1
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Kuril AK, Saravanan K, Subbappa PK. Analytical considerations for characterization of generic peptide product: A regulatory insight. Anal Biochem 2024; 694:115633. [PMID: 39089363 DOI: 10.1016/j.ab.2024.115633] [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: 05/11/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
The Peptide therapeutics market was evaluated to be around USD 45.67 BN in 2023 and is projected to witness massive growth at a CAGR of around 5.63 % from 2024 to 2032 (USD 80.4 BN). Generic peptides are expected to reach USD 27.1 billion by 2032 after the patent monopoly of the pioneer peptides expires, and generic peptides become accessible. The generic manufacturers are venturing into peptide-based therapeutics for the aforementioned reasons. There is an abundance of material accessible regarding the characterization of peptides, which can be quite confusing for researchers. The FDA believes that an ANDA applicant may now demonstrate that the active component in a proposed generic synthetic peptide drug product is the "same" as the active ingredient in a peptide of rDNA origin that has previously been approved. To ensure the efficacy, safety, and quality of peptide therapies during development, regulatory bodies demand comprehensive characterization utilizing several orthogonal methodologies. This article elaborates the peptide characterization by segmenting into different segments as per the critical quality attribute from identification of the peptide to the physicochemical property of the peptide therapeutics which will be required to demonstrate the sameness with reference product based on the size of the peptide chain and molecular weight of the peptides. Article insights briefly on each individual technique and the orthogonal techniques for each test were explained. The impurities requirements in the generic peptides as per the regulatory requirement were also discussed.
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Affiliation(s)
| | - K Saravanan
- Bhagwant University, Sikar Road, Ajmer, Rajasthan, India
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2
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Malarvannan M, Ravichandiran V, Paul D. Advances in analytical technologies for emerging drug modalities and their separation challenges in LC-MS systems. J Chromatogr A 2024; 1732:465226. [PMID: 39111181 DOI: 10.1016/j.chroma.2024.465226] [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: 05/31/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/23/2024]
Abstract
The last few years have seen a rise in the identification and development of bio-therapeutics through the use of cutting-edge delivery methods or bio-formulations, which has created bio-analytical difficulties. Every year, new bio-pharmaceutical product innovations come out, but the analytical development of these products is challenging. Quantifying the products and components of conjugated molecular structures is essential for preclinical and clinical research in order to guide therapeutic development, given their intrinsic complexity. Furthermore, a significant amount of information is needed for the measurement of these unique modalities by LC-MS techniques. Numerous LC-MS based methods have been developed, including AEX-HPLC-MS, RP-IP-LCMS, HILIC-MS, LCHRMS, Microflow-LC-MS, ASMS, Hybrid LBA/LC-MS, and more. However, these methods continue to face problems, prompting the development of alternative approaches. Therefore, developing bio-molecules that are this complicated and, low in concentration requires a skilled LC-MS based approach and knowledgeable personnel. This review covers general novel modalities classifications, sample preparation techniques, current status and bio-analytical strategies for analyzing various novel modalities, including gene bio-therapeutics, oligonucleotides, antibody-drug conjugates, monoclonal antibodies and PROTACs. It also covers how these strategies have been used in the past and how they are being used now to address challenges in the development of LC-MS based methods, as well as improvement strategies, current advancements and recent developed methods. We additionally covered on the benefits and drawbacks of different LC-MS based techniques for the examination of bio-pharmaceutical products and the future perspectives.
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Affiliation(s)
- M Malarvannan
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India
| | - V Ravichandiran
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India
| | - David Paul
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India.
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3
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Bu G, Zhao X, Wang M, Ti G, Chen F, Duan X, Huang Y, Li P. Identification of calcium chelating peptides from peanut protein hydrolysate and absorption activity of peptide-calcium complex. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:6676-6686. [PMID: 38545944 DOI: 10.1002/jsfa.13493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND Peanut peptides have good chelating ability with metal ions. However, there are few studies on the chelation mechanism of peanut peptides with calcium and absorption properties of peptide-calcium complex. RESULTS Peptides with high calcium chelating rate were isolated and purified from peanut protein hydrolysate (PPH), and the chelation rate of component F21 was higher (81.4 ± 0.8%). Six peptides were identified from component F21 by liquid chromatography-tandem mass spectrometry, and the frequency of acidic amino acids and arginine in the amino acid sequence was higher in all six peptides. Peanut peptide-calcium complex (PPH21-Ca) was prepared by selecting component F21 (PPH21). Ultraviolet analysis indicated that the chelate reaction occurred between peanut peptide and calcium ions. Fourier transform infrared analysis showed that the chelating sites were carboxyl and amino groups on the amino acid residues of peptides. Scanning electron microscopy revealed that the surface of peanut peptide had a smooth block structure, but the surface of the complex had a granular morphology. Caco-2 cell model tests revealed that the bioavailability of PPH21-Ca was 58.4 ± 0.5%, which was significantly higher than that of inorganic calcium at 37.0 ± 0.4%. CONCLUSION Peanut peptides can chelate calcium ions by carboxyl and amino groups, and the peptide-calcium complex had higher bioavailability. This study provides a theoretical basis for the development of new calcium supplement products that are absorbed easily. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Guanhao Bu
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Xiaoling Zhao
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Mengli Wang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Guanghui Ti
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Fusheng Chen
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Xiaojie Duan
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Yanan Huang
- Henan Province Nanjie Village (Group) Co., Ltd, Luohe, China
| | - Panxin Li
- Henan Province Nanjie Village (Group) Co., Ltd, Luohe, China
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4
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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5
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Waltho A, Popp O, Lenz C, Pluska L, Lambert M, Dötsch V, Mertins P, Sommer T. K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific ubiquitin interactors. Life Sci Alliance 2024; 7:e202402740. [PMID: 38803224 PMCID: PMC11109483 DOI: 10.26508/lsa.202402740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024] Open
Abstract
The ubiquitin (Ub) code denotes the complex Ub architectures, including Ub chains of different lengths, linkage types, and linkage combinations, which enable ubiquitination to control a wide range of protein fates. Although many linkage-specific interactors have been described, how interactors are able to decode more complex architectures is not fully understood. We conducted a Ub interactor screen, in humans and yeast, using Ub chains of varying lengths, as well as homotypic and heterotypic branched chains of the two most abundant linkage types-lysine 48-linked (K48) and lysine 63-linked (K63) Ub. We identified some of the first K48/K63-linked branch-specific Ub interactors, including histone ADP-ribosyltransferase PARP10/ARTD10, E3 ligase UBR4, and huntingtin-interacting protein HIP1. Furthermore, we revealed the importance of chain length by identifying interactors with a preference for Ub3 over Ub2 chains, including Ub-directed endoprotease DDI2, autophagy receptor CCDC50, and p97 adaptor FAF1. Crucially, we compared datasets collected using two common deubiquitinase inhibitors-chloroacetamide and N-ethylmaleimide. This revealed inhibitor-dependent interactors, highlighting the importance of inhibitor consideration during pulldown studies. This dataset is a key resource for understanding how the Ub code is read.
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Affiliation(s)
- Anita Waltho
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-University zu Berlin, Berlin, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Christopher Lenz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Lukas Pluska
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-University zu Berlin, Berlin, Germany
| | - Mahil Lambert
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Volker Dötsch
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Thomas Sommer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-University zu Berlin, Berlin, Germany
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6
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Maya-Aguirre CA, Torres A, Gutiérrez-Castañeda LD, Salazar LM, Abreu-Villaça Y, Manhães AC, Arenas NE. Changes in the proteome of Apis mellifera acutely exposed to sublethal dosage of glyphosate and imidacloprid. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:45954-45969. [PMID: 38980489 PMCID: PMC11269427 DOI: 10.1007/s11356-024-34185-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024]
Abstract
Uncontrolled use of pesticides has caused a dramatic reduction in the number of pollinators, including bees. Studies on the effects of pesticides on bees have reported effects on both metabolic and neurological levels under chronic exposure. In this study, variations in the differential expression of head and thorax-abdomen proteins in Africanized A. mellifera bees treated acutely with sublethal doses of glyphosate and imidacloprid were studied using a proteomic approach. A total of 92 proteins were detected, 49 of which were differentially expressed compared to those in the control group (47 downregulated and 2 upregulated). Protein interaction networks with differential protein expression ratios suggested that acute exposure of A. mellifera to sublethal doses of glyphosate could cause head damage, which is mainly associated with behavior and metabolism. Simultaneously, imidacloprid can cause damage associated with metabolism as well as, neuronal damage, cellular stress, and impairment of the detoxification system. Regarding the thorax-abdomen fractions, glyphosate could lead to cytoskeleton reorganization and a reduction in defense mechanisms, whereas imidacloprid could affect the coordination and impairment of the oxidative stress response.
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Affiliation(s)
- Carlos Andrés Maya-Aguirre
- Instituto de Biotecnología, Facultad de Ciencias, Universidad Nacional de Colombia, Ciudad Universitaria, Avenida Carrera 30 N° 45-03, Bogota, D.C, Colombia
- Grupo Ciencias Básicas en Salud-CBS-FUCS, Fundación Universitaria de Ciencias de La Salud, Hospital Infanti L Universitario de San José, Carrera 54 No.67A-80, Bogota, D.C., Colombia
| | - Angela Torres
- Departmento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Ciudad Universitaria, Avenida Carrera 30 N° 45-03, Bogota, D.C., Colombia
| | - Luz Dary Gutiérrez-Castañeda
- Grupo Ciencias Básicas en Salud-CBS-FUCS, Fundación Universitaria de Ciencias de La Salud, Hospital Infanti L Universitario de San José, Carrera 54 No.67A-80, Bogota, D.C., Colombia
| | - Luz Mary Salazar
- Departmento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Ciudad Universitaria, Avenida Carrera 30 N° 45-03, Bogota, D.C., Colombia
| | - Yael Abreu-Villaça
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade Do Estado Do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20550-170, Brazil
| | - Alex Christian Manhães
- Laboratório de Neurofisiologia, Departamento de Ciências Fisiológicas, Instituto de Biologia Roberto Alcantara Gomes, Universidade Do Estado Do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20550-170, Brazil
| | - Nelson Enrique Arenas
- Facultad de Medicina, Universidad de Cartagena, Campus Zaragocilla, Barrio Zaragocilla, Carrera 50a #24-63, Cartagena de Indias, Bolivar, Colombia.
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7
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Jarvis RP, Li J, Lin R, Ling Q, Lyu Y, Sun Y, Yao Z. Reply: Does the polyubiquitination pathway operate inside intact chloroplasts to remove proteins? THE PLANT CELL 2024:koae105. [PMID: 38738499 DOI: 10.1093/plcell/koae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/19/2024] [Indexed: 05/14/2024]
Affiliation(s)
- R Paul Jarvis
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Jialong Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qihua Ling
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuping Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yi Sun
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Zujie Yao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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8
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Hoare M, Tan R, Welle KA, Swovick K, Hryhorenko JR, Ghaemmaghami S. Methionine Alkylation as an Approach to Quantify Methionine Oxidation Using Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:433-440. [PMID: 38324783 PMCID: PMC10921467 DOI: 10.1021/jasms.3c00337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
Post-translational oxidation of methionine residues can destabilize proteins or modify their functions. Although levels of methionine oxidation can provide important information regarding the structural integrity and regulation of proteins, their quantitation is often challenging as analytical procedures in and of themselves can artifactually oxidize methionines. Here, we develop a mass-spectrometry-based method called Methionine Oxidation by Blocking with Alkylation (MObBa) that quantifies methionine oxidation by selectively alkylating and blocking unoxidized methionines. Thus, alkylated methionines can be used as a stable proxy for unoxidized methionines. Using proof of concept experiments, we demonstrate that MObBa can be used to measure methionine oxidation levels within individual synthetic peptides and on proteome-wide scales. MObBa may provide a straightforward experimental strategy for mass spectrometric quantitation of methionine oxidation.
