1
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Larsen DN, Kaczmarek JZ, Palarasah Y, Graversen JH, Højrup P. Epitope mapping of SARS-CoV-2 RBDs by hydroxyl radical protein footprinting reveals the importance of including negative antibody controls. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141011. [PMID: 38499233 DOI: 10.1016/j.bbapap.2024.141011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 03/20/2024]
Abstract
Understanding protein-protein interactions is crucial for drug design and investigating biological processes. Various techniques, such as CryoEM, X-ray spectroscopy, linear epitope mapping, and mass spectrometry-based methods, can be employed to map binding regions on proteins. Commonly used mass spectrometry-based techniques are cross-linking and hydrogen‑deuterium exchange (HDX). Another approach, hydroxyl radical protein footprinting (HRPF), identifies binding residues on proteins but faces challenges due to high initial costs and complex setups. This study introduces a generally applicable method using Fenton chemistry for epitope mapping in a standard mass spectrometry laboratory. It emphasizes the importance of controls, particularly the inclusion of a negative antibody control, not widely utilized in HRPF epitope mapping. Quantification by TMT labelling is introduced to reduce false positives, enabling direct comparison between sample conditions and biological triplicates. Additionally, six technical replicates were incorporated to enhance the depth of analysis. Observations on the receptor-binding domain (RBD) of SARS-CoV-2 Spike Protein, Alpha and Delta variants, revealed both binding and opening regions. Significantly changed peptides upon mixing with a negative control antibody suggested structural alterations or nonspecific binding induced by the antibody alone. Integration of negative control antibody experiments and high overlap between biological triplicates led to the exclusion of 40% of significantly changed regions. The final identified binding region correlated with existing literature on neutralizing antibodies against RBD. The presented method offers a straightforward implementation for HRPF analysis in a generic mass spectrometry-based laboratory. Enhanced data reliability was achieved through increased technical and biological replicates alongside negative antibody controls.
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Affiliation(s)
- Daniel Nyberg Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark; Ovodan Biotech A/S, Havnegade 36, DK-5000 Odense, Denmark
| | | | - Yaseelan Palarasah
- Department of Inflammation, Institute of Molecular Medicine, Faculty of Health and Medical Sciences, University of Southern Denmark, Odense, Denmark
| | - Jonas Heilskov Graversen
- Department of Inflammation, Institute of Molecular Medicine, Faculty of Health and Medical Sciences, University of Southern Denmark, Odense, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark; Ovodan Biotech A/S, Havnegade 36, DK-5000 Odense, Denmark.
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2
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Diab GAA, da Silva MAR, Rocha GFSR, Noleto LFG, Rogolino A, de Mesquita JP, Jiménez‐Calvo P, Teixeira IF. A Solar to Chemical Strategy: Green Hydrogen as a Means, Not an End. GLOBAL CHALLENGES (HOBOKEN, NJ) 2024; 8:2300185. [PMID: 38868607 PMCID: PMC11165522 DOI: 10.1002/gch2.202300185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/24/2023] [Indexed: 06/14/2024]
Abstract
Green hydrogen is the key to the chemical industry achieving net zero emissions. The chemical industry is responsible for almost 2% of all CO2 emissions, with half of it coming from the production of simple commodity chemicals, such as NH3, H2O2, methanol, and aniline. Despite electrolysis driven by renewable power sources emerging as the most promising way to supply all the green hydrogen required in the production chain of these chemicals, in this review, it is worth noting that the photocatalytic route may be underestimated and can hold a bright future for this topic. In fact, the production of H2 by photocatalysis still faces important challenges in terms of activity, engineering, and economic feasibility. However, photocatalytic systems can be tailored to directly convert sunlight and water (or other renewable proton sources) directly into chemicals, enabling a solar-to-chemical strategy. Here, a series of recent examples are presented, demonstrating that photocatalysis can be successfully employed to produce the most important commodity chemicals, especially on NH3, H2O2, and chemicals produced by reduction reactions. The replacement of fossil-derived H2 in the synthesis of these chemicals can be disruptive, essentially safeguarding the transition of the chemical industry to a low-carbon economy.
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Affiliation(s)
- Gabriel A. A. Diab
- Department of ChemistryFederal University of São CarlosRod. Washington Luís km 235 – SPSão CarlosSP13565‐905Brazil
| | - Marcos A. R. da Silva
- Department of ChemistryFederal University of São CarlosRod. Washington Luís km 235 – SPSão CarlosSP13565‐905Brazil
| | - Guilherme F. S. R. Rocha
- Department of ChemistryFederal University of São CarlosRod. Washington Luís km 235 – SPSão CarlosSP13565‐905Brazil
| | - Luis F. G. Noleto
- Department of ChemistryFederal University of São CarlosRod. Washington Luís km 235 – SPSão CarlosSP13565‐905Brazil
| | - Andrea Rogolino
- Cavendish LaboratoryUniversity of CambridgeCambridgeCB3 0HEUK
| | - João P. de Mesquita
- Department of ChemistryFederal University of São CarlosRod. Washington Luís km 235 – SPSão CarlosSP13565‐905Brazil
- Departamento de QuímicaUniversidade Federal dos Vales Jequitinhonha e MucuriRodovia MGT 367 – Km 583, n° 5000, Alto da JacubaDiamantinaMG39100Brazil
| | - Pablo Jiménez‐Calvo
- Department for Materials SciencesFriedrich‐Alexander‐Universität Erlangen‐NürnbergMartensstrasse 7D‐91058ErlangenGermany
- Chemistry of Thin Film MaterialsFriedrich‐Alexander‐Universität Erlangen‐NürnbergIZNF, Cauerstraße 3D‐91058ErlangenGermany
| | - Ivo F. Teixeira
- Department of ChemistryFederal University of São CarlosRod. Washington Luís km 235 – SPSão CarlosSP13565‐905Brazil
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3
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Zhang W, Issa K, Tang T, Zhang H. Role of Hydroperoxyl Radicals in Heterogeneous Oxidation of Oxygenated Organic Aerosols. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4727-4736. [PMID: 38411392 DOI: 10.1021/acs.est.3c09024] [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: 02/28/2024]
Abstract
Heterogeneous oxidative aging of organic aerosols (OA) occurs ubiquitously in the atmosphere, initiated by oxidants, such as the hydroxyl radicals (•OH). Hydroperoxyl radicals (HO2•) are also an important oxidant in the troposphere, and its gas-phase chemistry has been well studied. However, the role of HO2• in heterogeneous OA oxidation remains elusive. Here, we carry out •OH-initiated heterogeneous oxidation of several OA model systems under different HO2• conditions in a flow tube reactor and characterize the molecular oxidation products using a suite of mass spectrometry instrumentation. By using hydrogen-deuterium exchange (HDX) with thermal desorption iodide-adduct chemical ionization mass spectrometry, we provide direct observation of organic hydroperoxide (ROOH) formation from heterogeneous HO2• and peroxy radicals (RO2•) reactions for the first time. The ROOH may contribute substantially to the oxidation products, varied with the parent OA chemical structure. Furthermore, by regulating RO2• reaction pathways, HO2• also greatly influence the overall composition of the oxidized OA. Last, we suggest that the RO2• + HO2• reactions readily occur at the OA particle interface rather than in the particle bulk. These findings provide new mechanistic insights into the heterogeneous OA oxidation chemistry and help fill the critical knowledge gap in understanding atmospheric OA oxidative aging.
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Affiliation(s)
- Wen Zhang
- Department of Chemistry, University of California, Riverside, California 92507, United States
| | - Kassem Issa
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California 92507, United States
| | - Tiffany Tang
- Department of Chemistry, University of California, Riverside, California 92507, United States
| | - Haofei Zhang
- Department of Chemistry, University of California, Riverside, California 92507, United States
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4
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Cajka T, Hricko J, Rakusanova S, Brejchova K, Novakova M, Rudl Kulhava L, Hola V, Paucova M, Fiehn O, Kuda O. Hydrophilic Interaction Liquid Chromatography-Hydrogen/Deuterium Exchange-Mass Spectrometry (HILIC-HDX-MS) for Untargeted Metabolomics. Int J Mol Sci 2024; 25:2899. [PMID: 38474147 DOI: 10.3390/ijms25052899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/17/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Liquid chromatography with mass spectrometry (LC-MS)-based metabolomics detects thousands of molecular features (retention time-m/z pairs) in biological samples per analysis, yet the metabolite annotation rate remains low, with 90% of signals classified as unknowns. To enhance the metabolite annotation rates, researchers employ tandem mass spectral libraries and challenging in silico fragmentation software. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) may offer an additional layer of structural information in untargeted metabolomics, especially for identifying specific unidentified metabolites that are revealed to be statistically significant. Here, we investigate the potential of hydrophilic interaction liquid chromatography (HILIC)-HDX-MS in untargeted metabolomics. Specifically, we evaluate the effectiveness of two approaches using hypothetical targets: the post-column addition of deuterium oxide (D2O) and the on-column HILIC-HDX-MS method. To illustrate the practical application of HILIC-HDX-MS, we apply this methodology using the in silico fragmentation software MS-FINDER to an unknown compound detected in various biological samples, including plasma, serum, tissues, and feces during HILIC-MS profiling, subsequently identified as N1-acetylspermidine.
