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Samgina TY, Vasileva ID, Zubarev RA, Lebedev AT. EThcD as a Unique Tool for the Top-Down De Novo Sequencing of Intact Natural Ranid Amphibian Peptides. Anal Chem 2024; 96:12057-12064. [PMID: 38979842 DOI: 10.1021/acs.analchem.4c02109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
De novo sequencing of any novel peptide/protein is a difficult task. Full sequence coverage, isomeric amino acid residues, inter- and intramolecular S-S bonds, and numerous other post-translational modifications make the investigators employ various chemical modifications, providing a variety of specific fragmentation MSn patterns. The chemical processes are time-consuming, and their yields never reach 100%, while the subsequent purification often leads to the loss of minor components of the initial peptide mixture. Here, we present the advantages of the EThcD method that enables establishing the full sequence of natural intact peptides of ranid frogs in de novo top-down mode without any chemical modifications. The method provides complete sequence coverage, including the cyclic disulfide section, and reliable identification of isomeric leucine/isoleucine residues. The proposed approach demonstrated its efficiency in the analysis of peptidomes of ranid frogs from several populations of Rana arvalis, Rana temporaria, and Pelophylax esculentus complexes.
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Affiliation(s)
- Tatiana Yu Samgina
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Irina D Vasileva
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Roman A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, Stockholm 17177, Sweden
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow 117198, Russia
| | - Albert T Lebedev
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
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2
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Tageldin A, Omolo CA, Nyandoro VO, Elhassan E, Kassam SZF, Peters XQ, Govender T. Engineering dynamic covalent bond-based nanosystems for delivery of antimicrobials against bacterial infections. J Control Release 2024; 371:237-257. [PMID: 38815705 DOI: 10.1016/j.jconrel.2024.05.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Nanodrug delivery systems (NDDS) continue to be explored as novel strategies enhance therapy outcomes and combat microbial resistance. The need for the formulation of smart drug delivery systems for targeting infection sites calls for the engineering of responsive chemical designs such as dynamic covalent bonds (DCBs). Stimuli response due to DCBs incorporated into nanosystems are emerging as an alternative way to target infection sites, thus enhancing the delivery of antibacterial agents. This leads to the eradication of bacterial infections and the reduction of antimicrobial resistance. Incorporating DCBs on the backbone of the nanoparticles endows the systems with several properties, including self-healing, controlled disassembly, and stimuli responsiveness, which are beneficial in the delivery and release of the antimicrobial at the infection site. This review provides a comprehensive and current overview of conventional DCBs-based nanosystems, stimuli-responsive DCBs-based nanosystems, and targeted DCBs-based nanosystems that have been reported in the literature for antibacterial delivery. The review emphasizes the DCBs used in their design, the nanomaterials constructed, the drug release-triggering stimuli, and the antibacterial efficacy of the reported DCBs-based nanosystems. Additionally, the review underlines future strategies that can be used to improve the potential of DCBs-based nanosystems to treat bacterial infections and overcome antibacterial resistance.
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Affiliation(s)
- Abdelrahman Tageldin
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| | - Calvin A Omolo
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa; Department of Pharmaceutics and Pharmacy Practice, School of Pharmacy and Health Sciences, United States International University-Africa, P. O. Box 14634-00800, Nairobi, Kenya.
| | - Vincent O Nyandoro
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| | - Eman Elhassan
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| | - Sania Z F Kassam
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| | - Xylia Q Peters
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| | - Thirumala Govender
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa.
