for answering important biological questions. Structural proteomics can help to determine, for example, the detailed structure of the interfaces between proteins that may be important drug targets and the interactions between proteins and ligands. In this review, we have tried to provide a brief overview of structural proteomics methodologies, illustrated with examples from our laboratory and from the literature.
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Affiliation(s)
- Jason J Serpa
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC V8Z 7X8, Canada
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15
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Mädler S, Boeri Erba E, Zenobi R. MALDI-ToF mass spectrometry for studying noncovalent complexes of biomolecules. Top Curr Chem (Cham) 2012; 331:1-36. [PMID: 22371170 DOI: 10.1007/128_2011_311] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been demonstrated to be a valuable tool to investigate noncovalent interactions of biomolecules. The direct detection of noncovalent assemblies is often more troublesome than with electrospray ionization. Using dedicated sample preparation techniques and carefully optimized instrumental parameters, a number of biomolecule assemblies were successfully analyzed. For complexes dissociating under MALDI conditions, covalent stabilization with chemical cross-linking is a suitable alternative. Indirect methods allow the detection of noncovalent assemblies by monitoring the fading of binding partners or altered H/D exchange patterns.
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Affiliation(s)
- Stefanie Mädler
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
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Lambert W, Söderberg CAG, Rutsdottir G, Boelens WC, Emanuelsson C. Thiol-exchange in DTSSP crosslinked peptides is proportional to cysteine content and precisely controlled in crosslink detection by two-step LC-MALDI MSMS. Protein Sci 2011; 20:1682-91. [PMID: 21780214 DOI: 10.1002/pro.699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 07/04/2011] [Accepted: 07/07/2011] [Indexed: 11/06/2022]
Abstract
The lysine-specific crosslinker 3,3'-dithiobis(sulfosuccinimidylpropionate) (DTSSP) is commonly used in the structural characterization of proteins by chemical crosslinking and mass spectrometry and we here describe an efficient two-step LC-MALDI-TOF/TOF procedure to detect crosslinked peptides. First MS data are acquired, and the properties of isotope-labeled DTSSP are used in data analysis to identify candidate crosslinks. MSMS data are then acquired for a restricted number of precursor ions per spot for final crosslink identification. We show that the thiol-catalyzed exchange between crosslinked peptides, which is due to the disulfide bond in DTSSP and known to possibly obscure data, can be precisely quantified using isotope-labeled DTSSP. Crosslinked peptides are recognized as 8 Da doublet peaks and a new isotopic peak with twice the intensity appears in the middle of the doublet as a consequence of the thiol-exchange. False-positive crosslinks, formed exclusively by thiol-exchange, yield a 1:2:1 isotope pattern, whereas true crosslinks, formed by two lysine residues within crosslinkable distance in the native protein structure, yield a 1:0:1 isotope pattern. Peaks with a 1:X:1 isotope pattern, where 0 < X < 2, can be trusted as true crosslinks, with a defined proportion of the signal [2X/(2 + X)] being noise from the thiol-exchange. The thiol-exchange was correlated with the protein cysteine content and was minimized by shortening the trypsin incubation time, and for two molecular chaperone proteins with known structure all crosslinks fitted well to the structure data. The thiol-exchange can thus be controlled and isotope-labeled DTSSP safely used to detect true crosslinks between lysine residues in proteins.
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Affiliation(s)
- Wietske Lambert
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden.
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Clark DF, Go EP, Toumi ML, Desaire H. Collision induced dissociation products of disulfide-bonded peptides: ions result from the cleavage of more than one bond. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:492-8. [PMID: 21472567 PMCID: PMC3543116 DOI: 10.1007/s13361-010-0064-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 11/19/2010] [Accepted: 12/16/2010] [Indexed: 05/04/2023]
Abstract
Disulfide bonds are a post-translational modification (PTM) that can be scrambled or shuffled to non-native bonds during recombinant expression, sample handling, or sample purification. Currently, mapping of disulfide bonds is not easy because of various sample requirements and data analysis difficulties. One step towards facilitating this difficult work is developing a better understanding of how disulfide-bonded peptides fragment during collision induced dissociation (CID). Most automated analysis algorithms function based on the assumption that the preponderance of product ions observed during the dissociation of disulfide-bonded peptides result from the cleavage of just one peptide bond, and in this report we tested that assumption by extensively analyzing the product ions generated when several disulfide-bonded peptides are subjected to CID on a quadrupole time of flight (QTOF) instrument. We found that one of the most common types of product ions generated resulted from two peptide bond cleavages, or a double cleavage. We found that for several of the disulfide-bonded peptides analyzed, the number of double cleavage product ions outnumbered those of single cleavages. The influence of charge state and precursor ion size was investigated, to determine if those parameters dictated the amount of double cleavage product ions formed. It was found in this sample set that no strong correlation existed between the charge state or peptide size and the portion of product ions assigned as double cleavages. These data show that these ions could account for many of the product ions detected in CID data of disulfide bonded peptides. We also showed the utility of double cleavage product ions on a peptide with multiple cysteines present. Double cleavage products were able to fully characterize the bonding pattern of each cysteine where typical single b/y cleavage products could not.