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Affiliation(s)
- Tomas Cajka
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Jiri Hricko
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Stanislava Rakusanova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Kristyna Brejchova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Michaela Novakova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Lucie Rudl Kulhava
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Veronika Hola
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Michaela Paucova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Ondrej Kuda
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
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5
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Osipenko S, Bashilov A, Vishnevskaya A, Rumiantseva L, Levashova A, Kovalenko A, Tupertsev B, Kireev A, Nikolaev E, Kostyukevich Y. Investigating the Metabolism of Plants Germinated in Heavy Water, D 2O, and H 218O-Enriched Media Using High-Resolution Mass Spectrometry. Int J Mol Sci 2023; 24:15396. [PMID: 37895078 PMCID: PMC10607710 DOI: 10.3390/ijms242015396] [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: 08/08/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 10/29/2023] Open
Abstract
Mass spectrometry has been an essential technique for the investigation of the metabolic pathways of living organisms since its appearance at the beginning of the 20th century. Due to its capability to resolve isotopically labeled species, it can be applied together with stable isotope tracers to reveal the transformation of particular biologically relevant molecules. However, low-resolution techniques, which were used for decades, had limited capabilities for untargeted metabolomics, especially when a large number of compounds are labelled simultaneously. Such untargeted studies may provide new information about metabolism and can be performed with high-resolution mass spectrometry. Here, we demonstrate the capabilities of high-resolution mass spectrometry to obtain insights on the metabolism of a model plant, Lepidium sativum, germinated in D2O and H218O-enriched media. In particular, we demonstrated that in vivo labeling with heavy water helps to identify if a compound is being synthesized at a particular stage of germination or if it originates from seed content, and tandem mass spectrometry allows us to highlight the substructures with incorporated isotope labels. Additionally, we found in vivo labeling useful to distinguish between isomeric compounds with identical fragmentation patterns due to the differences in their formation rates that can be compared by the extent of heavy atom incorporation.
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Affiliation(s)
- Sergey Osipenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Anton Bashilov
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
- Institute for Translational Medicine and Biotechnology, First Moscow State Medical University, 119991 Moscow, Russia
| | - Anna Vishnevskaya
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Lidiia Rumiantseva
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Anna Levashova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Anna Kovalenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Boris Tupertsev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Albert Kireev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia; (S.O.); (A.B.); (A.V.); (L.R.); (A.L.); (A.K.); (B.T.); (A.K.); (E.N.)
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6
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Li PL, Huang CH, Mao L, Li J, Sheng ZG, Zhu BZ. An unprecedented free radical mechanism for the formation of DNA adducts by the carcinogenic N-sulfonated metabolite of aristolochic acids. Free Radic Biol Med 2023; 205:332-345. [PMID: 37179032 DOI: 10.1016/j.freeradbiomed.2023.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/29/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
The carcinogenicity of aristolochic acids (AAs) has been attributed mainly to the formation of stable DNA-aristolactam (DNA-AL) adducts by its reactive N-sulfonated metabolite N-sulfonatooxyaristolactam (N-OSO3--AL). The most accepted mechanism for such DNA-AL adduct formation is via the postulated but never unequivocally-confirmed aristolactam nitrenium ion. Here we found that both sulfate radical and two ALI-derived radicals (N-centered and C-centered spin isomers) were produced by N-OSO3--ALI, which were detected and unequivocally identified by complementary applications of ESR spin-trapping, HPLC-MS coupled with deuterium-exchange methods. Both the formation of the three radical species and DNA-ALI adducts can be significantly inhibited (up to 90%) by several well-known antioxidants, typical radical scavengers, and spin-trapping agents. Taken together, we propose that N-OSO3--ALI decomposes mainly via a new N-O bond homolysis rather than the previously proposed heterolysis pathway, yielding reactive sulfate and ALI-derived radicals, which are together and in concert responsible for forming DNA-ALI adducts. This study presents strong and direct evidence for the production of free radical intermediates during N-OSO3--ALI decomposition, providing an unprecedented free radical perspective and conceptual breakthrough, which can better explain and understand the molecular mechanism for the formation of DNA-AA adducts, the carcinogenicity of AAs and their potential prevention.
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Affiliation(s)
- Pei-Lin Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Chun-Hua Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China.
| | - Li Mao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jun Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zhi-Guo Sheng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ben-Zhan Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, PR China; Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA.
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7
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Kostyukevich Y, Stekolshikova E, Levashova A, Kovalenko A, Vishnevskaya A, Bashilov A, Kireev A, Tupertsev B, Rumiantseva L, Khaitovich P, Osipenko S, Nikolaev E. Untargeted Lipidomics after D 2O Administration Reveals the Turnover Rate of Individual Lipids in Various Organs of Living Organisms. Int J Mol Sci 2023; 24:11725. [PMID: 37511483 PMCID: PMC10380497 DOI: 10.3390/ijms241411725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The administration of low doses of D2O to living organisms was used for decades for the investigation of metabolic pathways and for the measurement of the turnover rate for specific compounds. Usually, the investigation of the deuterium uptake in lipids is performed by measuring the deuteration level of the palmitic acid residue using GC-MS instruments, and to our knowledge, the application of the modern untargeted LC-MS/MS lipidomics approaches was only reported a few times. Here, we investigated the deuterium uptake for >500 lipids for 13 organs and body liquids of mice (brain, lung, heart, liver, kidney, spleen, plasma, urine, etc.) after 4 days of 100% D2O administration. The maximum deuteration level was observed in the liver, plasma, and lung, while in the brain and heart, the deuteration level was lower. Using MS/MS, we demonstrated the incorporation of deuterium in palmitic and stearic fragments in lipids (PC, PE, TAG, PG, etc.) but not in the corresponding free forms. Our results were analyzed based on the metabolic pathways of lipids.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Elena Stekolshikova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Anna Levashova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Scientific Center of Biomedical Technologies of the Federal Medical and Biological Agency, Krasnogorsky District, Village Light Mountains, Bld. 1, 143442 Moscow, Russia
| | - Anna Kovalenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Anna Vishnevskaya
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Anton Bashilov
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Albert Kireev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Boris Tupertsev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Lidiia Rumiantseva
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Sergey Osipenko
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
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8
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Damont A, Legrand A, Cao C, Fenaille F, Tabet JC. Hydrogen/deuterium exchange mass spectrometry in the world of small molecules. MASS SPECTROMETRY REVIEWS 2023; 42:1300-1331. [PMID: 34859466 DOI: 10.1002/mas.21765] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 06/07/2023]
Abstract
The combined use of hydrogen/deuterium exchange (HDX) and mass spectrometry (MS), referred to as HDX-MS, is a powerful tool for exploring molecular edifices and has been used for over 60 years. Initially for structural and mechanistic investigation of low-molecular weight organic compounds, then to study protein structure and dynamics, then, the craze to study small molecules by HDX-MS accelerated and has not stopped yet. The purpose of this review is to present its different facets with particular emphasis on recent developments and applications. Reversible H/D exchanges of mobilizable protons as well as stable exchanges of non-labile hydrogen are considered whether they are taking place in solution or in the gas phase, or enzymatically in a biological media. Some fundamental principles are restated, especially for gas-phase processes, and an overview of recent applications, ranging from identification to quantification through the study of metabolic pathways, is given.
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Affiliation(s)
- Annelaure Damont
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - Anaïs Legrand
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - Chenqin Cao
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - François Fenaille
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
| | - Jean-Claude Tabet
- Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, Université Paris-Saclay, CEA, INRAE, Gif-sur-Yvette, France
- Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, Paris, France
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9
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Hatvany JB, Gallagher ES. Hydrogen/deuterium exchange for the analysis of carbohydrates. Carbohydr Res 2023; 530:108859. [PMID: 37290371 DOI: 10.1016/j.carres.2023.108859] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/10/2023]
Abstract
Carbohydrates and glycans are integral to many biological processes, including cell-cell recognition and energy storage. However, carbohydrates are often difficult to analyze due to the high degree of isomerism present. One method being developed to distinguish these isomeric species is hydrogen/deuterium exchange-mass spectrometry (HDX-MS). In HDX-MS, carbohydrates are exposed to a deuterated reagent and the functional groups with labile hydrogen atoms, including hydroxyls and amides, exchange with the 1 amu heavier isotope, deuterium. These labels can then be detected by MS, which monitors the mass increase with the addition of D-labels. The observed rate of exchange is dependent on the exchanging functional group, the accessibility of the exchanging functional group, and the presence of hydrogen bonds. Herein, we discuss how HDX has been applied in the solution-phase, gas-phase, and during MS ionization to label carbohydrates and glycans. Additionally, we compare differences in the conformations that are labeled, the labeling timeframes, and applications of each of these methods. Finally, we comment on future opportunities for development and use of HDX-MS to analyze glycans and glycoconjugates.
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Affiliation(s)
- Jacob B Hatvany
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA.