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3
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Liu Z, Zhang Z, Yang L, Zhang Y, Li D, Zhang Q, Niu C, Zhang B, Zhai Y, Wang Z. Effect and mechanism of C-terminal cysteine on the properties of HEV p222 protein. Virology 2024; 595:110091. [PMID: 38718446 DOI: 10.1016/j.virol.2024.110091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/07/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
Preliminary investigations have demonstrated that the cysteines located at the C-terminus of HEV ORF2 protein exhibits disulfide bonding capability during virus-like particles (VLPs) assembly. However, the effect and mechanism underlying the pairing of disulfide bonds formed by C627, C630, and C638 remains unclear. The p222 protein encompasses C-terminus and serves as a representative of HEV ORF2 to investigate the specific impacts of C627, C630, and C638. The three cysteines were subjected to site-directed mutagenesis and expressed in prokaryotes; Both the mutated proteins and p222 underwent polymerization except for p222A; Surprisingly, only p222 was observed as abundant spherical particles under transmission electron microscope (TEM); Stability and immunogenicity of the p222 exhibited higher than other mutated proteins; LC/MS/MS analysis identified four disulfide bonds in the p222. The novel findings suggest that the three cysteines contribute to structural and functional properties of ORF2 protein, highlighting the indispensability of each cysteine.
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Affiliation(s)
- Zhenzhen Liu
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Zhenzhen Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Lanping Yang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Yongwen Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Dong Li
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Qingling Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Chao Niu
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Baobao Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Yangyang Zhai
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Zhenhui Wang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China.
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4
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Heissel S, He Y, Jankevics A, Shi Y, Molina H, Viner R, Scheltema RA. Fast and Accurate Disulfide Bridge Detection. Mol Cell Proteomics 2024; 23:100759. [PMID: 38574859 PMCID: PMC11067345 DOI: 10.1016/j.mcpro.2024.100759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/08/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
Recombinant expression of proteins, propelled by therapeutic antibodies, has evolved into a multibillion dollar industry. Essential here is the quality control assessment of critical attributes, such as sequence fidelity, proper folding, and posttranslational modifications. Errors can lead to diminished bioactivity and, in the context of therapeutic proteins, an elevated risk for immunogenicity. Over the years, many techniques were developed and applied to validate proteins in a standardized and high-throughput fashion. One parameter has, however, so far been challenging to assess. Disulfide bridges, covalent bonds linking two cysteine residues, assist in the correct folding and stability of proteins and thus have a major influence on their efficacy. Mass spectrometry promises to be an optimal technique to uncover them in a fast and accurate fashion. In this work, we present a unique combination of sample preparation, data acquisition, and analysis facilitating the rapid and accurate assessment of disulfide bridges in purified proteins. Through microwave-assisted acid hydrolysis, the proteins are digested rapidly and artifact-free into peptides, with a substantial degree of overlap over the sequence. The nonspecific nature of this procedure, however, introduces chemical background, which is efficiently removed by integrating ion mobility preceding the mass spectrometric measurement. The nonspecific nature of the digestion step additionally necessitates new developments in data analysis, for which we extended the XlinkX node in Proteome Discoverer to efficiently process the data and ensure correctness through effective false discovery rate correction. The entire workflow can be completed within 1 h, allowing for high-throughput, high-accuracy disulfide mapping.
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Affiliation(s)
- Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA.
| | - Yi He
- Thermo Fisher Scientific, San Jose, California, USA
| | - Andris Jankevics
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Structural Proteomics Group, Department of Biochemistry and Systems Biology, University of Liverpool, Liverpool, UK
| | - Yuqi Shi
- Thermo Fisher Scientific, San Jose, California, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, California, USA.
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Structural Proteomics Group, Department of Biochemistry and Systems Biology, University of Liverpool, Liverpool, UK.
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5
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Fuentes-Lemus E, Hägglund P, López-Alarcón C, Davies MJ. Oxidative Crosslinking of Peptides and Proteins: Mechanisms of Formation, Detection, Characterization and Quantification. Molecules 2021; 27:15. [PMID: 35011250 PMCID: PMC8746199 DOI: 10.3390/molecules27010015] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 12/14/2022] Open
Abstract
Covalent crosslinks within or between proteins play a key role in determining the structure and function of proteins. Some of these are formed intentionally by either enzymatic or molecular reactions and are critical to normal physiological function. Others are generated as a consequence of exposure to oxidants (radicals, excited states or two-electron species) and other endogenous or external stimuli, or as a result of the actions of a number of enzymes (e.g., oxidases and peroxidases). Increasing evidence indicates that the accumulation of unwanted crosslinks, as is seen in ageing and multiple pathologies, has adverse effects on biological function. In this article, we review the spectrum of crosslinks, both reducible and non-reducible, currently known to be formed on proteins; the mechanisms of their formation; and experimental approaches to the detection, identification and characterization of these species.