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Affiliation(s)
- Margaret Hoare
- Department
of Biology, University of Rochester, Rochester, New York 14627, United States
| | - Ruiyue Tan
- Department
of Biology, University of Rochester, Rochester, New York 14627, United States
| | - Kevin A. Welle
- University
of Rochester Mass Spectrometry Resource Laboratory, Rochester, New York 14627, United States
| | - Kyle Swovick
- University
of Rochester Mass Spectrometry Resource Laboratory, Rochester, New York 14627, United States
| | - Jennifer R. Hryhorenko
- University
of Rochester Mass Spectrometry Resource Laboratory, Rochester, New York 14627, United States
| | - Sina Ghaemmaghami
- Department
of Biology, University of Rochester, Rochester, New York 14627, United States
- University
of Rochester Mass Spectrometry Resource Laboratory, Rochester, New York 14627, United States
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9
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Hartmann P, Bohdan K, Hommrich M, Juliá F, Vogelsang L, Eirich J, Zangl R, Farès C, Jacobs JB, Mukhopadhyay D, Mengeler JM, Vetere A, Sterling MS, Hinrichs H, Becker S, Morgner N, Schrader W, Finkemeier I, Dietz KJ, Griesinger C, Ritter T. Chemoselective umpolung of thiols to episulfoniums for cysteine bioconjugation. Nat Chem 2024; 16:380-388. [PMID: 38123842 PMCID: PMC10914617 DOI: 10.1038/s41557-023-01388-7] [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: 01/12/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023]
Abstract
Cysteine conjugation is an important tool in protein research and relies on fast, mild and chemoselective reactions. Cysteinyl thiols can either be modified with prefunctionalized electrophiles, or converted into electrophiles themselves for functionalization with selected nucleophiles in an independent step. Here we report a bioconjugation strategy that uses a vinyl thianthrenium salt to transform cysteine into a highly reactive electrophilic episulfonium intermediate in situ, to enable conjugation with a diverse set of bioorthogonal nucleophiles in a single step. The reactivity profile can connect several nucleophiles to biomolecules through a short and stable ethylene linker, ideal for introduction of infrared labels, post-translational modifications or NMR probes. In the absence of reactive exogenous nucleophiles, nucleophilic amino acids can react with the episulfonium intermediate for native peptide stapling and protein-protein ligation. Ready synthetic access to isotopologues of vinyl thianthrenium salts enables applications in quantitative proteomics. Such diverse applications demonstrate the utility of vinyl-thianthrenium-based bioconjugation as a fast, selective and broadly applicable tool for chemical biology.
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Affiliation(s)
- Philipp Hartmann
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Kostiantyn Bohdan
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Moritz Hommrich
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Fabio Juliá
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Lara Vogelsang
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Jürgen Eirich
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Rene Zangl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Frankfurt/Main, Germany
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | | | | | | | - Alessandro Vetere
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | | | - Heike Hinrichs
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Stefan Becker
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Frankfurt/Main, Germany
| | - Wolfgang Schrader
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Iris Finkemeier
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | | | - Tobias Ritter
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
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10
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Degliesposti G. Peptide-Based Mass Spectrometry for the Investigation of Protein Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:31-40. [PMID: 38507198 DOI: 10.1007/978-3-031-52193-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
In the last two decades, biological mass spectrometry has become the gold standard for the identification of proteins in biological samples. The technological advancement of mass spectrometers and the development of methods for ionization, gas phase transfer, peptide fragmentation as well as for acquisition of high-resolution mass spectrometric data marked the success of the technique. This chapter introduces peptide-based mass spectrometry as a tool for the investigation of protein complexes. It provides an overview of the main steps for sample preparation starting from protein fractionation, reduction, alkylation and focus on the final step of protein digestion. The basic concepts of biological mass spectrometry as well as details about instrumental analysis and data acquisition are described. Finally, the most common methods for data analysis and sequence determination are summarized with an emphasis on its application to protein-protein complexes.
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11
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Goulden T, Bodachivskyi I, Padula MP, Williams DBG. Concentrated ionic liquids for proteomics: Caveat emptor! Int J Biol Macromol 2023; 253:127438. [PMID: 37839603 DOI: 10.1016/j.ijbiomac.2023.127438] [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: 06/27/2023] [Revised: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
The use of concentrated ionic liquids (ILs) in the bioanalytical chemistry of proteins is sparse; typically, dilute aqueous IL solutions are used. Concentrated ILs have unique properties that may allow researchers to dissolve previously insoluble protein analytes, to increase the depth and robustness of sample preparation and the analysis of proteins. Previous research using concentrated ILs for this purpose is sparse and there is a need to systematically investigate the structure-activity relationship between the IL structure and its capacity to solubilise proteins. Here, bovine serum albumin was dissolved in various ionic liquids and monitored over time by light microscopy and SDS-PAGE. While qualitative, these measures provide a good estimate of, respectively, the dissolving power of an IL towards the given protein and the retained integrity of the protein. Hydrophilic ILs show the best solubilisation capacity and higher temperatures (in a restricted sense) improve the solubility of the protein. Higher temperatures and longer reaction times reduce the molecular weight of the protein, which could inhibit their applicability in proteomics, unless the conditions are judiciously controlled. Researchers should exercise caution when using concentrated ILs for protein analysis until the full scope and limitations are known, an aspect we are presently investigating.
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Affiliation(s)
- Thomas Goulden
- University of Technology Sydney, School of Mathematical and Physical Sciences, 15 Broadway, Sydney, NSW 2007, Australia
| | - Iurii Bodachivskyi
- University of Technology Sydney, School of Mathematical and Physical Sciences, 15 Broadway, Sydney, NSW 2007, Australia; V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar St, Kyiv 02094, Ukraine
| | - Matthew P Padula
- University of Technology Sydney, School of Life Sciences, 15 Broadway, Sydney, NSW 2007, Australia
| | - D Bradley G Williams
- University of Technology Sydney, School of Mathematical and Physical Sciences, 15 Broadway, Sydney, NSW 2007, Australia; University of Wollongong, School of Chemistry and Molecular Bioscience, Wollongong, NSW 2522, Australia.
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12
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Wang H, Sun WQ. Comparative proteomic analysis of regenerative acellular matrices: The effects of tissue source and processing method. J Biomed Mater Res B Appl Biomater 2023; 111:2002-2012. [PMID: 37466112 DOI: 10.1002/jbm.b.35300] [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: 11/22/2022] [Revised: 06/22/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023]
Abstract
Acellular tissue matrices are used in regenerative medicine from weak tissue re-enforcement to cosmetic augmentation. However, proteomic signatures leading to different clinical outcomes among matrices are not well understood. In an attempt to investigate the effects of tissue source and processing method, we examined by liquid chromatography tandem mass spectrometry (LC-MS/MS) the proteomic profiles of 12 regulatory agency-approved acellular matrices (AlloMax, AlloDerm, CollaMend, Heal-All, JayyaLife, ReGen, Renov, Strattice, SurgiMend, Surgisis, UniTrump and Vidasis). The compositions of acellular matrices varied greatly with the number of identified proteins ranging from 7 to 106. The content of individual proteins was between 0.0001% and 95.8% according to their abundances measured by the M/Z signal intensities. Most acellular matrices still contained numerous cellular proteins. AlloMax, AlloDerm, ReGen, Strattice, SurgiMend and Surgisis retained necessary structural and functional proteins to form the extracellular protein-protein interaction networks for cell adhesion, proliferation and tissue regeneration, whereas CollaMend, Heal-All, JayyaLife, Renov, UniTrump and Vidasis had only retained certain structural collagens. Principal component analysis showed that proteomic variations among acellular matrices were largely attributed to tissue source and processing method. Differences in proteomic profiles among acellular matrices offers insights into molecular interpretation for different clinical outcomes, and can serve as useful references for rational design of regenerative bio-scaffolds.
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Affiliation(s)
- Huidan Wang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wendell Q Sun
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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13
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Yeom S, Nam D, Bok KH, Kwon HK, Kim S, Lee SW, Kim HJ. Synthesis of S-Carbamidomethyl Cysteine and Its Use for Quantification of Cysteinyl Peptides by Targeted Proteomics. Anal Chem 2023; 95:14413-14420. [PMID: 37707799 DOI: 10.1021/acs.analchem.3c02768] [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: 09/15/2023]
Abstract
Proteomics has played a central role in the identification of reliable disease biomarkers, which are the basis of precision medicine, a promising approach for tackling recalcitrant diseases such as cancer, that elude conventional treatments. Among proteomic methodologies, targeted proteomics employing stable isotope-labeled (SIL) internal standards is particularly suited for the clinical translation of biomarker information owing to its high throughput and accuracy in the quantitative analysis of patient-derived proteomes. Using SIL internal standards ensures the utmost level of confidence in detection and precision in targeted MS experiments. For successfully establishing assays based on targeted proteomics, it is crucial to secure broad coverage when selecting the SIL standard peptide panel. However, cysteinyl peptides have often been excluded because of cysteine's high chemical reactivity. To address this limitation, a new cysteine building block was developed by incorporating a sulfhydryl group configured with an S-carbamidomethyl group, which is commonly used in proteome sampling. This compound was found to be chemically stable and applicable to a variety of solid-phase peptide synthesis (SPPS) campaigns. Furthermore, a direct comparison of the synthesized SIL peptides and tryptic endogenous peptides demonstrated the potential utility of an SPPS flow based on the new cysteine building block for improving the success of targeted proteomic applications.
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Affiliation(s)
- Suyeon Yeom
- Department of Chemistry and Center for ProteoGenome Research, Korea University, Seoul 02841, Republic of Korea
| | - Dowoon Nam
- Department of Chemistry and Center for ProteoGenome Research, Korea University, Seoul 02841, Republic of Korea
| | - Kwon Hee Bok
- Department of Chemistry and Center for ProteoGenome Research, Korea University, Seoul 02841, Republic of Korea
| | - Hye Kyeong Kwon
- Department of Chemistry and Center for ProteoGenome Research, Korea University, Seoul 02841, Republic of Korea
| | - Seungwoo Kim
- Department of Chemistry and Center for ProteoGenome Research, Korea University, Seoul 02841, Republic of Korea
| | - Sang-Won Lee
- Department of Chemistry and Center for ProteoGenome Research, Korea University, Seoul 02841, Republic of Korea
| | - Hak Joong Kim
- Department of Chemistry and Center for ProteoGenome Research, Korea University, Seoul 02841, Republic of Korea
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14
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Liu YD, Beardsley MI, Yang F. Expanding the Analytical Toolbox: Developing New Lys-C Peptide Mapping Methods with Minimized Assay-Induced Artifacts to Fully Characterize Antibodies. Pharmaceuticals (Basel) 2023; 16:1327. [PMID: 37765135 PMCID: PMC10536426 DOI: 10.3390/ph16091327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Peptide mapping is an important tool used to confirm that the correct sequence has been expressed for a protein and to evaluate protein post-translational modifications (PTMs) that may arise during the production, processing, or storage of protein drugs. Our new orally administered drug (Ab-1), a single-domain antibody, is highly stable and resistant to proteolysis. Analysis via the commonly used tryptic mapping method did not generate sufficient sequence coverage. Alternative methods were needed to study the Ab-1 drug substance (75 mg/mL) and drug product (3 mg/mL). To meet these analytical needs, we developed two new peptide mapping methods using lysyl endopeptidase (Lys-C) digestion. These newly developed protein digestion protocols do not require desalting/buffer-exchange steps, thereby reducing sample preparation time and improving method robustness. Additionally, the protein digestion is performed under neutral pH with methionine acting as a scavenger to minimize artifacts, such as deamidation and oxidation, which are induced during sample preparation. Further, the method for low-concentration samples performs comparably to the method for high-concentration samples. Both methods provide 100% sequence coverage for Ab-1, and, therefore, enable comprehensive characterization for its product quality attribute (PQA) assessment. Both methods can be used to study other antibody formats.