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10
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Williamson DL, Trimble TK, Nagy G. Hydrogen-Deuterium-Exchange-Based Mass Distribution Shifts in High-Resolution Cyclic Ion Mobility Separations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37098274 DOI: 10.1021/jasms.3c00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The mass distribution of ions influences separations in ion mobility spectrometry-mass spectrometry (IMS-MS). Herein, we introduce a method to induce mass distribution shifts for various analytes using hydrogen-deuterium exchange (HDX) immediately prior to ionization using a dual syringe approach. By replacing labile hydrogens on analytes with deuteriums, we were able to differentiate isomers using separations of isotopologues. For each analyte studied, every possible level of deuteration (from undeuterated to fully deuterated) was generated and then separated using cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS). The information gained from such separations (relative arrival times; tRel. values) was found to be orthogonal to conventional IMS-MS separations. Additionally, the observed shifts were linearly additive with increasing deuteration, suggesting that this methodology could be extended to analytes with a larger number of labile hydrogens. For one isomer pair, as few as two deuteriums were able to produce a large enough mass distribution shift to differentiate isomers. In another experiment, we found that the mass distribution shift was large enough to overcome the reduced mass contribution, resulting in a "flipped" arrival time where the heavier deuterated isotopologue arrived before the lighter one. In this work, we present a proof-of-concept demonstration that mass-distribution-based shifts, tRel. values, could potentially act as an added dimension to characterize molecules in IMS-MS. We anticipate, along with future work in this area, that mass-distribution-based shifts could enable the identification of unknown molecules through a database-driven approach in an analogous fashion to collision cross section (CCS) measurements.
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Affiliation(s)
- David L Williamson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Tyson K Trimble
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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11
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Olaleye O, Graf C, Spanov B, Govorukhina N, Groves MR, van de Merbel NC, Bischoff R. Determination of Binding Sites on Trastuzumab and Pertuzumab to Selective Affimers Using Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:775-783. [PMID: 36960982 PMCID: PMC10080681 DOI: 10.1021/jasms.3c00069] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a method to probe the solvent accessibility and conformational dynamics of a protein or a protein-ligand complex with respect to exchangeable amide hydrogens. Here, we present the application of HDX-MS to determine the binding sites of Affimer reagents to the monoclonal antibodies trastuzumab and pertuzumab, respectively. Intact and subunit level HDX-MS analysis of antibody-affimer complexes showed significant protection from HDX in the antibody Fab region upon affimer binding. Bottom-up HDX-MS experiments including online pepsin digestion revealed that the binding sites of the affimer reagents were mainly located in the complementarity-determining region (CDR) 2 of the heavy chain of the respective antibodies. Three-dimensional models of the binding interaction between the affimer reagents and the antibodies were built by homology modeling and molecular docking based on the HDX data.
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Affiliation(s)
- Oladapo Olaleye
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Christian Graf
- Novartis
Technical Research & Development Biologics, Hexal AG, Keltenring
1 + 3, 82041 Oberhaching, Germany
| | - Baubek Spanov
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Natalia Govorukhina
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Matthew R. Groves
- Drug
Design, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Nico C. van de Merbel
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- ICON
Bioanalytical Laboratories, Amerikaweg 18, 9407 TK Assen, The Netherlands
| | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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12
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Raznikov V, Raznikova M, Sulimenkov I, Zelenov V. Separation of mass spectra of hydrogen-deuterium exchanged ions obtained by electrospray of solutions of biopolymers with unknown primary structure. Anal Bioanal Chem 2023; 415:2193-2207. [PMID: 36943444 DOI: 10.1007/s00216-023-04625-7] [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: 01/10/2023] [Accepted: 02/21/2023] [Indexed: 03/23/2023]
Abstract
The work is dedicated to further development of our described method for analyzing mass spectra of biomolecules acquired as a result of hydrogen-deuterium exchange reactions (HDXs). The modified method consists of separating HDX distributions via their approximations by a minimum number of components corresponding to independent H/D substitutions and independent charge carrier retentions in different spatial isoforms or conformations of biomolecules with unknown primary structures. In this case, neither the natural isotopic distribution nor the exact number of active sites involved in HDXs and H+ or D+ attachments can be determined in advance. Original H/D electrospray mass spectra of an apamin solution were taken from our previous work. In that work, taking into account the natural isotopic distribution of apamin molecules, three main conformations of apamin ions were found as a result of separating the H/D mass spectra of the apamin solution for the gas flow with the addition of about 10% ND3 molecules. Using the proposed modified method that does not require knowledge of the primary structure of the biomolecules gave similar results with slight deviations of calculated HDX distributions of the apamin ions from those obtained earlier. The maximum difference between mean values of the calculated HDX distributions for ions of the same charge in both cases does not exceed a few percent. In addition, HDX mass spectra of the apamin complex with an adduct of unknown structure were processed. Such analysis gave also three main fractions of ions with relatively large contributions when ND3 was injected into a radio-frequency quadrupole. In the absence of ND3 flow, the results of calculations for apamin and its complex were close to each other too. The formation of the apamin complex most probably in solution was confirmed by performed calculations.
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Affiliation(s)
- Valery Raznikov
- Chernogolovka Branch of the N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow, 142432, Russia.
| | - Marina Raznikova
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, Moscow, 142432, Russia.
| | - Ilia Sulimenkov
- Chernogolovka Branch of the N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow, 142432, Russia
| | - Vladislav Zelenov
- Chernogolovka Branch of the N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow, 142432, Russia
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13
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Song D, Sun H, Ma L, Liu J, Gao Y, Zhang Q, Xiao P, Sun K, Shen M, Wang X, Zhou M. In-Vitro Diagnostic Reagent Evaluation of Commercially Available Cardiac Troponin I Assay Kits Using H/D Exchange Mass Spectrometry for Antibody-Epitope Mapping. Anal Chem 2023; 95:2278-2284. [PMID: 36647798 DOI: 10.1021/acs.analchem.2c03946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cardiac troponin I (cTnI) is the biomarker of choice and considered a gold standard for the diagnosis of acute myocardial infarction. However, the quantitative results of cTnI assay kits from different manufacturers are not comparable. Based on the H/D exchange mass spectrometry (HDX-MS) workflow, we developed an in-vitro diagnostic reagent antibody evaluation strategy to analyze the interactions of epitopes and antibody cocktails─(R195, F12, S13) and (D1, D2, pAb2). The HDX results indicate that the quantitative result bias of the different reagents originates from the ability of antibodies to recognize various cTnI complex forms, such as free cTnI, hydrolyzed cTnI, and cTnI combined with cTnT or TnC as binary or ternary complexes (cTnIC, cTnTIC), in blood based on different epitopes. The data obtained from the peptide HDX of interest after treatment with various antibody cocktails clearly indicated epitope specificity. The consistency of quantitative results can be improved by a thorough investigation into the epitopes recognized by the antibodies of various diagnostic kits, which will lead to the standardization of cTnI diagnosis.
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Affiliation(s)
- Dewei Song
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Haofeng Sun
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China.,School of Chemical and Engineering, Nanjing University of Science and Technology, Jiangsu 210094, China
| | - Lingyun Ma
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Jianyi Liu
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Yanhong Gao
- Laboratory Department of the First Medical Center of PLA General Hospital, Beijing 100039, China
| | - Qi Zhang
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China.,School of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Peng Xiao
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing 100029, China
| | - Keqi Sun
- Reference System Department, Maccura Biotechnology Co., Ltd., Chengdu 611713, China
| | - Min Shen
- Reference Laboratory, Medical System Biotechnology Co., Ltd., Ningbo 315104, China
| | - Xiaojian Wang
- Reference Laboratory, Beijing Strong Biotechnologies, Inc., Huairou, Beijing 101400, China
| | - Min Zhou
- School of Chemical and Engineering, Nanjing University of Science and Technology, Jiangsu 210094, China
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14
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Acter T, Lee S, Uddin N, Mow KM, Kim S. Characterization of petroleum‐related natural organic matter by ultrahigh‐resolution mass spectrometry. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Thamina Acter
- Department of Mathematical and Physical Sciences East West University Dhaka Bangladesh
| | - Seulgidaun Lee
- Department of Chemistry Kyungpook National University Daegu Republic of Korea
| | - Nizam Uddin
- Department of Nutrition and Food Engineering, Faculty of Allied Health Science Daffodil International University Dhaka Bangladesh
| | - Kamarum Monira Mow
- Department of Computer Science and Engineering East West University Dhaka Bangladesh
| | - Sunghwan Kim
- Department of Chemistry Kyungpook National University Daegu Republic of Korea
- Mass Spectrometry Based Convergence Research Institute Kyungpook National University Daegu Republic of Korea
- Green‐Nano Materials Research Center, Kyungpook National University Daegu Republic of Korea
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15
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Next Challenges for the Comprehensive Molecular Characterization of Complex Organic Mixtures in the Field of Sustainable Energy. Molecules 2022; 27:molecules27248889. [PMID: 36558021 PMCID: PMC9786309 DOI: 10.3390/molecules27248889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
The conversion of lignocellulosic biomass by pyrolysis or hydrothermal liquefaction gives access to a wide variety of molecules that can be used as fuel or as building blocks in the chemical industry. For such purposes, it is necessary to obtain their detailed chemical composition to adapt the conversion process, including the upgrading steps. Petroleomics has emerged as an integral approach to cover a missing link in the investigation bio-oils and linked products. It relies on ultra-high-resolution mass spectrometry to attempt to unravel the contribution of many compounds in complex samples by a non-targeted approach. The most recent developments in petroleomics partially alter the discriminating nature of the non-targeted analyses. However, a peak referring to one chemical formula possibly hides a forest of isomeric compounds, which may present a large chemical diversity concerning the nature of the chemical functions. This identification of chemical functions is essential in the context of the upgrading of bio-oils. The latest developments dedicated to this analytical challenge will be reviewed and discussed, particularly by integrating ion source features and incorporating new steps in the analytical workflow. The representativeness of the data obtained by the petroleomic approach is still an important issue.