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Affiliation(s)
- Eduardo Fuentes-Lemus
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen, Denmark; (E.F.-L.); (P.H.)
| | - Per Hägglund
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen, Denmark; (E.F.-L.); (P.H.)
| | - Camilo López-Alarcón
- Departamento de Química Física, Facultad de Química y de Farmacia, Pontificia Universidad Catolica de Chile, Santiago 7820436, Chile;
| | - Michael J. Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, 2200 Copenhagen, Denmark; (E.F.-L.); (P.H.)
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6
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Qiang J, Xu Z, Li Y, Wang H, Zhang Y. Carboxypeptidase Y Assisted Disulfide-Bond Identification with Linearized Database Search. Anal Chem 2021; 93:14940-14945. [PMID: 34735112 DOI: 10.1021/acs.analchem.1c03932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A disulfide bond is an important protein post-translational modification and plays a key role in regulating protein oxidation status, protein structure, and stability. Analysis of a disulfide bond using mass spectrometry is challenging because there lacks an efficient method to separate the disulfide-linked peptides from a complex protein digest, and the MS data requires sophisticated interpretation. Here, we developed a novel disulfide bond identification strategy, termed as "carboxypeptidase Y assisted disulfide-bond identification (CADI)". CADI is able to significantly reduce sample complexity by depleting ∼90% of the linear peptides while keeping the disulfide-bonded peptides. Furthermore, all CADI data can be directly analyzed by widely used protein database search engines, such as Mascot and MaxQuant. Our data show that CADI is able to sensitively identify disulfide bonds in peptides and proteins. However, CADI has not yet achieved a satisfied in-depth coverage on complex mammalian cell lysates due to the limited enzymatic activity of carboxypeptidase Y and low occurrences of disulfide bonds in a proteome. Altogether, CADI is a useful method that can get disulfide-linked peptides enriched and analyzed with regular search engines. CADI holds great potentials to deepen the analysis of disulfide bond and other types of cross-linked peptides on the proteome scale.
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Affiliation(s)
- Jiali Qiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhimin Xu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunxia Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong, Shanghai 201210, China
| | - Hongbin Wang
- The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Pudong, Shanghai 201210, China
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7
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Freitas D, Chen X, Cheng H, Davis A, Fallon B, Yan X. Recent Advances of In-Source Electrochemical Mass Spectrometry. Chempluschem 2021; 86:434-445. [PMID: 33689239 DOI: 10.1002/cplu.202100030] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/03/2021] [Indexed: 12/16/2022]
Abstract
Hyphenation of electrochemistry (EC) and mass spectrometry has become a powerful tool to study redox processes. Approaches that can achieve this hyphenation include integrating chromatography/electrophoresis between electroinduced redox reactions and detection of products, coupling an EC flow cell to a mass spectrometer, and performing electrochemical reactions inside the ion source of a mass spectrometer. The first two approaches have been well reviewed elsewhere. This Minireview highlights the inherent electrochemical properties of many mass spectrometry ion sources and their roles in the coupling of electrochemistry and mass spectrometric analysis. Development of modified ion sources that allow the compatibility of electrochemistry with ionization processes is also surveyed. Applications of different in-source electrochemical devices are provided including intermediate capturing, bioanalytical studies, nanoparticle formation, electrosynthesis, and electrode imaging.