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Affiliation(s)
| | | | - Feng Yang
- Department of Protein Analytical Chemistry, Genentech/Roche, South San Francisco, CA 94080, USA; (Y.D.L.); (M.I.B.)
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15
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Naplekov D, Jadeja S, Fučíková AM, Švec F, Sklenářová H, Lenčo J. Easy, Robust, and Repeatable Online Acid Cleavage of Proteins in Mobile Phase for Fast Quantitative LC-MS Bottom-Up Protein Analysis─Application for Ricin Detection. Anal Chem 2023; 95:12339-12348. [PMID: 37565982 PMCID: PMC10448442 DOI: 10.1021/acs.analchem.3c01772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Sample preparation involving the cleavage of proteins into peptides is the first critical step for successful bottom-up proteomics and protein analyses. Time- and labor-intensiveness are among the bottlenecks of the commonly used methods for protein sample preparation. Here, we report a fast online method for postinjection acid cleavage of proteins directly in the mobile phase typically used for LC-MS analyses in proteomics. The chemical cleavage is achieved in 0.1% formic acid within 35 s in a capillary heated to 195 °C installed upstream of the analytical column, enabling the generated peptides to be separated. The peptides generated by the optimized method covered the entire sequence except for one amino acid of trastuzumab used for the method development. The qualitative results are extraordinarily stable, even over a long period of time. Moreover, the method is also suitable for accurate and repeatable quantification. The procedure requires only one manual step, significantly decreasing sample transfer losses. To demonstrate its practical utility, we tested the method for the fast detection of ricin. Ricin can be unambiguously identified from an injection of 10 ng, and the results can be obtained within 7-8 min after receiving a suspicious sample. Because no sophisticated accessories and no additional reagents are needed, the method can be seamlessly transferred to any laboratory for high-throughput proteomic workflows.
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Affiliation(s)
- Denis
K. Naplekov
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Siddharth Jadeja
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Alena Myslivcová Fučíková
- Department
of Biology, Faculty of Science, University
of Hradec Králové, Hradecká 1285, 500 03 Hradec Králové, Czech Republic
| | - František Švec
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Hana Sklenářová
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Juraj Lenčo
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
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16
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Pohl T, Gervais A, Dirksen E, D'Alessio V, Bechtold-Peters K, Burkitt W, Cao L, Greven S, Lennard A, Li X, Lössner C, Niu B, Reusch D, O'Riordan T, Shearer J, Spencer D, Xu W, Yi L. Technical considerations for the implementation of the Multi-Attribute-Method by mass spectrometry in a Quality Control laboratory. Eur J Pharm Biopharm 2023:S0939-6411(23)00112-1. [PMID: 37146738 DOI: 10.1016/j.ejpb.2023.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023]
Abstract
Multi-attribute methods employing mass spectrometry are applied throughout the biopharmaceutical industry for product and process characterization purposes but are not yet widely accepted as a method for batch release and stability testing under good manufacturing practice (GMP) due to limited experience and level of comfort with the technical, compliance and regulatory aspects of its implementation at quality control (QC) laboratories. Here, current literature related to the development and application of the multi-attribute method by peptide mapping liquid chromatography mass spectrometry (MAM) is compiled with the aim of providing guidance for the implementation of MAM in a QC laboratory. This article, focusing on technical considerations, is the first part of a two-tiered publication, whereby the second part will focus on GMP compliance and regulatory aspects. This publication has been prepared by a group of industry experts representing 14 globally acting major biotechnology companies under the umbrella of the European Federation of Pharmaceutical Industries and Associations (EFPIA) Manufacturing & Quality Expert Group (MQEG).
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Affiliation(s)
- Thomas Pohl
- Biologics Analytical Development, Novartis Pharma AG, Klybeckstrasse 141, CH-4057 Basel, Switzerland
| | - Annick Gervais
- Analytical Development Sciences for Biologicals, UCB, Chemin du Foriest, 1420 Braine L'Alleud, Belgium
| | - Eef Dirksen
- Analytical Development and Quality Control, Byondis, Microweg 22, 6545 CM, Nijmegen, The Netherlands
| | - Valerio D'Alessio
- Analytical Development Biotech, Merck Serono S.p.A., Via Luigi Einaudi, 11, 00012 Guidonia Montecelio - Rome, Italy
| | - Karoline Bechtold-Peters
- Biologics Drug Product Development, Novartis Pharma AG, Klybeckstrasse 141, CH-4057 Basel, Switzerland
| | - Will Burkitt
- Biological Characterisation Product Development Sciences, UCB, 216 Bath Road, Slough, SL1 3WE, UK
| | - Li Cao
- Strategic External Development, GSK, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, USA
| | - Simone Greven
- Pharmaceuticals, Biological Development, Bayer AG, Friedrich-Ebert-Strasse 217-333, 42117 Wuppertal, Germany
| | - Andrew Lennard
- Amgen, 4 Uxbridge Business Park, Sanderson Road, Uxbridge, UB8 1DH, UK
| | - Xue Li
- Biologics Development, Bristol Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08901, USA
| | - Christopher Lössner
- Analytical Dev. Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Ben Niu
- Biotherapeutics, Bristol Myers Squibb, 4224 Campus Point Court, San Diego, California 92121, USA
| | - Dietmar Reusch
- Pharma Technical Development, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Tomás O'Riordan
- Eli Lilly Kinsale Limited, Dunderrow, Kinsale, Co. Cork, P17NY71, Ireland
| | - Justin Shearer
- Analytical Development, GSK, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, USA
| | - David Spencer
- BioPharmaceutical Development, Ipsen Biopharm Limited, 9 Ash Road, Wrexham Industrial Estate, Wrexham, LL13 9UF, UK
| | - Wei Xu
- Analytical Sciences, BioPharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, Maryland 20878, USA
| | - Linda Yi
- Analytical Development, Biogen, 5000 Davis Drive, Research Triangle Park, North Carolina 27709, USA
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17
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Eshghi A, Xie X, Hardie D, Chen MX, Izaguirre F, Newman R, Zhu Y, Kelly RT, Goodlett DR. Sample Preparation Methods for Targeted Single-Cell Proteomics. J Proteome Res 2023. [PMID: 37093777 DOI: 10.1021/acs.jproteome.2c00429] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
We compared three cell isolation and two proteomic sample preparation methods for single-cell and near-single-cell analysis. Whole blood was used to quantify hemoglobin (Hb) and glycated-Hb (gly-Hb) in erythrocytes using targeted mass spectrometry and stable isotope-labeled standard peptides. Each method differed in cell isolation and sample preparation as follows: 1) FACS and automated preparation in one-pot for trace samples (autoPOTS); 2) limited dilution via microscopy and a novel rapid one-pot sample preparation method that circumvented the need for the solid-phase extraction, low-volume liquid handling instrumentation and humidified incubation chamber; and 3) CellenONE-based cell isolation and the same one-pot sample preparation method used for limited dilution. Only the CellenONE device routinely isolated single-cells from which Hb was measured to be 540-660 amol per red blood cell (RBC), which was comparable to the calculated SI reference range for mean corpuscular hemoglobin (390-540 amol/RBC). FACSAria sorter and limited dilution could routinely isolate single-digit cell numbers, to reliably quantify CMV-Hb heterogeneity. Finally, we observed that repeated measures, using 5-25 RBCs obtained from N = 10 blood donors, could be used as an alternative and more efficient strategy than single RBC analysis to measure protein heterogeneity, which revealed multimodal distribution, unique for each individual.
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Affiliation(s)
- Azad Eshghi
- University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia V8Z 5N3, Canada
| | - Xiaofeng Xie
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604, United States
| | - Darryl Hardie
- University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia V8Z 5N3, Canada
| | - Michael X Chen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Laboratory Medicine, Pathology, and Medical Genetics, Vancouver Island Health Authority, Vancouver, British Columbia V9A 2P8, Canada
- Division of Medical Sciences, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Fabiana Izaguirre
- Cellenion SASU, 60 Avenue Rockefeller, Bâtiment BioSerra2, Lyon, Auvergne-Rhône-Alpes 69008, France
| | - Rachael Newman
- University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia V8Z 5N3, Canada
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604, United States
| | - David R Goodlett
- University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia V8Z 5N3, Canada
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Pomerania 80-309, Poland
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18
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Fu Q, Murray CI, Karpov OA, Van Eyk JE. Automated proteomic sample preparation: The key component for high throughput and quantitative mass spectrometry analysis. MASS SPECTROMETRY REVIEWS 2023; 42:873-886. [PMID: 34786750 DOI: 10.1002/mas.21750] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/11/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Sample preparation for mass spectrometry-based proteomics has many tedious and time-consuming steps that can introduce analytical errors. In particular, the steps around the proteolytic digestion of protein samples are prone to inconsistency. One route for reliable sample processing is the development and optimization of a workflow utilizing an automated liquid handling workstation. Diligent assessment of the sample type, protocol design, reagents, and incubation conditions can significantly improve the speed and consistency of preparation. When combining robust liquid chromatography-mass spectrometry with either discovery or targeted methods, automated sample preparation facilitates increased throughput and reproducible quantitation of biomarker candidates. These improvements in analysis are also essential to process the large patient cohorts necessary to validate a candidate biomarker for potential clinical use. This article reviews the steps in the workflow, optimization strategies, and known applications in clinical, pharmaceutical, and research fields that demonstrate the broad utility for improved automation of sample preparation in the proteomic field.
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Affiliation(s)
- Qin Fu
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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19
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Dewi KR, Ismayati M, Solihat NN, Yuliana ND, Kusnandar F, Riantana H, Heryani H, Halim A, Acter T, Uddin N, Kim S. Advances and key considerations of liquid chromatography–mass spectrometry for porcine authentication in halal analysis. J Anal Sci Technol 2023. [DOI: 10.1186/s40543-023-00376-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
AbstractThe halal food industries are rapidly expanding to fulfill global halal demands. Non-halal substances such as porcine proteins are often added intentionally or unintentionally to products. The development of highly selective and sensitive analytical tools is necessary, and liquid chromatography–mass spectrometry is a powerful tool that can cope with the challenge. The LC–MS method has great potential for halal authentication, because it has high sensitivity and low detection limit and detects several species markers and different tissue origins at once within one species. This article provides an understanding of recent advances in the application of LC–MS for the improvement of porcine authentication. Sample preparation, marker selection, separation and mass spectrometry conditions, quantitative assessment, and data processing for protein identification were all covered in detail to choose the most suitable method for the analytical needs.