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16
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Renawala HK, Topp EM. Fibrillation of human insulin B-chain by pulsed hydrogen-deuterium exchange mass spectrometry. Biophys J 2022; 121:4505-4516. [PMID: 36325616 PMCID: PMC9748358 DOI: 10.1016/j.bpj.2022.10.042] [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: 01/14/2022] [Revised: 08/15/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022] Open
Abstract
Insulin forms amyloid fibrils under slightly destabilizing conditions, and B-chain residues are thought to play an important role in insulin fibrillation. Here, pulsed hydrogen-deuterium exchange mass spectrometry (HDX-MS), far-UV circular dichroism spectroscopy, thioflavin T (ThioT) fluorescence, turbidity, and soluble fraction measurements were used to monitor the kinetics and mechanisms of fibrillation of human insulin B-chain (INSB) in acidic solution (1 mg/mL, pH 4.5) under stressed conditions (40°C, continuous shaking). Initially, INSB rapidly formed β-sheet-rich oligomers that were protected from HD exchange and showed weak ThioT binding. Subsequent fibril growth and maturation was accompanied by even greater protection from HD exchange and stronger ThioT binding. With peptic digestion of deuterated INSB, HDX-MS suggested early involvement of the N-terminal (1-11, 1-15) and central (12-15, 16-25) fragments in fibril-forming interactions, whereas the C-terminal fragment (25-30) showed limited involvement. The results provide mechanistic understanding of the intermolecular interactions and structural changes during INSB fibrillation under stressed conditions and demonstrate the application of pulsed HDX-MS to probe peptide fibrillation.
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Affiliation(s)
- Harshil K Renawala
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana; National Institute for Bioprocessing Research and Training, Dublin, Ireland.
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17
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Zu C, Wang NX, Brown CJ, Yang Q, Gilbert JR. Investigation of fragmentation pathways of protonated 2-methoxypyrimidine derivatives. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4883. [PMID: 36073665 DOI: 10.1002/jms.4883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/16/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Several representative pyrimidine derivatives were selected to undergo electrospray ionization (ESI) followed by collision-induced dissociation tandem mass spectrometry (CID MS/MS) experiments. Two competitive pathways were found to govern the formation of major fragment ions from protonated species of these molecules. The pathways were largely affected by the 2-O-methyl group but not significantly influenced by the substitution on C-5 site of the pyrimidine ring. These findings were supported by both deuterium labeling CID MS/MS experiments and theoretical calculations. The deuterium labeled pyrimidine ion molecules were generated in-source in ESI from the fully deuterated hydrazinyl pyrimidines, which were readily obtained through hydrogen/deuterium (H/D) exchange when dissolved in deuterium oxide (D2 O).
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Affiliation(s)
- Chengli Zu
- Crop Protection Research and Development, Corteva Agriscience Indianapolis, Indianapolis, Indiana, USA
| | - Nick X Wang
- Crop Protection Research and Development, Corteva Agriscience Indianapolis, Indianapolis, Indiana, USA
| | - Christopher J Brown
- Crop Protection Research and Development, Corteva Agriscience Indianapolis, Indianapolis, Indiana, USA
| | - Qiang Yang
- Crop Protection Research and Development, Corteva Agriscience Indianapolis, Indianapolis, Indiana, USA
| | - Jeffrey R Gilbert
- Crop Protection Research and Development, Corteva Agriscience Indianapolis, Indianapolis, Indiana, USA
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18
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In vivo detection of metabolic 2H-incorporation upon ingestion of 2H2O. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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19
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Zhang C, McElroy AC, Liberatore HK, Alexander NLM, Knappe DR. Stability of Per- and Polyfluoroalkyl Substances in Solvents Relevant to Environmental and Toxicological Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6103-6112. [PMID: 34734715 PMCID: PMC9065217 DOI: 10.1021/acs.est.1c03979] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Per- and polyfluoroalkyl substances (PFASs) are widely used anthropogenic chemicals. For environmental and toxicological analysis, it is important to understand the stability of PFASs, including novel per- and polyfluoroalkyl ether acids (PFEAs), in commonly used solvents. In this study, we investigated the effects of PFAS characteristics, solvent type, water-to-organic solvent ratio, and temperature on the stability of 21 PFASs including 18 PFEAs. None of the studied PFASs showed measurable degradation in deionized water, methanol, or isopropyl alcohol over 30 days; however, nine PFEAs degraded in the polar aprotic solvents acetonitrile, acetone, and dimethyl sulfoxide (DMSO). PFEA degradation followed first-order kinetics, and first-order rate constants increased with increasing temperature and with decreasing water-to-organic solvent ratio. Monoethers with a carboxylic acid functional group adjacent to a tertiary carbon (>CF-COOH) degraded more rapidly than multiethers in which the carboxylic acid moiety was adjacent to repeating -CF2O- groups. In contrast, monoethers with a carboxylic acid moiety adjacent to a secondary carbon (-CF2-COOH) were stable in all tested solvents. Using high-resolution mass spectrometry, we determined that PFEAs with a >CF-COOH group were stoichiometrically decarboxylated in aprotic solvents and formed products with a >CFH group; e.g., hexafluoropropylene oxide-dimer acid (HFPO-DA or GenX), HFPO-trimer acid, and HFPO-tetramer acid were stoichiometrically converted to Fluoroethers E-1, E-2, and E-3, respectively. PFEA degradation results highlight the importance of solvent choice when preparing dosing solutions and performing extractions for environmental and toxicological assessments of PFEAs.
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Affiliation(s)
- Chuhui Zhang
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Amie C. McElroy
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Hannah K. Liberatore
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Nancy Lee M. Alexander
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Detlef R.U. Knappe
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695, United States
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20
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Conformation Changes of Enkephalin in Coordination with Pb2+ Investigated by Gas Phase Hydrogen/Deuterium Exchange Mass Spectrometry Combined with Theoretical Calculations. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-021-1069-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Prakash G, Paul N, Oliver GA, Werz DB, Maiti D. C-H deuteration of organic compounds and potential drug candidates. Chem Soc Rev 2022; 51:3123-3163. [PMID: 35320331 DOI: 10.1039/d0cs01496f] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
C-H deuteration has been intricately developed to satisfy the urgent need for site-selectively deuterated organic frameworks. Deuteration has been primarily used to study kinetic isotope effects of reactions but recently its significance in pharmaceutical chemistry has been discovered. Deuterium labelled compounds have stolen the limelight since the inception of the first FDA-approved deuterated drug, for the treatment of chorea-associated Huntington's disease, and their pharmacological importance was realised by chemists, although surprisingly very late. Various approaches were developed to carry out site-selective deuteration. However, the most common and efficient method is hydrogen isotope exchange (HIE). This review summarises deuteration methods of various organic motifs containing C(sp2)-H and C(sp3)-H bonds utilizing C-H bond functionalisation as a key step along with a variety of catalysts, and exemplifies their biological relevance.
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Affiliation(s)
- Gaurav Prakash
- Department of Chemistry, IIT Bombay, Powai, Mumbai-400076, India.
| | - Nilanjan Paul
- Department of Chemistry, IIT Bombay, Powai, Mumbai-400076, India.
| | - Gwyndaf A Oliver
- Technische Universität Braunschweig, Institute of Organic Chemistry, Hagenring 30, 38106 Braunschweig, Germany.
| | - Daniel B Werz
- Technische Universität Braunschweig, Institute of Organic Chemistry, Hagenring 30, 38106 Braunschweig, Germany.
| | - Debabrata Maiti
- Department of Chemistry, IIT Bombay, Powai, Mumbai-400076, India.