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Affiliation(s)
- Dallas Freitas
- Department of Chemistry, Texas A&M University, 580 Ross St., College Station, TX 77843, USA
| | - Xi Chen
- Department of Chemistry, Texas A&M University, 580 Ross St., College Station, TX 77843, USA
| | - Heyong Cheng
- Department of Chemistry, Texas A&M University, 580 Ross St., College Station, TX 77843, USA
| | - Austin Davis
- Department of Chemistry, Texas A&M University, 580 Ross St., College Station, TX 77843, USA
| | - Blake Fallon
- Department of Chemistry, Texas A&M University, 580 Ross St., College Station, TX 77843, USA
| | - Xin Yan
- Department of Chemistry, Texas A&M University, 580 Ross St., College Station, TX 77843, USA
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8
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Dong Q, Yan X, Liang Y, Markey SP, Sheetlin SL, Remoroza CA, Wallace WE, Stein SE. Comprehensive Analysis of Tryptic Peptides Arising from Disulfide Linkages in NISTmAb and Their Use for Developing a Mass Spectral Library. J Proteome Res 2021; 20:1612-1629. [PMID: 33555887 PMCID: PMC9278810 DOI: 10.1021/acs.jproteome.0c00823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
This
work presents methods for identifying and then creating a
mass spectral library for disulfide-linked peptides originating from
the NISTmAb, a reference material of the humanized IgG1k monoclonal
antibody (RM 8671). Analyses involved both partially reduced and non-reduced
samples under neutral and weakly basic conditions followed by nanoflow
liquid chromatography tandem mass spectrometry (LC–MS/MS).
Spectra of peptides containing disulfide bonds are identified by both
MS1 ion and MS2 fragment ion data in order to completely map all the
disulfide linkages in the NISTmAb. This led to the detection of 383
distinct disulfide-linked peptide ions, arising from fully tryptic
cleavage, missed cleavage, irregular cleavage, complex Met/Trp oxidation
mixtures, and metal adducts. Fragmentation features of disulfide bonds
under low-energy collision dissociation were examined. These include
(1) peptide bond cleavage leaving disulfide bonds intact; (2) disulfide
bond cleavage, often leading to extensive fragmentation; and (3) double
cleavage products resulting from breakages of two peptide bonds or
both peptide and disulfide bonds. Automated annotation of various
complex MS/MS fragments enabled the identification of disulfide-linked
peptides with high confidence. Peptides containing each of the nine
native disulfide bonds were identified along with 86 additional disulfide
linkages arising from disulfide bond shuffling. The presence of shuffled
disulfides was nearly completely abrogated by refining digest conditions.
A curated spectral library of 702 disulfide-linked peptide spectra
was created from this analysis and is publicly available for free
download. Since all IgG1 antibodies have the same constant regions,
the resulting library can be used as a tool for facile identification
of “hard-to-find” disulfide-bonded peptides. Moreover,
we show that one may identify such peptides originating from IgG1
proteins in human serum, thereby serving as a means of monitoring
the completeness of protein reduction in proteomics studies. Data
are available via ProteomeXchange with identifier PXD023358.