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20
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Drack A, Rai A, Greening DW. Generation of Red Blood Cell Nanovesicles as a Delivery Tool. Methods Mol Biol 2023; 2628:321-336. [PMID: 36781795 DOI: 10.1007/978-1-0716-2978-9_21] [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] [Indexed: 02/15/2023]
Abstract
Extracellular vesicles (EVs) are natural membranous vesicles with immense potential as drug delivery tools. However, their large-scale production remains a huge technical challenge, is time consuming, and expensive. Thus, EV mimetics (nanovesicles) generated from easily sourced red blood cells (RBCs) have gained vested interest as an effective and scalable drug delivery system. Their surface proteins (e.g., CD47) inherited from parental RBCs also improve their biocompatibility and bioavailability. Here, we outline a step-by-step guide for large-scale production of RBC nanovesicles using one-step extrusion method coupled to rapid density-cushion centrifugation. We also outline protocol for their extensive biophysical characterization (size and morphology using single particle analysis and cryogenic electron microscopy), and in-depth mass spectrometry-based proteome characterization. Finally, we outline two strategies (active loading during extrusion vs. passive loading via diffusion) to incorporate pharmacological compound(s) into nanovesicles and detect their loading using spectrophotometry.
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Affiliation(s)
- Auriane Drack
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Biochemistry and Chemistry, La Trobe University, Melbourne, VIC, Australia
| | - Alin Rai
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia
| | - David W Greening
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Department of Biochemistry and Chemistry, La Trobe University, Melbourne, VIC, Australia.
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia.
- Central Clinical School, Monash University, Melbourne, VIC, Australia.
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia.
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21
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Cardozo G, Mastrogiovanni M, Zeida A, Viera N, Radi R, Reyes AM, Trujillo M. Mitochondrial Peroxiredoxin 3 Is Rapidly Oxidized and Hyperoxidized by Fatty Acid Hydroperoxides. Antioxidants (Basel) 2023; 12:antiox12020408. [PMID: 36829967 PMCID: PMC9952270 DOI: 10.3390/antiox12020408] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
Human peroxiredoxin 3 (HsPrx3) is a thiol-based peroxidase responsible for the reduction of most hydrogen peroxide and peroxynitrite formed in mitochondria. Mitochondrial disfunction can lead to membrane lipoperoxidation, resulting in the formation of lipid-bound fatty acid hydroperoxides (LFA-OOHs) which can be released to become free fatty acid hydroperoxides (fFA-OOHs). Herein, we report that HsPrx3 is oxidized and hyperoxidized by fFA-OOHs including those derived from arachidonic acid and eicosapentaenoic acid peroxidation at position 15 with remarkably high rate constants of oxidation (>3.5 × 107 M-1s-1) and hyperoxidation (~2 × 107 M-1s-1). The endoperoxide-hydroperoxide PGG2, an intermediate in prostanoid synthesis, oxidized HsPrx3 with a similar rate constant, but was less effective in causing hyperoxidation. Biophysical methodologies suggest that HsPrx3 can bind hydrophobic structures. Indeed, molecular dynamic simulations allowed the identification of a hydrophobic patch near the enzyme active site that can allocate the hydroperoxide group of fFA-OOHs in close proximity to the thiolate in the peroxidatic cysteine. Simulations performed using available and herein reported kinetic data indicate that HsPrx3 should be considered a main target for mitochondrial fFA-OOHs. Finally, kinetic simulation analysis support that mitochondrial fFA-OOHs formation fluxes in the range of nM/s are expected to contribute to HsPrx3 hyperoxidation, a modification that has been detected in vivo under physiological and pathological conditions.
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Affiliation(s)
- Giuliana Cardozo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Mauricio Mastrogiovanni
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Nicolás Viera
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
| | - Aníbal M. Reyes
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
- Correspondence: (A.M.R.); (M.T.)
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo 11800, Uruguay
- Correspondence: (A.M.R.); (M.T.)
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22
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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23
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Langó T, Kuffa K, Tóth G, Turiák L, Drahos L, Tusnády GE. Comprehensive Discovery of the Accessible Primary Amino Group-Containing Segments from Cell Surface Proteins by Fine-Tuning a High-Throughput Biotinylation Method. Int J Mol Sci 2022; 24:ijms24010273. [PMID: 36613715 PMCID: PMC9820203 DOI: 10.3390/ijms24010273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Cell surface proteins, including transmembrane and other surface-anchored proteins, play a key role in several critical cellular processes and have a strong diagnostic value. The development of quick and robust experimental methods remains vital for the accurate and comprehensive characterization of the cell surface subproteome of individual cells. Here we present a high-throughput technique which relies on the biotinylation of the accessible primary amino groups in the extracellular segments of the proteins, using HL60 as a model cell line. Several steps of the method have been thoroughly optimized to capture labeled surface proteins selectively and in larger quantities. These include the following: improving the efficiency of the cell surface biotinylation; reducing the endogen protease activity; applying an optimal amount of affinity column and elution steps for labeled peptide enrichment; and examining the effect of various solid-phase extraction methods, different HPLC gradients, and various tandem mass spectrometry settings. Using the optimized workflow, we identified at least 1700 surface-associated individual labeled peptides (~6000-7000 redundant peptides) from the model cell surface in a single nanoHPLC-MS/MS run. The presented method can provide a comprehensive and specific list of the cell surface available protein segments that could be potential targets in various bioinformatics and molecular biology research.
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Affiliation(s)
- Tamás Langó
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
- Correspondence:
| | - Katalin Kuffa
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány P. stny. 1/C, H-1117 Budapest, Hungary
| | - Gábor Tóth
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
| | - Gábor E. Tusnády
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
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24
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Antoshina DV, Balandin SV, Bogdanov IV, Vershinina MA, Sheremeteva EV, Toropygin IY, Finkina EI, Ovchinnikova TV. Antimicrobial Activity and Immunomodulatory Properties of Acidocin A, the Pediocin-like Bacteriocin with the Non-Canonical Structure. MEMBRANES 2022; 12:1253. [PMID: 36557160 PMCID: PMC9780942 DOI: 10.3390/membranes12121253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Pediocin-like bacteriocins are among the natural antimicrobial agents attracting attention as scaffolds for the development of a new generation of antibiotics. Acidocin A has significant structural differences from most other members of this subclass. We studied its antibacterial and cytotoxic activity, as well as effects on the permeability of E. coli membranes in comparison with avicin A, the typical pediocin-like bacteriocin. Acidocin A had a more marked tendency to form an alpha-helical structure upon contact with detergent micelles, as was shown by CD spectroscopy, and demonstrated considerably less specific mode of action: it inhibited growth of Gram-positive and Gram-negative strains, which were unsusceptible to avicin A, and disrupted the integrity of outer and inner membranes of E. coli. However, the peptide retained a low toxicity towards normal and tumor human cells. The effect of mutations in the pediocin box of acidocin A (on average, a 2-4-fold decrease in activity) was less pronounced than is usually observed for such peptides. Using multiplex analysis, we showed that acidocin A and avicin A modulated the expression level of a number of cytokines and growth factors in primary human monocytes. Acidocin A induced the production of a number of inflammatory mediators (IL-6, TNFα, MIG/CXCL9, MCP-1/CCL2, MCP-3/CCL7, and MIP-1β) and inhibited the production of some anti-inflammatory factors (IL-1RA, MDC/CCL22). We assumed that the activity of acidocin A and similar peptides produced by lactic acid bacteria might affect the functional state of the human intestinal tract, not only through direct inhibition of various groups of symbiotic and pathogenic bacteria, but also via immunomodulatory effects.
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Affiliation(s)
- Daria V. Antoshina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey V. Balandin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ivan V. Bogdanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maria A. Vershinina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Elvira V. Sheremeteva
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ilia Yu. Toropygin
- V.N. Orekhovich Research Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Ekaterina I. Finkina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Bioorganic Chemistry, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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25
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van der Pan K, Kassem S, Khatri I, de Ru AH, Janssen GMC, Tjokrodirijo RTN, al Makindji F, Stavrakaki E, de Jager AL, Naber BAE, de Laat IF, Louis A, van den Bossche WBL, Vogelezang LB, Balvers RK, Lamfers MLM, van Veelen PA, Orfao A, van Dongen JJM, Teodosio C, Díez P. Quantitative proteomics of small numbers of closely-related cells: Selection of the optimal method for a clinical setting. Front Med (Lausanne) 2022; 9:997305. [PMID: 36237552 PMCID: PMC9553008 DOI: 10.3389/fmed.2022.997305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Mass spectrometry (MS)-based proteomics profiling has undoubtedly increased the knowledge about cellular processes and functions. However, its applicability for paucicellular sample analyses is currently limited. Although new approaches have been developed for single-cell studies, most of them have not (yet) been standardized and/or require highly specific (often home-built) devices, thereby limiting their broad implementation, particularly in non-specialized settings. To select an optimal MS-oriented proteomics approach applicable in translational research and clinical settings, we assessed 10 different sample preparation procedures in paucicellular samples of closely-related cell types. Particularly, five cell lysis protocols using different chemistries and mechanical forces were combined with two sample clean-up techniques (C18 filter- and SP3-based), followed by tandem mass tag (TMT)-based protein quantification. The evaluation was structured in three phases: first, cell lines from hematopoietic (THP-1) and non-hematopoietic (HT-29) origins were used to test the approaches showing the combination of a urea-based lysis buffer with the SP3 bead-based clean-up system as the best performer. Parameters such as reproducibility, accessibility, spatial distribution, ease of use, processing time and cost were considered. In the second phase, the performance of the method was tested on maturation-related cell populations: three different monocyte subsets from peripheral blood and, for the first time, macrophages/microglia (MAC) from glioblastoma samples, together with T cells from both tissues. The analysis of 50,000 cells down to only 2,500 cells revealed different protein expression profiles associated with the distinct cell populations. Accordingly, a closer relationship was observed between non-classical monocytes and MAC, with the latter showing the co-expression of M1 and M2 macrophage markers, although pro-tumoral and anti-inflammatory proteins were more represented. In the third phase, the results were validated by high-end spectral flow cytometry on paired monocyte/MAC samples to further determine the sensitivity of the MS approach selected. Finally, the feasibility of the method was proven in 194 additional samples corresponding to 38 different cell types, including cells from different tissue origins, cellular lineages, maturation stages and stimuli. In summary, we selected a reproducible, easy-to-implement sample preparation method for MS-based proteomic characterization of paucicellular samples, also applicable in the setting of functionally closely-related cell populations.
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Affiliation(s)
- Kyra van der Pan
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Sara Kassem
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Indu Khatri
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Leiden Computational Biology Center, LUMC, Leiden, Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, LUMC, Leiden, Netherlands
| | | | | | - Fadi al Makindji
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | | | - Anniek L. de Jager
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Brigitta A. E. Naber
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Inge F. de Laat
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Alesha Louis
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | | | | | | | | | | | - Alberto Orfao
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Jacques J. M. van Dongen
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- *Correspondence: Jacques J. M. van Dongen
| | - Cristina Teodosio
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Paula Díez
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain
- Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
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26
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Cataldo VA, Taimoory SM, Mohammadzadeh S, Guterman R, Trant J. A Solid Alkylation: Highly Recyclable, Flow Chemistry‐Ready, Resin‐Supported Thioimidazoliums Alkylate Sulfur‐Centered Nucleophile. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Vincenzo Alessandro Cataldo
- Max Planck Institute of Colloids and Interfaces: Max-Planck-Institut fur Kolloid und Grenzflachenforschung Colloid Chemistry Am Muhlenberg 1 Potsdam GERMANY
| | | | | | - Ryan Guterman
- Max Planck Institute of Colloids and Interfaces: Max-Planck-Institut fur Kolloid und Grenzflachenforschung Colloid Chemistry Potsdam GERMANY
| | - John Trant
- University of Windsor Chemistry and Biochemistry 401 Sunset Ave. N9B 3P4 Windsor CANADA
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27
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Ebhardt HA, Ponchon P, Theodosiadis K, Fuerer C, Courtet-Compondu MC, O'Regan J, Affolter M, Joubran Y. Reduction of multiple reaction monitoring protein target list using correlation analysis. J Dairy Sci 2022; 105:7216-7229. [PMID: 35879160 DOI: 10.3168/jds.2021-21647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/15/2022] [Indexed: 11/19/2022]
Abstract
High mass resolution mass spectrometry provides hundreds to thousands of protein identifications per sample, and quantification is typically performed using label-free quantification. However, the gold standard of quantitative proteomics is multiple reaction monitoring (MRM) using triple quadrupole mass spectrometers and stable isotope reference peptides. This raises the question how to reduce a large data set to a small one without losing essential information. Here we present the reduction of such a data set using correlation analysis of bovine dairy ingredients and derived products. We were able to explain the variance in the proteomics data set using only 9 proteins across all major dairy protein classes: caseins, whey, and milk fat globule membrane proteins. We term this method Trinity-MRM. The reproducibility of the protein extraction and Trinity-MRM methods was shown to be below 5% in independent experiments (multi-day single-user and single-day multi-user) using double cream. Further application of this reductionist approach might include screening of large sample cohorts for biologically interesting samples before analysis by high-resolution mass spectrometry or other omics methodologies.