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Affiliation(s)
| | | | | | - Heather Desaire
- To whom correspondence should be addressed. Phone: (785) 864-3015, Fax: 785-864-5396,
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Lauber MA, Reilly JP. Novel amidinating cross-linker for facilitating analyses of protein structures and interactions. Anal Chem 2011; 82:7736-43. [PMID: 20795639 DOI: 10.1021/ac101586z] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel bifunctional thioimidate cross-linking reagent (diethyl suberthioimidate) that modifies amines without sacrificing their native basicity is developed. Intermolecular cross-linking of neurotensin and intramolecular cross-linking of cytochrome c under physiological conditions is investigated with this reagent. Because it does not perturb the electrostatic properties of a protein, it is unlikely to lead to artifactual conclusions about native protein structure. The interpeptide cross-links formed with this reagent are easily separated from other tryptic fragments using strong cation exchange chromatography, and they have a readily identified mass spectrometric signature. The use of this novel amidinating protein cross-linking reagent holds great promise for efficient, large-scale structural analysis of complex systems.
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Affiliation(s)
- Matthew A Lauber
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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Santos LFA, Iglesias AH, Pilau EJ, Gomes AF, Gozzo FC. Traveling-wave ion mobility mass spectrometry analysis of isomeric modified peptides arising from chemical cross-linking. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:2062-2069. [PMID: 20864354 DOI: 10.1016/j.jasms.2010.08.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 08/19/2010] [Accepted: 08/24/2010] [Indexed: 05/29/2023]
Abstract
Traveling-wave ion mobility (TWIM) coupled to mass spectrometry (MS) has emerged as a powerful tool for structural and conformational analysis of proteins and peptides, allowing the analysis of isomeric peptides (or proteins) with the same sequence but modified at different residues. This work demonstrates the use of the novel TWIM-MS technique to separate isomeric peptide ions derived from chemical cross-linking experiments, which enables the acquisition of distinct product ion spectra for each isomer, clearly indicating modification on different sites. Experiments were performed with four synthetic peptides, for which variable degrees of mobility separation were achieved. In cases of partially overlapping mobility arrival time distributions (ATDs), extracting the ATDs of fragment ions belonging to each individual isomer allowed their separation into two distinct ATDs. Accumulation over regions from the specific ATDs generates the product ion spectrum of each isomer, or a spectrum highly enriched in their fragments. The population of both modified peptide isomers was correlated with the intrinsic reactivities of different Lys residues from reactions conducted at different pH conditions.
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Affiliation(s)
- Luiz F A Santos
- Institute of Chemistry, University of Campinas and Instituto Nacional de Ciencia e Tecnologia de Bioanalitica, Sao Paulo, Brazil
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Gardner MW, Brodbelt JS. Preferential Cleavage of N−N Hydrazone Bonds for Sequencing Bis-arylhydrazone Conjugated Peptides by Electron Transfer Dissociation. Anal Chem 2010; 82:5751-9. [DOI: 10.1021/ac100788a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Myles W. Gardner
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712
| | - Jennifer S. Brodbelt
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712
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Yang H, Liu N, Qiu X, Liu S. A new method for analysis of disulfide-containing proteins by matrix-assisted laser desorption ionization (MALDI) mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:2284-93. [PMID: 19815426 DOI: 10.1016/j.jasms.2009.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 08/24/2009] [Accepted: 08/24/2009] [Indexed: 05/24/2023]
Abstract
A simple and high-throughput method for the identification of disulfide-containing peptides utilizing peptide-matrix adducts is described. Some commonly used matrices in MALDI mass spectrometry were found to specifically react with sulfhydryl groups within peptide, thus allowing the observation of the peptide-matrix adduct ion [M + n + n' matrix + H]+ or [M + n + n' matrix + Na]+ (n = the number of cysteine residues, n' = 1, 2, ... , n) in MALDI mass spectra after chemical reduction of disulfide-linked peptides. Among several matrices tested, alpha-cyano-4-hydroxycinnamic acid (CHCA, molecular mass 189 Da) and alpha-cyano-3-hydroxycinnamic acid (3-HCCA) were found to be more effective for MALDI analysis of disulfide-containing peptides/proteins. Two reduced cysteines involved in a disulfide bridge resulted in a mass shift of 189 Da per cysteine, so the number of disulfide bonds could then be determined, while for the other matrices (sinapinic acid, ferulic acid, and caffeic acid), a similar addition reaction could not occur unless the reaction was carried out under alkaline conditions. The underlying mechanism of the reaction of the matrix addition at sulfhydryl groups is proposed, and several factors that might affect the formation of the peptide-matrix adducts were investigated. In general, this method is fast, effective, and robust to identify disulfide bonds in proteins/peptides.
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Affiliation(s)
- Hongmei Yang
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P.R. China
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22
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United we stand: combining structural methods. Curr Opin Struct Biol 2008; 18:617-22. [DOI: 10.1016/j.sbi.2008.07.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 07/29/2008] [Indexed: 01/20/2023]
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