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Affiliation(s)
- Qian Dong
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Xinjian Yan
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Yuxue Liang
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Sanford P Markey
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Sergey L Sheetlin
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Concepcion A Remoroza
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - William E Wallace
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Stephen E Stein
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
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Yang X, Xia Y. Mapping Complex Disulfide Bonds via Implementing Photochemical Reduction Online with Liquid Chromatography-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:307-314. [PMID: 33136395 DOI: 10.1021/jasms.0c00324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Assigning disulfide linkage is a crucial task for protein identification. The current bottom-up proteomics workflow has limitations in characterizing peptide digests containing multiple disulfide bonds due to the difficulty of controlling partial reduction via conventional chemical reduction methods. Previously, our lab reported the development of an acetone/2-propanol (IPA) photoinitiating system for rapid (on second time scale) and tunable disulfide bond reduction. Herein, we incorporated this reaction system onto a liquid chromatography-mass spectrometry (LC-MS) system for bottom-up protein analysis applications. The photochemical reduction reaction was implemented in a flow microreactor which allowed for up to 15 s 254 nm UV irradiation. The microreactor was installed post LC separation and right before electrospray ionization, while a T-junction was used to introduce the photoinitiating solution to the LC eluent before entering the microreactor. The degree of disulfide reduction was tunable from partial reduction to complete reduction for peptides containing one or multiple disulfide bonds. Significantly improved sequence coverage was obtained from complete disulfide reduction, while assignment of the disulfide connectivity was facilitated from partial disulfide reduction when coupled with tandem mass spectrometry via collision-induced dissociation. As a proof-of-concept test, trypsin digests of lysozyme (four disulfide bonds) and bovine serum albumin (BSA, 17 disulfide bonds) were analyzed by the LC-MS system coupled with online reduction. Sequence coverage was improved from 35% to 100% and 13% to 87% for lysozyme and BSA, respectively. All four disulfide bonds of lysozyme were determined. For BSA, nine disulfide bonds were characterized and eight adjacent disulfide bonds were narrowed down.
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Affiliation(s)
- Xiaoyue Yang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
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10
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Kuo CM, Wei SY, Du SH, Lin JL, Chu CH, Chen CH, Tai JH, Chen SH. Comprehensive Workflow for Mapping Disulfide Linkages Including Free Thiols and Error Checking by On-Line UV-Induced Precolumn Reduction and Spiked Control. Anal Chem 2020; 93:1544-1552. [PMID: 33378175 DOI: 10.1021/acs.analchem.0c03866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mapping highly complicated disulfide linkages and free thiols via liquid chromatography-tandem mass spectrometry (LC-MS2) is challenging because of the difficulties in optimizing sample preparation to acquire critical MS data and detecting mispairings. Herein, we report a highly efficient and comprehensive workflow using an on-line UV-induced precolumn reduction tandem mass spectrometry (UV-LC-MS2) coupled with two-stage data analysis and spiked control. UV-LC-MS2 features a gradient run of acetonitrile containing a tunable percentage of photoinitiators (acetone/alcohol) that drives the sample to the MS through a UV-flow cell and reverse phase column to separate UV-induced products for subsequent fragmentation via low energy collision-induced dissociation. This allowed the alkylated thiol-containing and UV-reduced cysteine-containing peptides to be identified by a nontargeted database search. Expected or unexpected disulfide/thiol mapping was then carried out based on the search results, and data were derived from partially reduced species by photochemical reaction. Complete assignments of native and scrambled disulfide linkages of insulin, α-lactalbumin, and bovine serum albumin (BSA) as well as the free C34-BSA were demonstrated using none or single enzyme digestion. This workflow was applied to characterize unknown disulfide/thiol patterns of the recombinant cyclophilin 1 monomer (rTvCyP1 mono) from the human pathogen Trichomonas vaginalis. α-Lactalbumin was judiciously chosen as a spiked control to minimize mispairings due to sample preparation. rTvCyP1 was determined to contain a high percentage of thiol (>80%). The rest of rTvCyP1 mono were identified to contain two disulfide/thiol patterns, of which C41-C169 linkage was confirmed to exist as C53-C181 in rTvCyP2, a homologue of rTvCyP1. This platform identifies heterogeneous protein disulfide/thiol patterns in a de-novo fashion with artifact control, opening up an opportunity to characterize crude proteins for many applications.