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Affiliation(s)
- Holger A Ebhardt
- Nestlé Development Centre Nutrition, Askeaton, County Limerick, Ireland, V94 E7P9
| | - Pierre Ponchon
- Nestlé Development Centre Nutrition, Askeaton, County Limerick, Ireland, V94 E7P9
| | | | - Christophe Fuerer
- Société des Produits Nestlé, Nestlé Research, Route du Jorat 57, 1000 Lausanne 26, Switzerland
| | | | - Jonathan O'Regan
- Nestlé Development Centre Nutrition, Askeaton, County Limerick, Ireland, V94 E7P9
| | - Michael Affolter
- Société des Produits Nestlé, Nestlé Research, Route du Jorat 57, 1000 Lausanne 26, Switzerland
| | - Yousef Joubran
- Nestlé Development Centre Nutrition, Askeaton, County Limerick, Ireland, V94 E7P9.
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28
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Skeens E, Gadzuk-Shea M, Shah D, Bhandari V, Schweppe DK, Berlow RB, Lisi GP. Redox-dependent structure and dynamics of macrophage migration inhibitory factor reveal sites of latent allostery. Structure 2022; 30:840-850.e6. [PMID: 35381187 DOI: 10.1016/j.str.2022.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/20/2022] [Accepted: 03/09/2022] [Indexed: 01/01/2023]
Abstract
Macrophage migration inhibitory factor (MIF) is a multifunctional immunoregulatory protein that is a key player in the innate immune response. Given its overexpression at sites of inflammation and in diseases marked by increasingly oxidative environments, a comprehensive understanding of how cellular redox conditions impact the structure and function of MIF is necessary. We used NMR spectroscopy and mass spectrometry to investigate biophysical signatures of MIF under varied solution redox conditions. Our results indicate that the MIF structure is modified and becomes increasingly dynamic in an oxidative environment, which may be a means to alter the MIF conformation and functional response in a redox-dependent manner. We identified latent allosteric sites within MIF through mutational analysis of redox-sensitive residues, revealing that a loss of redox-responsive residues attenuates CD74 receptor activation. Leveraging sites of redox sensitivity as targets for structure-based drug design therefore reveals an avenue to modulate MIF function in its "disease state."
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Affiliation(s)
- Erin Skeens
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, RI 02903, USA
| | - Meagan Gadzuk-Shea
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Dilip Shah
- Section of Neonatology, Department of Pediatrics, Cooper University Hospital, Camden, NJ 08103, USA
| | - Vineet Bhandari
- Section of Neonatology, Department of Pediatrics, Cooper University Hospital, Camden, NJ 08103, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Rebecca B Berlow
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - George P Lisi
- Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, RI 02903, USA.
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29
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A systematic evaluation of yeast sample preparation protocols for spectral identifications, proteome coverage and post-isolation modifications. J Proteomics 2022; 261:104576. [DOI: 10.1016/j.jprot.2022.104576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 11/20/2022]
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30
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Mustafa G, Komatsu S. Plant proteomic research for improvement of food crops under stresses: a review. Mol Omics 2021; 17:860-880. [PMID: 34870299 DOI: 10.1039/d1mo00151e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Crop improvement approaches have been changed due to technological advancements in traditional plant-breeding methods. Abiotic and biotic stresses limit plant growth and development, which ultimately lead to reduced crop yield. Proteins encoded by genomes have a considerable role in the endurance and adaptation of plants to different environmental conditions. Biotechnological applications in plant breeding depend upon the information generated from proteomic studies. Proteomics has a specific advantage to contemplate post-translational modifications, which indicate the functional effects of protein modifications on crop production. Subcellular proteomics helps in exploring the precise cellular responses and investigating the networking among subcellular compartments during plant development and biotic/abiotic stress responses. Large-scale mass spectrometry-based plant proteomic studies with a more comprehensive overview are now possible due to dramatic improvements in mass spectrometry, sample preparation procedures, analytical software, and strengthened availability of genomes for numerous plant species. Development of stress-tolerant or resilient crops is essential to improve crop productivity and growth. Use of high throughput techniques with advanced instrumentation giving efficient results made this possible. In this review, the role of proteomic studies in identifying the stress-response processes in different crops is summarized. Advanced techniques and their possible utilization on plants are discussed in detail. Proteomic studies accelerate marker-assisted genetic augmentation studies on crops for developing high yielding stress-tolerant lines or varieties under stresses.
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Affiliation(s)
- Ghazala Mustafa
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
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31
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Espinosa LA, Ramos Y, Andújar I, Torres EO, Cabrera G, Martín A, Roche D, Chinea G, Becquet M, González I, Canaán-Haden C, Nelson E, Rojas G, Pérez-Massón B, Pérez-Martínez D, Boggiano T, Palacio J, Lozada Chang SL, Hernández L, de la Luz Hernández KR, Markku S, Vitikainen M, Valdés-Balbín Y, Santana-Medero D, Rivera DG, Vérez-Bencomo V, Emalfarb M, Tchelet R, Guillén G, Limonta M, Pimentel E, Ayala M, Besada V, González LJ. In-solution buffer-free digestion allows full-sequence coverage and complete characterization of post-translational modifications of the receptor-binding domain of SARS-CoV-2 in a single ESI-MS spectrum. Anal Bioanal Chem 2021; 413:7559-7585. [PMID: 34739558 PMCID: PMC8569510 DOI: 10.1007/s00216-021-03721-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 11/04/2022]
Abstract
Subunit vaccines based on the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 provide one of the most promising strategies to fight the COVID-19 pandemic. The detailed characterization of the protein primary structure by mass spectrometry (MS) is mandatory, as described in ICHQ6B guidelines. In this work, several recombinant RBD proteins produced in five expression systems were characterized using a non-conventional protocol known as in-solution buffer-free digestion (BFD). In a single ESI-MS spectrum, BFD allowed very high sequence coverage (≥ 99%) and the detection of highly hydrophilic regions, including very short and hydrophilic peptides (2-8 amino acids), and the His6-tagged C-terminal peptide carrying several post-translational modifications at Cys538 such as cysteinylation, homocysteinylation, glutathionylation, truncated glutathionylation, and cyanylation, among others. The analysis using the conventional digestion protocol allowed lower sequence coverage (80-90%) and did not detect peptides carrying most of the above-mentioned PTMs. The two C-terminal peptides of a dimer [RBD(319-541)-(His)6]2 linked by an intermolecular disulfide bond (Cys538-Cys538) with twelve histidine residues were only detected by BFD. This protocol allows the detection of the four disulfide bonds present in the native RBD, low-abundance scrambling variants, free cysteine residues, O-glycoforms, and incomplete processing of the N-terminal end, if present. Artifacts generated by the in-solution BFD protocol were also characterized. BFD can be easily implemented; it has been applied to the characterization of the active pharmaceutical ingredient of two RBD-based vaccines, and we foresee that it can be also helpful to the characterization of mutated RBDs.
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Affiliation(s)
- Luis Ariel Espinosa
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Yassel Ramos
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Ivan Andújar
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Enso Onill Torres
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Gleysin Cabrera
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Alejandro Martín
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Diamilé Roche
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Glay Chinea
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Mónica Becquet
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Isabel González
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Camila Canaán-Haden
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Elías Nelson
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Gertrudis Rojas
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | | | | | - Tamy Boggiano
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | - Julio Palacio
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | | | - Lourdes Hernández
- Center of Molecular Immunology, 216 St., P.O. Box 16040, Havana, Cuba
| | | | - Saloheimo Markku
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT, Espoo, Finland
| | - Marika Vitikainen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044 VTT, Espoo, Finland
| | | | | | - Daniel G Rivera
- Laboratory of Synthetic and Biomolecular Chemistry, Faculty of Chemistry, University of Havana, Zapata & G, 10400, Havana, Cuba
| | | | - Mark Emalfarb
- Dyadic International, Inc, 140 Intercoastal Pointe Drive, Suite #404, Jupiter, FL, 33477, USA
| | - Ronen Tchelet
- Dyadic International, Inc, 140 Intercoastal Pointe Drive, Suite #404, Jupiter, FL, 33477, USA
| | - Gerardo Guillén
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Miladys Limonta
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Eulogio Pimentel
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Marta Ayala
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Vladimir Besada
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba
| | - Luis Javier González
- Center for Genetic Engineering and Biotechnology, Ave 31, e/ 158 y 190, Cubanacán, Playa, Havana, Cuba.
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32
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Cherepanov SM, Gerasimenko M, Yuhi T, Shabalova A, Zhu H, Yokoyama S, Salmina AB, Munesue SI, Harashima A, Yamamoto Y, Higashida H. An improved sample extraction method reveals that plasma receptor for advanced glycation end-products (RAGE) modulates circulating free oxytocin in mice. Peptides 2021; 146:170649. [PMID: 34543678 DOI: 10.1016/j.peptides.2021.170649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022]
Abstract
The receptor for advanced glycation end-products (RAGE) binds oxytocin (OT) and transports it from the blood to the brain. As RAGE's OT-binding capacity was lost in RAGE knockout (KO) mice, we predicted that circulating concentrations of unbound (free) OT should be elevated compared to wild-type (WT) mice. However, this hypothesis has not yet been investigated. Unfortunately, the evaluation of the dynamics of circulating free and bound plasma OT is unclear in immunoassays, in part because of interference from plasma proteins. A radioimmunoassay (RIA) is considered the gold standard method for overcoming this issue, but is more challenging to implement; thus, commercially available enzyme-linked immunosorbent assays (ELISAs) are more commonly used. Here, we developed a pre-treatment method to remove the interference-causing components from plasma before performing ELISA. The acetonitrile protein precipitation (PPT) approach was reliable, with fewer steps needed to measure free OT concentrations than by solid-phase extraction of plasma samples. PPT-extracted plasma samples yielded higher concentrations of OT in RAGE KO mice than in WT mice using ELISA. After peripheral OT injection, free OT plasma levels spiked immediately then rapidly declined in WT mice, but remained high in KO mice. These results suggest that plasma samples with PPT pre-treatment appear to be superior and that circulating soluble RAGE can most likely serve as a buffer for plasma OT, which indicates a novel physiological function of RAGE.