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Kostyukevich Y, Sosnin S, Osipenko S, Kovaleva O, Rumiantseva L, Kireev A, Zherebker A, Fedorov M, Nikolaev EN. PyFragMS-A Web Tool for the Investigation of the Collision-Induced Fragmentation Pathways. ACS OMEGA 2022; 7:9710-9719. [PMID: 35350354 PMCID: PMC8945079 DOI: 10.1021/acsomega.1c07272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/28/2022] [Indexed: 05/13/2023]
Abstract
Dissociation induced by the accumulation of internal energy via collisions of ions with neutral molecules is one of the most important fragmentation techniques in mass spectrometry (MS), and the identification of small singly charged molecules is based mainly on the consideration of the fragmentation spectrum. Many research studies have been dedicated to the creation of databases of experimentally measured tandem mass spectrometry (MS/MS) spectra (such as MzCloud, Metlin, etc.) and developing software for predicting MS/MS fragments in silico from the molecular structure (such as MetFrag, CFM-ID, CSI:FingerID, etc.). However, the fragmentation mechanisms and pathways are still not fully understood. One of the limiting obstacles is that protomers (positive ions protonated at different sites) produce different fragmentation spectra, and these spectra overlap in the case of the presence of different protomers. Here, we are proposing to use a combination of two powerful approaches: computing fragmentation trees that carry information of all consecutive fragmentations and consideration of the MS/MS data of isotopically labeled compounds. We have created PyFragMS-a web tool consisting of a database of annotated MS/MS spectra of isotopically labeled molecules (after H/D and/or 16O/18O exchange) and a collection of instruments for computing fragmentation trees for an arbitrary molecule. Using PyFragMS, we investigated how the site of protonation influences the fragmentation pathway for small molecules. Also, PyFragMS offers capabilities for performing database search when MS/MS data of the isotopically labeled compounds are taken into account.
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23
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Kim S, Kim D, Jung MJ, Kim S. Analysis of environmental organic matters by Ultrahigh-Resolution mass spectrometry-A review on the development of analytical methods. MASS SPECTROMETRY REVIEWS 2022; 41:352-369. [PMID: 33491249 DOI: 10.1002/mas.21684] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 06/12/2023]
Abstract
Owing to the increasing environmental and climate changes globally, there is an increasing interest in the molecular-level understanding of environmental organic compound mixtures, that is, the pursuit of complete and detailed knowledge of the chemical compositions and related chemical reactions. Environmental organic molecule mixtures, including those in air, soil, rivers, and oceans, have extremely complex and heterogeneous chemical compositions. For their analyses, ultrahigh-resolution and sub-ppb level mass accuracy, achievable using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), are important. FT-ICR MS has been successfully used to analyze complex environmental organic molecule mixtures such as natural, soil, particulate, and dissolved organic matter. Despite its success, many limitations still need to be overcome. Sample preparation, ionization, structural identification, chromatographic separation, and data interpretation are some key areas that have been the focus of numerous studies. This review describes key developments in analytical techniques in these areas to aid researchers seeking to start or continue investigations for the molecular-level understanding of environmental organic compound mixtures.
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Affiliation(s)
- Sungjune Kim
- Department of Chemistry, Kyungpook National University, Daegu, Korea
| | - Donghwi Kim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology, Geoje, Korea
| | - Maeng-Joon Jung
- Department of Chemistry, Kyungpook National University, Daegu, Korea
| | - Sunghwan Kim
- Department of Chemistry, Kyungpook National University, Daegu, Korea
- Mass Spectrometry Convergence Research Center and Green-Nano Materials Research Center, Daegu, Korea
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24
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Osipenko S, Zherebker A, Rumiantseva L, Kovaleva O, Nikolaev EN, Kostyukevich Y. Oxygen Isotope Exchange Reaction for Untargeted LC-MS Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:390-398. [PMID: 35077167 DOI: 10.1021/jasms.1c00383] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
LC-MS is a key technique for the identification of small molecules in complex samples. Accurate mass, retention time, and fragmentation spectra from LC-MS experiments are compared to reference values for pure chemical standards. However, this information is often unavailable or insufficient, leading to an assignment to a list of candidates instead of a single hit; therefore, additional features are desired to filter candidates. One such promising feature is the number of specific functional groups of a molecule that can be counted via derivatization or isotope-exchange techniques. Hydrogen/deuterium exchange (HDX) is the most widespread implementation of isotope exchange for mass spectrometry, while oxygen 16O/18O exchange is not applied as frequently as HDX. Nevertheless, it is known that some functional groups may be selectively exchanged in 18O enriched media. Here, we propose an implementation of 16O/18O isotope exchange to highlight various functional groups. We evaluated the possibility of using the number of exchanged oxygen atoms as a descriptor to filter database candidates in untargeted LC-MS-based workflows. It was shown that 16O/18O exchange provides 62% (median, n = 45) search space reduction for a panel of drug molecules. Additionally, it was demonstrated that studying the fragmentation spectra after 16O/18O can aid in eliminating false positives and, in some cases, help to annotate fragments formed with water traces in the collisional cell.
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Affiliation(s)
- Sergey Osipenko
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Alexander Zherebker
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Lidiia Rumiantseva
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Oxana Kovaleva
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Evgeny N Nikolaev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
| | - Yury Kostyukevich
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Nobel Str., 3, 121205 Moscow, Russia
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25
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Fu QL, Fujii M, Watanabe A, Kwon E. Formula Assignment Algorithm for Deuterium-Labeled Ultrahigh-Resolution Mass Spectrometry: Implications of the Formation Mechanism of Halogenated Disinfection Byproducts. Anal Chem 2022; 94:1717-1725. [PMID: 35019276 DOI: 10.1021/acs.analchem.1c04298] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ultrahigh-resolution mass spectrometry (UHR-MS) coupled with isotope labeling has attracted significant attention in elucidating the mechanisms of the transformation of dissolved organic matter (DOM). Herein, we developed a novel formula assignment algorithm based on deuterium (D)-labeled UHR-MS, namely, FTMSDeu, for the first time. This algorithm was employed to determine the precursor molecules of halogenated disinfection byproducts (Xn-DBPs) and to evaluate the relative contribution of electrophilic addition and substitution reactions in Xn-DBP formation according to the H/D exchange of DOM molecules. Further, tandem mass spectrometry with homologous-based network analysis was used to validate the formula assignment accuracy of FTMSDeu in the identification of iodinated disinfection byproducts. Electrophilic substitution accounted for 82-98, 71-89, and 43-45% of the formation for Cl-, Br-, and I-containing Xn-DBPs, respectively, indicating the dominant role of the electrophilic substitution in chlorinated disinfection byproducts with low Br and I concentrations. The absence of putative precursors in some Xn-DBPs also suggests that Xn-DBP formation includes secondary reactions (e.g., oxidation and hydrolysis) in addition to the electrophilic addition and/or substitution of halogens. These findings highlight the significance of isotopically labeled UHR-MS techniques in revealing the transformation of DOM in natural and engineered systems.
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Affiliation(s)
- Qing-Long Fu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China.,Department of Civil and Environmental Engineering, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-Ku, Tokyo 152-8550, Japan.,State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, Wuhan 430074, China
| | - Manabu Fujii
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-Ku, Tokyo 152-8550, Japan
| | - Akari Watanabe
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-Ku, Tokyo 152-8550, Japan
| | - Eunsang Kwon
- Research and Analytical Center for Giant Molecules, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-Ku, Sendai 980-8578, Japan
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26
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Zhang S, Hong Y. Measuring Cysteine Exposure in Unfolded Proteins with Tetraphenylethene Maleimide and its Analogs. Methods Mol Biol 2022; 2378:3-18. [PMID: 34985690 DOI: 10.1007/978-1-0716-1732-8_1] [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: 06/14/2023]
Abstract
When proteostasis is challenged and becomes unbalanced, unfolded proteins can accumulate in the cells. Protein unfolding causes conformational changes and subsequent differentials in side-chain solvent accessibility and reactivity. In particular, when protein unfolds, non-disulfide-bonded cysteines that are usually buried in the native state can become surface exposed and thus accessible. A series of fluorogenic dyes including tetraphenylethene maleimide (TPE-MI) and its analogs were developed to capture cysteine exposure in unfolded proteins as a measure of unfolded protein load and proteostasis capacity in cells. These dyes are inherently non-fluorescent but show fluorescence turn-on effect when conjugated to unfolded proteins via reacting with exposed cysteines on the protein. Reacting with small biothiols such as glutathione does not induce fluorescence of these dyes. Here we describe the routine workflow to characterize unfolded proteins in vitro or unfolded proteomes in cells by TPE-MIs.
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Affiliation(s)
- Shouxiang Zhang
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Yuning Hong
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia.
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27
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Han C, Han G, Yao S, Yuan L, Liu X, Cao Z, Mannodi‐Kanakkithodi A, Sun Y. Defective Ultrathin ZnIn 2 S 4 for Photoreductive Deuteration of Carbonyls Using D 2 O as the Deuterium Source. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103408. [PMID: 34796666 PMCID: PMC8787392 DOI: 10.1002/advs.202103408] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/16/2021] [Indexed: 05/17/2023]
Abstract
Deuterium (D) labeling is of great value in organic synthesis, pharmaceutical industry, and materials science. However, the state-of-the-art deuteration methods generally require noble metal catalysts, expensive deuterium sources, or harsh reaction conditions. Herein, noble metal-free and ultrathin ZnIn2 S4 (ZIS) is reported as an effective photocatalyst for visible light-driven reductive deuteration of carbonyls to produce deuterated alcohols using heavy water (D2 O) as the sole deuterium source. Defective two-dimensional ZIS nanosheets (D-ZIS) are prepared in a surfactant assisted bottom-up route exhibited much enhanced performance than the pristine ZIS counterpart. A systematic study is carried out to elucidate the contributing factors and it is found that the in situ surfactant modification enabled D-ZIS to expose more defect sites for charge carrier separation and active D-species generation, as well as high specific surface area, all of which are beneficial for the desirable deuteration reaction. This work highlights the great potential in developing low-cost semiconductor-based photocatalysts for organic deuteration in D2 O, circumventing expensive deuterium reagents and harsh conditions.