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Affiliation(s)
- Chin-Ming Kuo
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Shih-Yao Wei
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Shu-Han Du
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Jung-Lee Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chien-Hsin Chu
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | | | - Jung-Hsiang Tai
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
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11
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Samodova D, Hosfield CM, Cramer CN, Giuli MV, Cappellini E, Franciosa G, Rosenblatt MM, Kelstrup CD, Olsen JV. ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping. Mol Cell Proteomics 2020; 19:2139-2157. [PMID: 33020190 PMCID: PMC7710147 DOI: 10.1074/mcp.tir120.002129] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/29/2020] [Indexed: 01/01/2023] Open
Abstract
Trypsin is the protease of choice in bottom-up proteomics. However, its application can be limited by the amino acid composition of target proteins and the pH of the digestion solution. In this study we characterize ProAlanase, a protease from the fungus Aspergillus niger that cleaves primarily on the C-terminal side of proline and alanine residues. ProAlanase achieves high proteolytic activity and specificity when digestion is carried out at acidic pH (1.5) for relatively short (2 h) time periods. To elucidate the potential of ProAlanase in proteomics applications, we conducted a series of investigations comprising comparative multi-enzymatic profiling of a human cell line proteome, histone PTM analysis, ancient bone protein identification, phosphosite mapping and de novo sequencing of a proline-rich protein and disulfide bond mapping in mAb. The results demonstrate that ProAlanase is highly suitable for proteomics analysis of the arginine- and lysine-rich histones, enabling high sequence coverage of multiple histone family members. It also facilitates an efficient digestion of bone collagen thanks to the cleavage at the C terminus of hydroxyproline which is highly prevalent in collagen. This allows to identify complementary proteins in ProAlanase- and trypsin-digested ancient bone samples, as well as to increase sequence coverage of noncollagenous proteins. Moreover, digestion with ProAlanase improves protein sequence coverage and phosphosite localization for the proline-rich protein Notch3 intracellular domain (N3ICD). Furthermore, we achieve a nearly complete coverage of N3ICD protein by de novo sequencing using the combination of ProAlanase and tryptic peptides. Finally, we demonstrate that ProAlanase is efficient in disulfide bond mapping, showing high coverage of disulfide-containing regions in a nonreduced mAb.
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Affiliation(s)
- Diana Samodova
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Maria V Giuli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Enrico Cappellini
- Evolutionary Genomics SectionGlobe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Christian D Kelstrup
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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12
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Affiliation(s)
- Thomas Herl
- Institute of Analytical Chemistry, Chemo- and BiosensorsUniversity of Regensburg Universitätsstraße 31 93053 Regensburg Germany
| | - Frank‐Michael Matysik
- Institute of Analytical Chemistry, Chemo- and BiosensorsUniversity of Regensburg Universitätsstraße 31 93053 Regensburg Germany
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13
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Mao F, Yu K, He J, Zhou Q, Zhang G, Wang W, Li N, Zhang H, Jiang J. Real-time monitoring of electroreduction and labelling of disulfide-bonded peptides and proteins by mass spectrometry. Analyst 2019; 144:6898-6904. [PMID: 31638109 DOI: 10.1039/c9an01420a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The accurate determination of disulfide bonds for protein identification is in high demand. In this study, a simple electrochemical-mass spectrometry (EC-MS) method that possesses advantages of real-time information, simultaneous disulfide bond electroreduction and tagging was developed. In this EC-MS, an ITO glass corner functions as a counter electrode and spray system, and allows the direct sampling of the droplet-scale reacting solution in real-time. The application of this method was successfully demonstrated by electrochemical reduction of oxidized glutathione (GSSG) with one disulfide bond as well as insulin with multiple disulfide bonds. The preferred electroreduction of intermolecular-bonded disulfides for insulin has been observed and the intramolecular bond was not favored. Moreover, simultaneously tagging the formed thiol residues from electroreduction of GSSG using electrogenerated intermediates such as dopamine orthoquinone (DQ) and benzoquinone (Q) was performed. A proof-of-concept was also demonstrated with a large molecule, β-lactoglobulin A. The relationship between signal strength and operating parameters was also studied. This method successfully detected the reduction reaction of the disulfide bond in the polypeptide and protein. The detection limit (S/N ≥ 3) is 0.398 μg mL-1. These results suggest that this EC-MS platform can count cysteine moieties in proteins using a single drop of sample and in real-time and is promising for protein identification experiments.
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Affiliation(s)
- Fengjiao Mao
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, P.R. China.