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Affiliation(s)
- Stanislav M Cherepanov
- Department of Basic Research on Social Recognition and Memory, Research Center for Child Mental Development, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Maria Gerasimenko
- Department of Basic Research on Social Recognition and Memory, Research Center for Child Mental Development, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Teruko Yuhi
- Department of Basic Research on Social Recognition and Memory, Research Center for Child Mental Development, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Anna Shabalova
- Department of Basic Research on Social Recognition and Memory, Research Center for Child Mental Development, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Hong Zhu
- Department of Basic Research on Social Recognition and Memory, Research Center for Child Mental Development, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Shigeru Yokoyama
- Department of Basic Research on Social Recognition and Memory, Research Center for Child Mental Development, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Alla B Salmina
- Laboratory for Social Brain Studies, Research Institute of Molecular Medicine and Pathobiochemistry, and Department of Biochemistry, Krasnoyarsk State Medical University named after Prof. V. F. Voino-Yasentsky, Krasnoyarsk, 660022, Russia
| | - Shei-Ichi Munesue
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Ai Harashima
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Yasuhiko Yamamoto
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Haruhiro Higashida
- Department of Basic Research on Social Recognition and Memory, Research Center for Child Mental Development, Kanazawa University, Kanazawa, 920-8640, Japan.
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33
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Bispo M, Suhani S, van Dijl JM. Empowering antimicrobial photodynamic therapy of Staphylococcus aureus infections with potassium iodide. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 225:112334. [PMID: 34678616 DOI: 10.1016/j.jphotobiol.2021.112334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/26/2021] [Accepted: 10/07/2021] [Indexed: 11/30/2022]
Abstract
Infections caused by the Gram-positive bacterium Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA), impose a great burden on global healthcare systems. Thus, there is an urgent need for alternative approaches to fight staphylococcal infections, such as targeted antimicrobial photodynamic therapy (aPDT). We recently reported that targeted aPDT with the S. aureus-specific immunoconjugate 1D9-700DX can be effectively applied to eradicate MRSA. Nonetheless, the efficacy of aPDT in the human body may be diminished by powerful antioxidant activities. In particular, we observed that the efficacy of aPDT with 1D9-700DX towards MRSA was reduced in human plasma. Here we show that this antagonistic effect can be attributed to human serum albumin, which represents the largest pool of free thiols in plasma for trapping reactive oxygen species. Importantly, we also show that our targeted aPDT approach with 1D9-700DX can be empowered by the non-toxic inorganic salt potassium iodide (KI), which reacts with the singlet oxygen produced upon aPDT, resulting in the formation of free iodine. The targeted iodine formation allows full eradication of MRSA (more than 6-log reduction) without negatively affecting other non-targeted bacterial species or human cells. Altogether, we show that the addition of KI allows a drastic reduction of both the amount of the immunoconjugate 1D9-700DX and the irradiation time needed for effective elimination of MRSA by aPDT in the presence of human serum albumin.
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Affiliation(s)
- Mafalda Bispo
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Sabrina Suhani
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
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34
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [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: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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35
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Pagel O, Kollipara L, Sickmann A. Tandem Mass Tags for Comparative and Discovery Proteomics. Methods Mol Biol 2021; 2228:117-131. [PMID: 33950487 DOI: 10.1007/978-1-0716-1024-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Relative or comparative proteomics provides valuable insights about the altered protein abundances across different biological samples in a single (labeled) or series (label-free) of LC-MS measurement(s). Chemical labeling of peptides using isobaric mass tags for identification and quantification of different proteomes simultaneously has become a routine in the so-called discovery proteomics in the past decade. One of the earliest isobaric tags-based technologies is TMT (tandem mass tags), which relies on the comparison of the unique "reporter ions" intensities for relative peptide/protein quantification. This differential labeling approach has evolved over time with respect to its multiplexing capability, i.e., from just 2 samples (TMTduplex) to 10 samples (TMT10plex) and a nowadays of up to 16 samples (TMTpro 16plex). Here, we describe a straightforward protocol to perform relatively deep proteome quantitative analyses using TMT10plex.
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Affiliation(s)
- Oliver Pagel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, Dortmund, Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, Dortmund, Germany. .,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland. .,Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany.
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36
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Coughlan C, Bruce KD, Burgy O, Boyd TD, Michel CR, Garcia-Perez JE, Adame V, Anton P, Bettcher BM, Chial HJ, Königshoff M, Hsieh EWY, Graner M, Potter H. Exosome Isolation by Ultracentrifugation and Precipitation and Techniques for Downstream Analyses. ACTA ACUST UNITED AC 2021; 88:e110. [PMID: 32633898 DOI: 10.1002/cpcb.110] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Exosomes are 50- to 150-nm-diameter extracellular vesicles secreted by all mammalian cells except mature red blood cells and contribute to diverse physiological and pathological functions within the body. Many methods have been used to isolate and analyze exosomes, resulting in inconsistencies across experiments and raising questions about how to compare results obtained using different approaches. Questions have also been raised regarding the purity of the various preparations with regard to the sizes and types of vesicles and to the presence of lipoproteins. Thus, investigators often find it challenging to identify the optimal exosome isolation protocol for their experimental needs. Our laboratories have compared ultracentrifugation and commercial precipitation- and column-based exosome isolation kits for exosome preparation. Here, we present protocols for exosome isolation using two of the most commonly used methods, ultracentrifugation and precipitation, followed by downstream analyses. We use NanoSight nanoparticle tracking analysis and flow cytometry (Cytek® ) to determine exosome concentrations and sizes. Imaging flow cytometry can be utilized to both size exosomes and immunophenotype surface markers on exosomes (ImageStream® ). High-performance liquid chromatography followed by nano-flow liquid chromatography-mass spectrometry (LCMS) of the exosome fractions can be used to determine the presence of lipoproteins, with LCMS able to provide a proteomic profile of the exosome preparations. We found that the precipitation method was six times faster and resulted in a ∼2.5-fold higher concentration of exosomes per milliliter compared to ultracentrifugation. Both methods yielded extracellular vesicles in the size range of exosomes, and both preparations included apoproteins. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Pre-analytic fluid collection and processing Basic Protocol 2: Exosome isolation by ultracentrifugation Alternate Protocol 1: Exosome isolation by precipitation Basic Protocol 3: Analysis of exosomes by NanoSight nanoparticle tracking analysis Alternate Protocol 2: Analysis of exosomes by flow cytometry and imaging flow cytometry Basic Protocol 4: Downstream analysis of exosomes using high-performance liquid chromatography Basic Protocol 5: Downstream analysis of the exosome proteome using nano-flow liquid chromatography-mass spectrometry.
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Affiliation(s)
- Christina Coughlan
- University of Colorado Alzheimer's and Cognition Center, Department of Neurology, Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Kimberley D Bruce
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Olivier Burgy
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus. INSERM U1231, Faculty of Medicine and Pharmacy, University of Bourgogne-Franche Comté, Dijon, France
| | - Timothy D Boyd
- University of Colorado Alzheimer's and Cognition Center, Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Cole R Michel
- School of Pharmacy, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Josselyn E Garcia-Perez
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Vanesa Adame
- University of Colorado Alzheimer's and Cognition Center, Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Paige Anton
- Department of Pharmaceutical Sciences, University of Colorado Alzheimer's and Cognition Center, Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Brianne M Bettcher
- University of Colorado Alzheimer's and Cognition Center, Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Heidi J Chial
- University of Colorado Alzheimer's and Cognition Center, Department of Neurology, Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Melanie Königshoff
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Elena W Y Hsieh
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado
| | - Michael Graner
- Department of Pediatrics, Section of Allergy and Immunology, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado
| | - Huntington Potter
- University of Colorado Alzheimer's and Cognition Center, Department of Neurology, Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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37
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Chiari L, Carpentier P, Kieffer-Jaquinod S, Gogny A, Perard J, Ravanel S, Cobessi D, Ménage S, Dumas R, Hamelin O. LEAFY protein crystals with a honeycomb structure as a platform for selective preparation of outstanding stable bio-hybrid materials. NANOSCALE 2021; 13:8901-8908. [PMID: 33949561 DOI: 10.1039/d1nr00268f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Well-organized protein assemblies offer many properties that justify their use for the design of innovative bionanomaterials. Herein, crystals of the oligomerization domain of the LEAFY protein from Ginkgo biloba, organized in a honeycomb architecture, were used as a modular platform for the selective grafting of a ruthenium-based complex. The resulting bio-hybrid crystalline material was fully characterized by UV-visible and Raman spectroscopy and by mass spectrometry and LC-MS analysis after selective enzymatic digestion. Interestingly, insertion of complexes within the tubular structure affords an impressive increase in stability of the crystals, eluding the use of stabilizing cross-linking strategies.
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Affiliation(s)
- Lucile Chiari
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-LCBM, UMR5249, 38000, Grenoble, France.
| | - Philippe Carpentier
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-LCBM, UMR5249, 38000, Grenoble, France. and ESRF, the European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | - Alice Gogny
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-LCBM, UMR5249, 38000, Grenoble, France.
| | - Julien Perard
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-LCBM, UMR5249, 38000, Grenoble, France.
| | - Stéphane Ravanel
- Univ. Grenoble Alpes, CEA, CNRS, INRAE, IRIG-DBSCI-LPCV 38000, Grenoble, France
| | - David Cobessi
- Univ. Grenoble Alpes, CEA, CNRS, IBS 38000, Grenoble, France
| | - Stéphane Ménage
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-LCBM, UMR5249, 38000, Grenoble, France.
| | - Renaud Dumas
- Univ. Grenoble Alpes, CEA, CNRS, INRAE, IRIG-DBSCI-LPCV 38000, Grenoble, France
| | - Olivier Hamelin
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-LCBM, UMR5249, 38000, Grenoble, France.
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38
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Petyuk VA, Yu L, Olson HM, Yu F, Clair G, Qian WJ, Shulman JM, Bennett DA. Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss. J Proteome Res 2021; 20:2266-2282. [PMID: 33900085 PMCID: PMC9190253 DOI: 10.1021/acs.jproteome.0c00747] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteinaceous aggregates containing α-synuclein protein called Lewy bodies in the substantia nigra is a hallmark of Parkinson's disease. The molecular mechanisms of Lewy body formation and associated neuronal loss remain largely unknown. To gain insights into proteins and pathways associated with Lewy body pathology, we performed quantitative profiling of the proteome. We analyzed substantia nigra tissue from 51 subjects arranged into three groups: cases with Lewy body pathology, Lewy body-negative controls with matching neuronal loss, and controls with no neuronal loss. Using a label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach, we characterized the proteome both in terms of protein abundances and peptide modifications. Statistical testing for differential abundance of the most abundant 2963 proteins, followed by pathway enrichment and Bayesian learning of the causal network structure, was performed to identify likely drivers of Lewy body formation and dopaminergic neuronal loss. The identified pathways include (1) Arp2/3 complex-mediated actin nucleation; (2) synaptic function; (3) poly(A) RNA binding; (4) basement membrane and endothelium; and (5) hydrogen peroxide metabolic process. According to the data, the endothelial/basement membrane pathway is tightly connected with both pathologies and likely to be one of the drivers of neuronal loss. The poly(A) RNA-binding proteins, including the ones relevant to other neurodegenerative disorders (e.g., TDP-43 and FUS), have a strong inverse correlation with Lewy bodies and may reflect an alternative mechanism of nigral neurodegeneration.