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Affiliation(s)
- Chuang Han
- Department of ChemistryUniversity of CincinnatiCincinnatiOH45221USA
| | - Guanqun Han
- Department of ChemistryUniversity of CincinnatiCincinnatiOH45221USA
| | - Shukai Yao
- School of Materials EngineeringPurdue UniversityWest LafayetteIN47907USA
| | - Lan Yuan
- School of Chemistry and Chemical EngineeringWuhan University of Science and TechnologyWuhan430081China
| | - Xingwu Liu
- Syncat@BeijingSynfuels CHINA Company, Ltd.Beijing101407China
| | - Zhi Cao
- Syncat@BeijingSynfuels CHINA Company, Ltd.Beijing101407China
| | | | - Yujie Sun
- Department of ChemistryUniversity of CincinnatiCincinnatiOH45221USA
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28
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Shi C, Jia H, Chen S, Huang J, Peng Y, Guo W. Hydrogen/Deuterium Exchange Aiding Metabolite Identification in Single-Cell Nanospray High-Resolution Mass Spectrometry Analysis. Anal Chem 2021; 94:650-657. [PMID: 34931818 DOI: 10.1021/acs.analchem.1c02057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The identification of metabolites in single-cell or small-volume tissue samples using single-cell mass spectrometry (MS) is challenging. In this study, hydrogen/deuterium (H/D) exchange was combined with microsampling nanospray high-resolution mass spectrometry (HRMS) to improve the efficiency and confidence level of metabolite identification in a single cell using commercial software. A nanospray ion source showed an improved reaction depth of 8% for H/D exchange compared with an electrospray ion source. In total, 273 metabolites were identified in Allium cepa L. single cells by searching commercial databases. Generally, more than one candidate is given for a precursor ion by MS or tandem MS (MS2) databases such as ChemSpider, MetDNA, MassBank, and mzCloud. With the help of the H/D exchange technique, the number of candidates decreased and reduction of the search space by a factor of 8 was achieved. In addition, two enzymolysis products of isoalliin, the transient intermediate and its isomer, were tracked at the single-cell level using the proposed method.
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Affiliation(s)
- Changzhi Shi
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hetian Jia
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Sisi Chen
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Juan Huang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan 430074, China
| | - Yue'e Peng
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Wei Guo
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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29
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Raznikov VV, Zelenov VV, Aparina EV, Sulimenkov IV, Raznikova MO. Formation of Deuterium-Substituted Ions from a Solution Introduced into a Radio-Frequency Quadrupole under the Action of a Gas Jet Passed through an Electron Ionization Ion Source. JOURNAL OF ANALYTICAL CHEMISTRY 2021. [DOI: 10.1134/s1061934821130116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Song X, Li J, Mofidfar M, Zare RN. Distinguishing between Isobaric Ions Using Microdroplet Hydrogen-Deuterium Exchange Mass Spectrometry. Metabolites 2021; 11:728. [PMID: 34822386 PMCID: PMC8625015 DOI: 10.3390/metabo11110728] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Isobaric ions having the same mass-to-charge ratio cannot be separately identified by mass spectrometry (MS) alone, but this limitation can be overcome by using hydrogen-deuterium exchange (HDX) in microdroplets. Because isobaric ions may contain a varied number of exchangeable sites and different types of functional groups, each one produces a unique MS spectral pattern after droplet spray HDX without the need for MS/MS experiments or introduction of ion mobility measurements. As an example of the power of this approach, isobaric ions in urinary metabolic profiles are identified and used to distinguish between healthy individuals and those having bladder cancer.
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Affiliation(s)
- Xiaowei Song
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; (X.S.); (M.M.)
- Department of Chemistry, Fudan University, Shanghai 200438, China;
| | - Jia Li
- Department of Chemistry, Fudan University, Shanghai 200438, China;
| | - Mohammad Mofidfar
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; (X.S.); (M.M.)
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; (X.S.); (M.M.)
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31
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Song X, Zang Q, Zare RN. Hydrogen-Deuterium Exchange Desorption Electrospray Ionization Mass Spectrometry Visualizes an Acidic Tumor Microenvironment. Anal Chem 2021; 93:10411-10417. [PMID: 34279072 DOI: 10.1021/acs.analchem.1c02026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report that microdroplet hydrogen-deuterium exchange (HDX) detected by desorption electrospray ionization mass spectrometry imaging (DESI-MSI) allows the measurement of the acidity of a tissue sample. The integration of HDX and DESI-MSI has been applied to visualize the acidic tumor microenvironment (TME). HDX-DESI-MSI enables the simultaneous collection of regional pH variation and its corresponding in-depth metabolomic changes. This technique is a cost-effective tool for providing insight into the pH-dependent tumor metabolism heterogeneity.
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Affiliation(s)
- Xiaowei Song
- Stanford University, Department of Chemistry, Stanford, California 94305, United States.,Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Qingce Zang
- Institute of Materia Medica, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100050, China
| | - Richard N Zare
- Stanford University, Department of Chemistry, Stanford, California 94305, United States
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32
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Murashima H, Fujihara A. Gas-Phase Adsorption of N 2 on Protonated Molecules and Its Application to the Structural Elucidation of Small Molecules. Mass Spectrom (Tokyo) 2021; 10:A0096. [PMID: 34136324 PMCID: PMC8188007 DOI: 10.5702/massspectrometry.a0096] [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: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 11/23/2022] Open
Abstract
The gas-phase adsorption of N2 on protonated serine (Ser, C3H7NO3), threonine (Thr, C4H9NO3), glycine (Gly, C2H5NO2), and 2-aminoethanol (C2H7NO) was investigated using a tandem mass spectrometer equipped with an electrospray ionization source and a cold ion trap. N2 molecules were adsorbed on the free X–H (X=O and N) groups of protonated molecules. Gas-phase N2 adsorption-mass spectrometry detected the presence of free X–H groups in the molecular structures, and was applied to the structural elucidation of small molecules. When the 93 structures with an elemental composition of C3H7NO3 were filtered using the gas-phase N2 adsorption-mass spectrometry results for Ser, the number of possible molecular structures was reduced to 8 via the quantification of the X–H groups. Restricting and minimizing the number of possible candidates were effective steps in the structural elucidation process. Gas-phase N2 adsorption-mass spectrometry combined with mass spectrometry-based techniques has the potential for being useful for elucidating the molecular structures of a variety of molecules.
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Affiliation(s)
- Hiromori Murashima
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan
| | - Akimasa Fujihara
- Department of Chemistry, Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan
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33
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Okuda A, Inoue R, Morishima K, Saio T, Yunoki Y, Yagi-Utsumi M, Yagi H, Shimizu M, Sato N, Urade R, Kato K, Sugiyama M. Deuteration Aiming for Neutron Scattering. Biophys Physicobiol 2021; 18:16-27. [PMID: 33954079 PMCID: PMC8049778 DOI: 10.2142/biophysico.bppb-v18.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/03/2021] [Indexed: 01/17/2023] Open
Abstract
The distinguished feature of neutron as a scattering probe is an isotope effect, especially the large difference in neutron scattering length between hydrogen and deuterium. The difference renders the different visibility between hydrogenated and deuterated proteins. Therefore, the combination of deuterated protein and neutron scattering enables the selective visualization of a target domain in the complex or a target protein in the multi-component system. Despite of this fascinating character, there exist several problems for the general use of this method: difficulty and high cost for protein deuteration, and control and determination of deuteration ratio of the sample. To resolve them, the protocol of protein deuteration techniques is presented in this report. It is strongly expected that this protocol will offer more opportunity for conducting the neutron scattering studies with deuterated proteins.