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14
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Adhikari S, Xia Y, McLuckey SA. Top-Down Analysis of Disulfide-Linked Proteins Using Photoinduced Radical Reactions and ET-DDC. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 444:116173. [PMID: 31372092 PMCID: PMC6675022 DOI: 10.1016/j.ijms.2019.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Top-down characterization of proteins via tandem mass spectrometry (MS/MS) can be challenging due to the presence of multiple disulfide bond linkages; which significantly inhibit the backbone cleavage efficiency for the formation of structurally informative fragment ions. In this study, we present a strategy of pairing a solution-phase photoinitiating system with dipolar direct current induced collisional activation of electron transfer products (ET-DDC) of proteins for a top-down MS/MS approach. The photoinitiating system allows for a rapid scission of all the disulfide linkages in the protein (on the time scale of seconds) with high efficiency (near to complete reduction); while ET-DDC collisional activation improves the fragmentation efficiency for the protein via broadband activation of all the first-generation charge reduced precursor ions (e.g., electron transfer no-dissociation or ETnoD products) from electron transfer reactions over a wide mass-to-charge range. As a result, this approach enabled the generation of extensive sequence informative fragment ion yields for a rapid and enhanced structural characterization of disulfide-linked proteins.
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Affiliation(s)
- Sarju Adhikari
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yu Xia
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
- Address reprint requests to: Dr. Scott A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 494-5270, Fax: (765) 494-0239,
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15
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Tiwari MK, Hägglund PM, Møller IM, Davies MJ, Bjerrum MJ. Copper ion / H 2O 2 oxidation of Cu/Zn-Superoxide dismutase: Implications for enzymatic activity and antioxidant action. Redox Biol 2019; 26:101262. [PMID: 31284117 PMCID: PMC6614508 DOI: 10.1016/j.redox.2019.101262] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 01/25/2023] Open
Abstract
Copper ion-catalyzed oxidation of yeast SOD1 (ySOD1) was examined to determine early oxidative modifications, including oxidation of a crucial disulfide bond, and the structural and functional repercussions of these events. The study used distinct oxidative conditions: Cu2+/H2O2, Cu2+/H2O2/AscH− and Cu2+/H2O2/glucose. Capillary electrophoresis experiments and quantification of protein carbonyls indicate that ySOD1 is highly susceptible to oxidative modification and that changes can be detected within 0.1 min of the initiation of the reaction. Oxidation-induced structural perturbations, characterized by circular dichroism, revealed the formation of partially-unfolded ySOD1 species in a dose-dependent manner. Consistent with these structural changes, pyrogallol assay indicates a partial loss of enzymatic activity. ESI-MS analyses showed seven distinct oxidized ySOD1 species under mild oxidation within 0.1 min. LC/MS analysis after proteolytic digestion demonstrated that the copper-coordinating active site histidine residues, His47 and His49, were converted into 2-oxo-histidine. Furthermore, the Cu and Zn bridging residue, His64 is converted into aspartate/asparagine. Importantly, the disulfide-bond Cys58-Cys147 which is critical for the structural and functional integrity of ySOD1 was detected as being oxidized at Cys147. We propose, based on LC/MS analyses, that disulfide-bond oxidation occurs without disulfide bond cleavage. Modifications were also detected at Met85 and five surface-exposed Lys residues. Based on these data we propose that the Cys58-Cys147 bond may act as a sacrificial target for oxidants and protect ySOD1 from oxidative inactivation arising from exposure to Cu2+/H2O2 and auto-inactivation during extended enzymatic turnover. Oxidation of yeast superoxide dismutase (ySOD1) by Cu2+/H2O2 is examined. Rapid modification of His, Met, Cys and Lys residues detected by LC-MS methods. Oxidation of active site His residues and partial protein unfolding are early events. The Cys58-Cys147 disulfide bond is oxidized and may act as a sacrificial target. Excess exogenous Cu2+ decreases protein damage and can reverse loss of activity.