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Affiliation(s)
- Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Heather M Olson
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Joshua M Shulman
- Departments of Neurology, Molecular & Human Genetics, and Neuroscience, Baylor College of Medicine, Houston, Texas 77030, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, United States
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois 60612, United States
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39
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Human Plasma Extracellular Vesicle Isolation and Proteomic Characterization for the Optimization of Liquid Biopsy in Multiple Myeloma. Methods Mol Biol 2021; 2261:151-191. [PMID: 33420989 DOI: 10.1007/978-1-0716-1186-9_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer cells secrete membranous extracellular vesicles (EVs) which contain specific oncogenic molecular cargo (including oncoproteins, oncopeptides, and RNA) into their microenvironment and the circulation. As such, EVs including exosomes (small EVs) and microvesicles (large EVs) represent important circulating biomarkers for various diseases, including cancer and its progression. These circulating biomarkers offer a potentially minimally invasive and repeatable targets for analysis (liquid biopsy) that could aid in the diagnosis, risk stratification, and monitoring of cancer. Although their potential as cancer biomarkers has been promising, the identification and quantification of EVs in clinical samples remain challenging. Like EVs, other types of circulating biomarkers (including cell-free nucleic acids, cf-NAs; or circulating tumor cells, CTCs) may represent a complementary or alternative approach to cancer diagnosis. In the context of multiple myeloma (MM), a systemic cancer type that causes cancer cells to accumulate in the bone marrow, the specific role for EVs as biomarkers for diagnosis and monitoring remains undefined. Tumor heterogeneity along with the various subtypes of MM (such as non-secretory MM) that cannot be monitored using conventional testing (e.g. sequential serological testing and bone marrow biopsies) render liquid biopsy and circulating tumor-derived EVs a promising approach. In this protocol, we describe the isolation and purification of EVs from peripheral blood plasma (PBPL) collected from healthy donors and patients with MM for a biomarker discovery strategy. Our results demonstrate detection of circulating EVs from as little as 1 mL of MM patients' PBPL. High-resolution mass spectrometry (MS)-based proteomics promises to provide new avenues in identifying novel markers for detection, monitoring, and therapeutic intervention of disease. We describe biophysical characterization and quantitative proteomic profiling of disease-specific circulating EVs which may provide important implications for the development of cancer diagnostics in MM.
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40
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Shigeri Y, Nakata M, Kubota HY, Tomari N, Yamamoto Y, Uegaki K, Haramoto Y, Bumb C, Tanaka Y, Kinumi T, Inagaki H. Identification of Novel Proteins in Foam Nests of the Japanese Forest Green Tree Frog, Rhacophorus arboreus. Zoolog Sci 2021; 38:8-19. [PMID: 33639713 DOI: 10.2108/zs200113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/08/2020] [Indexed: 11/17/2022]
Abstract
Foam nests of frogs are natural biosurfactants that contain potential compounds for biocompatible materials, Drug Delivery System (DDS), emulsifiers, and bioremediation. To elucidate the protein components in the foam nests of Rhacophorus arboreus, which is an endemic Japanese frog species commonly seen during the rainy season, we performed amino acid analysis, SDS-PAGE electrophoresis, and matrix-assisted laser desorption/ionization mass spectrometry using intact foam nests. Many proteins were detected in these foam nests, ranging from a few to several hundred kDa, with both essential and non-essential amino acids. Next, we performed transcriptome analysis using a next-generation sequencer on total RNAs extracted from oviducts before egg-laying. The soluble foam nests were purified by LC-MS and analyzed using Edman degradation, and the identified N-terminal sequences were matched to the transcriptome data. Four proteins that shared significant sequence homologies with extracellular superoxide dismutase of Nanorana parkeri, vitelline membrane outer layer protein 1 homolog of Xenopus tropicalis, ranasmurfin of Polypedates leucomystax, and alpha-1-antichymotrypsin of Sorex araneus were identified. Prior to purification of the foam nests, they were treated with both a reducing reagent and an alkylating agent, and LC-MS/ MS analyses were performed. We identified 22 proteins in the foam nests that were homologous with proteinase inhibitors, ribonuclease, glycoproteins, antimicrobial protein and barrier, immunoglobulin-binding proteins, glycoprotein binding protein, colored protein, and keratin-associated protein. The presence of these proteins in foam nests, along with small molecules, such as carbohydrates and sugars, would protect them against microbial and parasitic attack, oxidative stress, and a shortage of moisture.
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Affiliation(s)
- Yasushi Shigeri
- Department of Chemistry, Wakayama Medical University, Wakayama 641-0011, Japan,
| | - Makoto Nakata
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan
| | - Hiroshi Y Kubota
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Naohiro Tomari
- Kyoto Municipal Institute of Industrial Technology and Culture, Shimogyo-ku, Kyoto 600-8813, Japan
| | - Yoshihiro Yamamoto
- Kyoto Municipal Institute of Industrial Technology and Culture, Shimogyo-ku, Kyoto 600-8813, Japan
| | - Koichi Uegaki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Yoshikazu Haramoto
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Chloe Bumb
- Department of Chemistry, Wakayama Medical University, Wakayama 641-0011, Japan.,Faculty of Pharmacy, University of Strasbourg, 67401, Illkirch, Cedex, France
| | - Yoshie Tanaka
- Department of Chemistry, Wakayama Medical University, Wakayama 641-0011, Japan
| | - Tomoya Kinumi
- Research Institute for Material and Chemical Measurement, National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba C-3, Ibaraki 305-8563, Japan
| | - Hidetoshi Inagaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
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41
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Moyer TB, Parsley NC, Sadecki PW, Schug WJ, Hicks LM. Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products. Nat Prod Rep 2021; 38:489-509. [PMID: 32929442 PMCID: PMC7956910 DOI: 10.1039/d0np00046a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.
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Affiliation(s)
- Tessa B Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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42
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Murphy EL, Joy AP, Ouellette RJ, Barnett DA. Optimization of cysteine residue alkylation using an on-line LC-MS strategy: Benefits of using a cocktail of haloacetamide reagents. Anal Biochem 2021; 619:114137. [PMID: 33582115 DOI: 10.1016/j.ab.2021.114137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/31/2022]
Abstract
Several common reagents for the alkylation of cysteine residues of model intact proteins were evaluated for reaction speed, yield of alkylated product and degree of over-alkylation using an online LC-MS platform. The efficiency of the alkylation reaction is found to be dependent on the (1) reagent, (2) peptide/protein, (3) reagent concentration and (4) reaction time. At high reagent concentrations, iodoacetic acid was found to produce significant levels of over-alkylation products wherein methionine residues become modified. For optimal performance of the alkylation reaction, we found the use of a cocktail of chloroacetamide, bromoacetamide and iodoacetamide worked best. The alkylating efficiency of each haloacetamide is a balance between the characteristics of the halogen leaving group and the steric hindrance of the alkylation site on the peptide or protein. A key aspect of using a cocktail of haloacetamides is that they all produce the same modification (+57.0209 Da) to the cysteine residues of the protein while the alkylation efficiency of each site may differ for each of the three reagents. Over-alkylation effects appear to be lower with the cocktail due to a lower concentration of each reagent. The haloacetamide cocktail could be useful when considering complex mixtures of proteins.
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Affiliation(s)
- EmmaRae L Murphy
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada; Department of Process Engineering and Applied Science, Dalhousie University, Sexton Campus Chemical Engineering Building, PO Box 15000, Halifax, Nova Scotia, B3H4R2, Canada
| | - Andrew P Joy
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada
| | - Rodney J Ouellette
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada
| | - David A Barnett
- Atlantic Cancer Research Institute, Hotel Dieu Pavilion, 35 Providence Street, Moncton, New Brunswick, E1C8X3, Canada; Department of Chemistry and Biochemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L1G8, Canada.
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43
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Rai A, Fang H, Fatmous M, Claridge B, Poh QH, Simpson RJ, Greening DW. A Protocol for Isolation, Purification, Characterization, and Functional Dissection of Exosomes. Methods Mol Biol 2021; 2261:105-149. [PMID: 33420988 DOI: 10.1007/978-1-0716-1186-9_9] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Extracellular vesicles (EVs) are membrane-enclosed vesicles released by cells. They carry proteins, nucleic acids, and metabolites which can be transferred to a recipient cell, locally or at a distance, to elicit a functional response. Since their discovery over 30 years ago, the functional repertoire of EVs in both physiological (e.g., organ morphogenesis, embryo implantation) and pathological (e.g., cancer, neurodegeneration) conditions has cemented their crucial role in intercellular communication. Moreover, because the cargo encapsulated within circulating EVs remains protected from degradation, their diagnostic as well as therapeutic (such as drug delivery tool) applications have garnered vested interest. Global efforts have been made to purify EV subtypes from biological fluids and in vitro cell culture media using a variety of strategies and techniques, with a major focus on EVs of endocytic origin called exosomes (30-150 nm in size). Given that the secretome comprises of soluble secreted proteins, protein aggregates, RNA granules, and EV subtypes (such as exosomes, shed microvesicles, apoptotic bodies), it is imperative to purify exosomes to homogeneity if we are to perform biochemical and biophysical characterization and, importantly, functional dissection. Besides understanding the composition of EV subtypes, defining molecular bias of how they reprogram target cells also remains of paramount importance in this area of active research. Here, we outline a systematic "how to" protocol (along with useful insights/tips) to obtain highly purified exosomes and perform their biophysical and biochemical characterization. This protocol employs a mass spectrometry-based proteomics approach to characterize the protein composition of exosomes. We also provide insights on different isolation strategies and their usefulness in various downstream applications. We outline protocols for lipophilic labeling of exosomes to study uptake by a recipient cell, investigating cellular reprogramming using proteomics and studying functional response to exosomes in the Transwell-Matrigel™ Invasion assay.
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Affiliation(s)
- Alin Rai
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Haoyun Fang
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Monique Fatmous
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Bethany Claridge
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Qi Hui Poh
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Richard J Simpson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - David W Greening
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia.
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Kaushal P, Lee C. N-terminomics - its past and recent advancements. J Proteomics 2020; 233:104089. [PMID: 33359939 DOI: 10.1016/j.jprot.2020.104089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/22/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023]
Abstract
N-terminomics is a rapidly evolving branch of proteomics that encompasses the study of protein N-terminal sequence. A proteome-wide collection of such sequences has been widely used to understand the proteolytic cascades and in annotating the genome. Over the last two decades, various N-terminomic strategies have been developed for achieving high sensitivity, greater depth of coverage, and high-throughputness. We, in this review, cover how the field of N-terminomics has evolved to date, including discussion on various sample preparation and N-terminal peptide enrichment strategies. We also compare different N-terminomic methods and highlight their relative benefits and shortcomings in their implementation. In addition, an overview of the currently available bioinformatics tools and data analysis pipelines for the annotation of N-terminomic datasets is also included. SIGNIFICANCE: It has been recognized that proteins undergo several post-translational modifications (PTM), and a number of perturbed biological pathways are directly associated with modifications at the terminal sites of a protein. In this regard, N-terminomics can be applied to generate a proteome-wide landscape of mature N-terminal sequences, annotate their source of generation, and recognize their significance in the biological pathways. Besides, a system-wide study can be used to study complicated proteolytic machinery and protease cleavage patterns for potential therapeutic targets. Moreover, due to unprecedented improvements in the analytical methods and mass spectrometry instrumentation in recent times, the N-terminomic methodologies now offers an unparalleled ability to study proteoforms and their implications in clinical conditions. Such approaches can further be applied for the detection of low abundant proteoforms, annotation of non-canonical protein coding sites, identification of candidate disease biomarkers, and, last but not least, the discovery of novel drug targets.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea.