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Affiliation(s)
- Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Tomohide Saio
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Yasuhiro Yunoki
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan
| | - Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
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34
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Zhou T, Fleming JR, Lange S, Hessel AL, Bogomolovas J, Stronczek C, Grundei D, Ghassemian M, Biju A, Börgeson E, Bullard B, Linke WA, Chen J, Kovermann M, Mayans O. Molecular Characterisation of Titin N2A and Its Binding of CARP Reveals a Titin/Actin Cross-linking Mechanism. J Mol Biol 2021; 433:166901. [PMID: 33647290 PMCID: PMC8052292 DOI: 10.1016/j.jmb.2021.166901] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022]
Abstract
Striated muscle responds to mechanical overload by rapidly up-regulating the expression of the cardiac ankyrin repeat protein, CARP, which then targets the sarcomere by binding to titin N2A in the I-band region. To date, the role of this interaction in the stress response of muscle remains poorly understood. Here, we characterise the molecular structure of the CARP-receptor site in titin (UN2A) and its binding of CARP. We find that titin UN2A contains a central three-helix bundle fold (ca 45 residues in length) that is joined to N- and C-terminal flanking immunoglobulin domains by long, flexible linkers with partial helical content. CARP binds titin by engaging an α-hairpin in the three-helix fold of UN2A, the C-terminal linker sequence, and the BC loop in Ig81, which jointly form a broad binding interface. Mutagenesis showed that the CARP/N2A association withstands sequence variations in titin N2A and we use this information to evaluate 85 human single nucleotide variants. In addition, actin co-sedimentation, co-transfection in C2C12 cells, proteomics on heart lysates, and the mechanical response of CARP-soaked myofibrils imply that CARP induces the cross-linking of titin and actin myofilaments, thereby increasing myofibril stiffness. We conclude that CARP acts as a regulator of force output in the sarcomere that preserves muscle mechanical performance upon overload stress.
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Affiliation(s)
- Tiankun Zhou
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | - Stephan Lange
- Division of Cardiology, School of Medicine, University of California, San Diego 92093, CA, USA; Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Anthony L Hessel
- Institute of Physiology II, University Hospital Münster, Münster, Germany
| | - Julius Bogomolovas
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Chiara Stronczek
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - David Grundei
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Majid Ghassemian
- Department of Chemistry and Biochemistry, University of California, San Diego 92093, CA, USA
| | - Andrea Biju
- Division of Cardiology, School of Medicine, University of California, San Diego 92093, CA, USA
| | - Emma Börgeson
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Belinda Bullard
- Department of Biology, University of York, York YO10 5DD, UK
| | - Wolfgang A Linke
- Institute of Physiology II, University Hospital Münster, Münster, Germany
| | - Ju Chen
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.
| | - Olga Mayans
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.
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35
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Ray AD, Clemens G, Holman SW. Application of open port sampling interface mass spectrometry (OPSI-MS) to deuterium exchange as an aid for structural elucidation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35 Suppl 2:e8536. [PMID: 31336014 DOI: 10.1002/rcm.8536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/19/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Deuterium exchange has been demonstrated to provide additional information to accurate mass measurement and collision-induced dissociation on unknown chemical structures. An enhanced method for rapid deuterium exchange could make this technique more routine for structural elucidation. Open port sampling interface mass spectrometry (OPSI-MS) with an aprotic solvent offers a rapid method for performing deuterium incorporation. METHODS Samples of standard drug molecules have been analysed by OPSI-MS directly from solids using a make-up flow of acetonitrile + 0.1% trifluoroacetic acid. The resultant spectra were compared with those obtained by OPSI-MS analysis of the samples dissolved in deuterium oxide (D2 O). Solutions of these molecules in acetonitrile/D2 O were analysed using an Atmospheric Solids Analysis Probe (ASAP) at different temperatures to compare the suitability of this technique. RESULTS The number of exchangeable hydrogens was obtained through deuterium exchange using the OPSI source, although there was some incomplete exchange or back-exchange observed. Molecules with one to five exchangeable hydrogens were successfully analysed. ASAP analysis produced more complicated spectra with higher levels of incomplete or back-exchanged ions; this was more pronounced at higher temperatures. CONCLUSIONS The use of OPSI provides a method for the rapid determination of the number of exchangeable hydrogens within a molecule. This yields useful information as an aid to the structural elucidation of unknowns. ASAP produces incomplete exchange and cannot be used for incorporation studies.
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Affiliation(s)
- Andrew D Ray
- Global Product Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield, SK10 2NA, UK
| | - Graeme Clemens
- Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield, SK10 2NA, UK
| | - Stephen W Holman
- Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield, SK10 2NA, UK
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36
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Rodrigues MO, Eberlin MN, Neto BAD. How and Why to Investigate Multicomponent Reactions Mechanisms? A Critical Review. CHEM REC 2021; 21:2762-2781. [PMID: 33538117 DOI: 10.1002/tcr.202000165] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/04/2021] [Indexed: 01/03/2023]
Abstract
We review the most innovative efforts and greatest challenges faced when elucidating multicomponent reactions (MCRs) mechanisms. When compared to traditional reactions, the often two or more concurrent reactions pathways and the greater number of possible intermediates in MCRs turn their mechanistic investigation both a harder and trickier task. The common approaches used to investigate reaction mechanisms are often unable to clarify MCRs mechanisms; hence few but clever approaches are currently used to determine these mechanisms and to depict their key transformations. Their complexity has required most innovative approaches and the use of a number of unique techniques that have shed light over the favored pathway selected from the myriad of alternatives theoretically available for MCRs. This review focuses on the most successful efforts applied by a few leading groups to perform these puzzlingly investigations.
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Affiliation(s)
- Marcelo O Rodrigues
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal, 70904-970, Brazil.,School of Physics and Astronomy, Nottingham University, NG72RD, Nottingham, U.K
| | - Marcos N Eberlin
- MackMass Laboratory, PPGENM, School of Engineering, Mackenzie Presbyterian University, São Paulo, SP, 01302-907, Brazil
| | - Brenno A D Neto
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, Distrito Federal, 70904-970, Brazil
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37
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Tian Y, Bao Q, Wang N, Wan N, Lv L, Hao H, He C, Ye H. Time-Resolved Acetaldehyde-Based Accessibility Profiling Maps Ligand-Target Interactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:519-530. [PMID: 33382614 DOI: 10.1021/jasms.0c00382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Elucidating ligand-protein interactions is important in understanding the biochemical machinery for given proteins. Previously, formaldehyde (FH)-based labeling has been employed to obtain such structural knowledge, since reactive residues that participate in ligand-target interactions display reduced accessibility to FH-labeling reagents, and thus can be identified by quantitative proteomics. Although being rapid and efficient for probing proteinaceous lysine accessibility, here, we report an acetaldehyde (AcH)-labeling approach that complements with FH for probing ligand-target interactions. AcH labeling examines lysine accessibility at a more moderate reaction speed and hence delivers a cleaner reaction when compared to that of FH. The subsequent application of AcH to label RNase A without and with ligands has assisted to assign lysines involved in ligand-RNase A binding by detecting the time-dependent changes in accessibility profiles. We further employed multiple reaction monitoring (MRM) to quantify these ligand-binding-responsive sites when a variety of potential ligands were queried. We noted that the time-resolved abundance changes of these peptides can sensitively determine the ligand-binding sites and differentiate binding affinities among these ligands, which was confirmed by native mass spectrometry (MS) and molecular docking. Lastly, we demonstrated that the binding sites can be recognized by monitoring the chemical accessibility of these responsive peptides in cell lysates. Together, we believe that the proposed combined use of AcH-based lysine accessibility profiling, native MS, and MRM screening is a powerful toolbox in characterizing ligand-target interactions, mapping topography, and interrogating affinities and holds promise for future applications in a complex cellular environment.
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Affiliation(s)
- Yang Tian
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Qiuyu Bao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Nian Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Ning Wan
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Langlang Lv
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Haiping Hao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Chaoyong He
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Hui Ye
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
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Rampler E, Abiead YE, Schoeny H, Rusz M, Hildebrand F, Fitz V, Koellensperger G. Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics-Standardization, Coverage, and Throughput. Anal Chem 2021; 93:519-545. [PMID: 33249827 PMCID: PMC7807424 DOI: 10.1021/acs.analchem.0c04698] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Evelyn Rampler
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Yasin El Abiead
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Harald Schoeny
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Mate Rusz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Institute of Inorganic
Chemistry, University of Vienna, Währinger Straße 42, 1090 Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Veronika Fitz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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39
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Desmet S, Brouckaert M, Boerjan W, Morreel K. Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. Comput Struct Biotechnol J 2020; 19:72-85. [PMID: 33384856 PMCID: PMC7753198 DOI: 10.1016/j.csbj.2020.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023] Open
Abstract
Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed.
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Affiliation(s)
- Sandrien Desmet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marlies Brouckaert
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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40
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Luo Y, Li H. Structure-Based Inhibitor Discovery of Class I Histone Deacetylases (HDACs). Int J Mol Sci 2020; 21:E8828. [PMID: 33266366 PMCID: PMC7700698 DOI: 10.3390/ijms21228828] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022] Open
Abstract
Class I histone deacetylases (HDACs) are promising targets for epigenetic therapies for a range of diseases such as cancers, inflammations, infections and neurological diseases. Although six HDAC inhibitors are now licensed for clinical treatments, they are all pan-inhibitors with little or no HDAC isoform selectivity, exhibiting undesirable side effects. A major issue with the currently available HDAC inhibitors is that they have limited specificity and target multiple deacetylases. Except for HDAC8, Class I HDACs (1, 2 and 3) are recruited to large multiprotein complexes to function. Therefore, there are rising needs to develop new, hopefully, therapeutically efficacious HDAC inhibitors with isoform or complex selectivity. Here, upon the introduction of the structures of Class I HDACs and their complexes, we provide an up-to-date overview of the structure-based discovery of Class I HDAC inhibitors, including pan-, isoform-selective and complex-specific inhibitors, aiming to provide an insight into the discovery of additional HDAC inhibitors with greater selectivity, specificity and therapeutic utility.