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Affiliation(s)
- Manish K Tiwari
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Per M Hägglund
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
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16
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Li X, Yang X, Hoang V, Liu YH. Characterization of Protein Disulfide Linkages by MS In-Source Dissociation Comparing to CID and ETD Tandem MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:519-528. [PMID: 30478816 DOI: 10.1007/s13361-018-2103-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/18/2018] [Accepted: 11/01/2018] [Indexed: 05/19/2023]
Abstract
Direct characterization of disulfide linkages in proteins by mass spectrometry has been challenging. Here, we report analysis of disulfide linkages in insulin variant, endothelin 3, and relaxin 2 by in-source dissociation (ISD) during LC-MS. A duplet insulin peptide from Glu-C digestion that contains peptides p1 and p2 (from chains A and B, respectively) was selected as a model peptide. This duplet peptide has an inter-chain disulfide bond between p1 and p2, and an intra-chain disulfide bond in p1. To compare the gas-phase fragmentation, it was subjected to ISD MS and MS/MS methods, including collision-induced dissociation (CID) and electron transfer dissociation (ETD). The pattern and efficiency of peptide backbone and disulfide cleavage varied with these dissociation methods. ETD, CID, and ISD were able to generate single backbone, double backbone, and triple (double backbone and single disulfide bond) cleavages in this model peptide, respectively. Specifically, CID did not cleave disulfide bonds and ETD was able to only cleave the inter-chain disulfide bond at low efficiency, limiting their usage in this disulfide analysis. In contrast, ISD was able to cleave the intra-chain disulfide bond in addition to peptide backbone, creating multiple fragment ions that allow accurate assignment of both intra- and inter-chain disulfide linkages. ISD was also successfully applied to determine double disulfide linkages in endothelin 3 and relaxin 2 peptides. This study contributes to the fundamental understanding of disulfide bond cleavages in different gas-phase fragmentations and provides an efficient cleavage strategy for identification of disulfide bonds in proteins by ISD ESI-MS. Graphical Abstract.
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Affiliation(s)
- Xiaojuan Li
- Bioprocess Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA.
| | - Xiaoyu Yang
- Bioprocess Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Van Hoang
- Bioprocess Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Yan-Hui Liu
- Bioprocess Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
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17
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Corona discharge electrospray ionization of formate-containing solutions enables in-source reduction of disulfide bonds. Anal Bioanal Chem 2018; 411:4729-4737. [PMID: 30397758 DOI: 10.1007/s00216-018-1447-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/12/2018] [Accepted: 10/22/2018] [Indexed: 01/05/2023]
Abstract
Disulfide bonds are critical linkages for maintaining protein structure and enzyme activity. These linkages, however, can limit peptide sequencing efforts by mass spectrometry (MS) and often require chemical reduction and alkylation. Under such conditions, information regarding cysteine connectivity is lost. Online partial disulfide reduction within the electrospray (ESI) source has recently been established as a means to identify complex cysteine linkage patterns in a liquid chromatography-MS experiment without the need for sample pre-treatment. Corona discharge (CD) is invoked as the causative factor of this in-source reduction (ISR); however, evidence remains largely circumstantial. In this study, we demonstrate that instrumental factors-nebulizing gas, ESI capillary material, organic solvent content, ESI spray needle-to-MS distance-all modulate the degree of reduction observed for the single disulfide in oxytocin, further implicating CD in ISR. Rigorous analysis of solution conditions, however, reveals that corona discharge alone can induce only minor disulfide reduction. We establish that CD-ESI of peptide solutions containing formic acid or its conjugate base results in a dramatic increase in disulfide reduction. It is also determined that ISR is exacerbated at low pH for complex peptides containing multiple disulfide bonds and possessing higher-order structure, as well as for a small protein. Overall, our results demonstrate that ESI of formate/formic acid-containing solutions under corona discharge conditions facilitates disulfide ISR, likely by a similar reduction pathway measured in γ-radiolysis studies nearly three decades ago.
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