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Relative Abundance of Alpha-Amylase/Trypsin Inhibitors in Selected Sorghum Cultivars. Molecules 2020; 25:molecules25245982. [PMID: 33348658 PMCID: PMC7774315 DOI: 10.3390/molecules25245982] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
Sorghum is of growing interest and considered as a safe food for wheat related disorders. Besides the gluten, α-amylase/trypsin-inhibitors (ATIs) have been identified as probable candidates for these disorders. Several studies focused on wheat-ATIs although there is still a lack of data referring to the relative abundance of sorghum-ATIs. The objective of this work was therefore to contribute to the characterization of sorghum ATI profiles by targeted proteomics tools. Fifteen sorghum cultivars from different regions were investigated with raw proteins ranging from 7.9 to 17.0 g/100 g. Ammonium bicarbonate buffer in combination with urea was applied for protein extraction, with concentration from 0.588 ± 0.047 to 4.140 ± 0.066 mg/mL. Corresponding electrophoresis data showed different protein profiles. UniProtKB data base research reveals two sorghum ATIs, P81367 and P81368; both reviewed and a targeted LC–MS/MS method was developed to analyze these. Quantifier peptides ELAAVPSR (P81367) and TYMVR (P81368) were identified and retained as biomarkers for relative quantification. Different reducing and alkylating agents were assessed and combination of tris (2 carboxyethyl) phosphine/iodoacetamide gave the best response. Linearity was demonstrated for the quantifier peptides with standard recovery between 92.2 and 107.6%. Nine sorghum cultivars presented up to 60 times lower ATI contents as compared to wheat samples. This data suggests that sorghum can effectively be considered as a good alternative to wheat.
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46
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Bhopatkar AA, Rangachari V. Are granulins copper sequestering proteins? Proteins 2020; 89:450-461. [PMID: 33252789 DOI: 10.1002/prot.26031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023]
Abstract
Granulins (GRN 1-7) are short (~6 kDa), cysteine-rich proteins that are generated upon the proteolytic processing of progranulin (PGRN). These peptides, along with their precursor, have been implicated in multiple pathophysiological roles, especially in neurodegenerative diseases. Previously we showed that GRN-3 and GRN-5 are fully disordered in the reduced form implicating redox sensitive attributes to the proteins. Redox-based modulations are often carried out by metalloproteins in mitigating oxidative stress and maintaining metal-homeostasis within cells. To probe whether GRNs play a role in metal sequestration, we tested the metal binding propensity of the reduced forms of GRNs -3 and - 5 under neutral and acidic pH mimicking cytosolic and lysosomal conditions, respectively. We found, at neutral pH, both GRNs selectively bind Cu and no other divalent metal cations, with a greater specificity for Cu(I). Binding of Cu did not result in a disorder-to-order structural transition but partly triggered the multimerization of GRNs via uncoordinated cystines at both pH conditions. Overall, the results indicate that GRNs -3 and - 5 have surprisingly strong affinity for Cu in the pM range, comparable to other known copper sequestering proteins. The results also hint at a potential of GRNs to reduce Cu(II) to Cu(I), a process that has significance in mitigating Cu-induced ROS cytotoxicity in cells. Together, this report uncovers metal-coordinating property of GRNs for the first time, which may have profound significance in their structure and pathophysiological functions.
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Affiliation(s)
- Anukool A Bhopatkar
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences and, University of Southern Mississippi, Hattiesburg, Mississippi, USA
| | - Vijayaraghavan Rangachari
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA
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Jiang S, Carroll L, Rasmussen LM, Davies MJ. Oxidation of protein disulfide bonds by singlet oxygen gives rise to glutathionylated proteins. Redox Biol 2020; 38:101822. [PMID: 33338920 PMCID: PMC7750407 DOI: 10.1016/j.redox.2020.101822] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/20/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023] Open
Abstract
Disulfide bonds play a key function in determining the structure of proteins, and are the most strongly conserved compositional feature across proteomes. They are particularly common in extracellular environments, such as the extracellular matrix and plasma, and in proteins that have structural (e.g. matrix) or binding functions (e.g. receptors). Recent data indicate that disulfides vary markedly with regard to their rate of reaction with two-electron oxidants (e.g. HOCl, ONOOH), with some species being rapidly and readily oxidized. These reactions yielding thiosulfinates that can react further with a thiol to give thiolated products (e.g. glutathionylated proteins with glutathione, GSH). Here we show that these ‘oxidant-mediated thiol-disulfide exchange reactions’ also occur during photo-oxidation reactions involving singlet oxygen (1O2). Reaction of protein disulfides with 1O2 (generated by multiple sensitizers in the presence of visible light and O2), yields reactive intermediates, probably zwitterionic peroxyl adducts or thiosulfinates. Subsequent exposure to GSH, at concentrations down to 2 μM, yields thiolated adducts which have been characterized by both immunoblotting and mass spectrometry. The yield of GSH adducts is enhanced in D2O buffers, and requires the presence of the disulfide bond. This glutathionylation can be diminished by non-enzymatic (e.g. tris-(2-carboxyethyl)phosphine) and enzymatic (glutaredoxin) reducing systems. Photo-oxidation of human plasma and subsequent incubation with GSH yields similar glutathionylated products with these formed primarily on serum albumin and immunoglobulin chains, demonstrating potential in vivo relevance. These reactions provide a novel pathway to the formation of glutathionylated proteins, which are widely recognized as key signaling molecules, via photo-oxidation reactions. Disulfide bonds (DSBs) are critical to protein structure and function. DSBs are rapidly oxidized by singlet oxygen and other oxidants to reactive species. These DSB-derived intermediates react with GSH to give glutathionylated proteins. Glutathionylation can be diminished by reductants, but does not repair DSB damage. Oxidation of human plasma DSBs gives glutathionylated albumin and immunoglobulins.
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Affiliation(s)
- Shuwen Jiang
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Luke Carroll
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Lars M Rasmussen
- Center for Individualized Medicine in Arterial Diseases (CIMA), Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, 2200, Denmark.
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Efficient Confirmation of Plant Viral Proteins and Identification of Specific Viral Strains by nanoLC-ESI-Q-TOF Using Single-Leaf-Tissue Samples. Pathogens 2020; 9:pathogens9110966. [PMID: 33228257 PMCID: PMC7699591 DOI: 10.3390/pathogens9110966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/11/2020] [Accepted: 11/17/2020] [Indexed: 12/03/2022] Open
Abstract
Plant viruses are important pathogens that cause significant crop losses. A plant protein extraction protocol that combines crushing the tissue by a pestle in liquid nitrogen with subsequent crushing by a roller-ball crusher in urea solution, followed by RuBisCO depletion, reduction, alkylation, protein digestion, and ZipTip purification allowed us to substantially simplify the sample preparation by removing any other precipitation steps and to detect viral proteins from samples, even with less than 0.2 g of leaf tissue, by a medium resolution nanoLC-ESI-Q-TOF. The presence of capsid proteins or polyproteins of fourteen important viruses from seven different families (Geminiviridae, Luteoviridae, Bromoviridae, Caulimoviridae, Virgaviridae, Potyviridae, and Secoviridae) isolated from ten different economically important plant hosts was confirmed through many identified pathogen-specific peptides from a protein database of host proteins and potential pathogen proteins assembled separately for each host and based on existing online plant virus pathogen databases. The presented extraction protocol, combined with a medium resolution LC-MS/MS, represents a cost-efficient virus protein confirmation method that proved to be effective at identifying virus strains (as demonstrated for PPV, WDV) and distinct disease species of BYDV, as well as putative new viral protein sequences from single-plant-leaf tissue samples. Data are available via ProteomeXchange with identifier PXD022456.
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Moloney C, Brosnan B, Faulkner H, O’Regan J. An Analytical Method to Quantify Osteopontin in Dairy Powders and Infant Formulas by Signature Peptide Quantification with UHPLC-MS/MS. J AOAC Int 2020; 103:1646-1653. [DOI: 10.1093/jaoacint/qsaa058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/27/2020] [Accepted: 04/15/2020] [Indexed: 11/13/2022]
Abstract
Abstract
Background
Osteopontin (OPN) is an important protein in human milk, and is of growing interest to infant formula (IF) manufacturers. OPN is present at low quantities in bovine milk and its derived ingredients, and there is a need for an accurate quantitative method in complex matrixes such as IF and growing-up milks (GUMs).
Objective
The objective of this work was to validate a method to quantify OPN in several dairy powders produced from bovine milk, including skimmed milk powder (SMP), whey protein concentrate (WPC), demineralized WPC and α-lactalbumin-enriched WPC (α-lac WPC). The method was further validated in intact-protein IF and GUM powders produced using combinations of these ingredients.
Methods
Test samples were digested using trypsin, and the most appropriate peptide fragmentation transitions were identified by UHPLC-MS/MS. Quantification was made against a standard curve constructed from OPN reference material, and isotopically-labelled peptide standards were used as internal standards. Curve linearity was assessed, and samples were spiked at two OPN levels.
Results
The validation parameters were met in almost all cases, with precision RSDr and RSDiR values ranging from 0.26–7.43% and 1.22–12.70%, respectively, and spike recoveries ranging from 88–102%. The method was used to accurately measure OPN in bovine milk-based IF and GUM powders with intact protein systems, based on comparisons with mass balance calculations.
Conclusions
The results from this study show that the method is fit-for-purpose to support IF and GUM manufacturers in evaluating OPN contents of raw materials and products containing whole, intact protein systems from bovine milk.
Highlights
An LC-MS/MS method was developed to measure OPN in dairy powders, IF and GUMs containing whole, intact protein systems from bovine milk.
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Affiliation(s)
- Cian Moloney
- Nestle Development Centre Nutrition, Askeaton, Limerick, Ireland
| | - Brid Brosnan
- CAPPA, Centre for Advanced Photonics & Process Analysis, Cork Institute of Technology, Cork, Ireland
| | - Hope Faulkner
- CAPPA, Centre for Advanced Photonics & Process Analysis, Cork Institute of Technology, Cork, Ireland
| | - Jonathan O’Regan
- Nestle Development Centre Nutrition, Askeaton, Limerick, Ireland
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50
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Expression and purification of the antimicrobial peptide Bin1b in Escherichia coli tagged with the fusion proteins CusF3H+ and SmbP. Protein Expr Purif 2020; 178:105784. [PMID: 33129981 DOI: 10.1016/j.pep.2020.105784] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 11/22/2022]
Abstract
We have previously shown that the small metal-binding proteins CusF3H+ and SmbP can be used as fusion proteins for the expression and purification of recombinant proteins in Escherichia coli. Because of their small size, both around 10 kDa, they are suitable for the production of peptides to avoid meager yields after the final purification step of tag removal. Bin1b is a beta-defensin found in the epididymis of rats that has shown to have antimicrobial activity. Previous methodologies used to express this antimicrobial peptide in E. coli involve the expression of the peptide as inclusion bodies followed by in vitro refolding or the supplementation of the proteins necessary for proper folding of the peptide in the cytoplasm via a second plasmid. Here, we developed a methodology that forgoes these approaches and instead uses the fusion proteins CusF3H+ or SmbP and the E. coli strain SHuffle to obtain a soluble recombinant protein that contains the mature Bin1b peptide. The recombinant protein is purified using IMAC chromatography and is subsequently cleaved with enterokinase to separate the fusion protein from Bin1b. The purified peptide displays antimicrobial activity against E. coli, as previously shown. Furthermore, we also tested its antimicrobial activity against the Gram-positive bacteria Staphylococcus aureus and found that Bin1b is also capable of inhibiting the growth of this bacterium. In conclusion, we developed a practical methodology for the expression and purification of the bioactive Bin1b peptide in E. coli using the fusion proteins CusF3H+ and SmbP. This approach could be further applied for the production of more biologically active peptides.
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