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Affiliation(s)
- Yuxiang Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, No.132 Wai Huan Dong lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, Guangdong, China;
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, No.132 Wai Huan Dong lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, Guangdong, China;
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, Guangdong, China
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41
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Renawala HK, Chandrababu KB, Topp EM. Fibrillation of Human Calcitonin and Its Analogs: Effects of Phosphorylation and Disulfide Reduction. Biophys J 2020; 120:86-100. [PMID: 33220304 DOI: 10.1016/j.bpj.2020.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/24/2020] [Accepted: 11/10/2020] [Indexed: 11/16/2022] Open
Abstract
Some therapeutic peptides self-assemble in solution to form ordered, insoluble, β-sheet-rich amyloid fibrils. This physical instability can result in reduced potency, cause immunogenic side effects, and limit options for formulation. Understanding the mechanisms of fibrillation is key to developing rational mitigation strategies. Here, amide hydrogen-deuterium exchange with mass spectrometric analysis (HDX-MS) coupled with proteolytic digestion was used to identify the early stage interactions leading to fibrillation of human calcitonin (hCT), a peptide hormone important in calcium metabolism. hCT fibrillation kinetics was sigmoidal, with lag, growth, and plateau phases as shown by thioflavin T and turbidity measurements. HDX-MS of fibrillating hCT (pH 7.4; 25°C) suggested early involvement of the N-terminal (1-11) and central (12-19) fragments in interactions during the lag phase, whereas C-terminal fragments (20-32 and 26-32) showed limited involvement during this period. The residue-level information was used to develop phosphorylated hCT analogs that showed modified fibrillation that depended on phosphorylation site. Phosphorylation in the central region resulted in complete inhibition of fibrillation for the phospho-Thr-13 hCT analog, whereas phosphorylation in the N-terminal and C-terminal regions inhibited but did not prevent fibrillation. Reduction of the Cys1-Cys7 disulfide bond resulted in faster fibrillation with involvement of different hCT residues as indicated by pulsed HDX-MS. Together, the results demonstrate that small structural changes have significant effects on hCT fibrillation and that understanding these effects can inform the rational development of fibrillation-resistant hCT analogs.
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Affiliation(s)
- Harshil K Renawala
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana
| | - Karthik B Chandrababu
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana; National Institute for Bioprocessing Research and Training, Dublin, Ireland.
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42
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Zherebker A, Yakimov B, Rubekina A, Kharybin O, Fedoros EI, Perminova IV, Shirshin E, Nikolaev EN. Photoreactivity of humic-like polyphenol material under irradiation with different wavelengths explored by FTICR MS and deuteromethylation. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2020; 26:292-300. [PMID: 32264711 DOI: 10.1177/1469066720917067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The goal of this study was to establish reactivity of lignin-derived synthetic polyphenolic material under irradiation by ultraviolet (254 nm) and visible (460 and 525 nm) light in order to deeper examine relationships between the optical properties of this complex mixture and its individual constituents. In all photoirradiation experiments, blue shift of the fluorescence spectrum was observed. We aimed at understanding whether these changes could be explained on the basis of the chromophore interactions hypothesis, which implies destruction of electron-acceptor pairs via free radical transformations to be responsible for the alteration of optical properties. For this, changes in molecular composition were explored by Fourier transform ion cyclotron resonance mass spectrometry. Irradiation with UV resulted in a pronounced oxidation of polyphenols, which was manifested in the van Krevelen diagram by the formation of components with higher O/C ratio. At the same time, irradiation by visible light had led to the appearance of more condensed molecules depleted of oxygen. Consideration of changes in relative contribution of 500 most abundant components in polyphenol materials revealed higher transformation yields under UV light as compared to the visible light. Further studies using deuteromethylation followed by Fourier transform ion cyclotron resonance mass spectrometry enabled to enumerate the number of carboxylic groups in individual components of the parent polyphenol material. It was shown that at all wavelengths irradiation mainly impacted carboxylic-rich unsaturated and aromatic compounds, which can be considered as strong electron-acceptors. We suggest that their transformation is responsible for the blue shift of fluorescence spectrum, thus emphasizing the role of chromophore interaction mechanism of the optical properties formation.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Boris Yakimov
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Rubekina
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Elena I Fedoros
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg, Russia
- Nobel LTD, Saint-Petersburg, Russia
| | - I V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Evgeny Shirshin
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
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43
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Zhang Y, Chen X, Zhang L, Shi Q, Zhao S, Xu C. Specification of the nitrogen functional group in a hydrotreated petroleum molecule using hydrogen/deuterium exchange electrospray ionization high-resolution mass spectrometry. Analyst 2020; 145:4442-4451. [PMID: 32529999 DOI: 10.1039/d0an00772b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrotreatment is extensively used for the production of clean fuel. Attaining an understanding of the structural conversion of the nitrogen species during hydrotreatment is very challenging due to the compositional complexity and the absence of a proper characterization method. In the presented work, we coupled hydrogen/deuterium exchange (HDX) with positive-ion electrospray ionization high-resolution mass spectrometry ((+) ESI HR MS) to investigate the difference between the composition of the nitrogen-containing species and the functional groups before and after hydrotreatment. The solvent and additive were optimized for HDX (+) ESI HRMS through systematic evaluations on model nitrogen-containing compounds. We found that adding deuterated water (D2O) and deuterated formic acid (DCOOD) significantly increased the degree of HDX and thus facilitated the identification of nitrogen functional groups. After application to the hydrotreated petroleum samples, the compositional variation of intermediate amine compounds during the heavy petroleum hydrotreatment process was clearly revealed.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory of Heavy Oil Processing & Petroleum Molecular Engineering Center (PMEC), China University of Petroleum, Beijing 102249, China.
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44
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Zherebker A, Lechtenfeld OJ, Sarycheva A, Kostyukevich Y, Kharybin O, Fedoros EI, Nikolaev EN. Refinement of Compound Aromaticity in Complex Organic Mixtures by Stable Isotope Label Assisted Ultrahigh-Resolution Mass Spectrometry. Anal Chem 2020; 92:9032-9038. [PMID: 32484343 DOI: 10.1021/acs.analchem.0c01208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) provides a unique opportunity for molecular analysis of natural complex mixtures. In many geochemical and environmental studies structure-propertry relations are based solely on the elemental compositional information. Several calculated parameters were proposed to increase reliability of structural attribution, among which aromaticity indices (AI and AImod) are widely used. Herein, we applied a combination of selective labeling reactions in order to obtain direct structural information on the individual components of lignin-derived polyphenolic material. Carboxylic (COOH), carbonyl (C═O), and hydroxyl (OH) groups were enumerated by esterification, reducing, and acetylation reactions, respectively, followed by FTICR MS analyses. Obtained information was enabled to constrain aromaticity accounting for the carbon skeleton only. We found that actual aromaticity of components may be both higher or lower than approximated values depending on the abundance of COOH, C═O, and OH groups. The results are of importance for the geochemical community studying terrestrial NOM with structural gradients.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig DE-04318, Germany
| | - Anastasia Sarycheva
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Yury Kostyukevich
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
| | - Elena I Fedoros
- N.N. Petrov National Medical Research Center of Oncology, Saint-Petersburg 197758, Russia.,Nobel LTD, Saint-Petersburg 192012, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Moscow, Russia
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45
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Ochiai N, Murashima H, Fujihara A. Quantification of hydroxy groups in carbohydrates using gas-phase N2 adsorption. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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46
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Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry. J Proteomics 2020; 222:103799. [DOI: 10.1016/j.jprot.2020.103799] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/23/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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47
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Kostyukevich Y, Zherebker A, Orlov A, Kovaleva O, Burykina T, Isotov B, Nikolaev EN. Hydrogen/Deuterium and 16O/ 18O-Exchange Mass Spectrometry Boosting the Reliability of Compound Identification. Anal Chem 2020; 92:6877-6885. [PMID: 32167749 DOI: 10.1021/acs.analchem.9b05379] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Accurate and reliable identification of chemical compounds is the ultimate goal of mass spectrometry analyses. Currently, identification of compounds is usually based on the measurement of the accurate mass and fragmentation spectrum, chromatographic elution time, and collisional cross section. Unfortunately, despite the growth of databases of experimentally measured MS/MS spectra (such as MzCloud and Metlin) and developing software for predicting MS/MS fragments in silico from SMILES patterns (such as MetFrag, CFM-ID, and Ms-Finder), the problem of identification is still unsolved. The major issue is that the elution time and fragmentation spectra depend considerably on the equipment used and are not the same for different LC-MS systems. It means that any additional descriptors depending only on the structure of the chemical compound will be of big help for LC-MS/MS-based omics. Our approach is based on the characterization of compounds by the number of labile hydrogen and oxygen atoms in the molecule, which can be measured using hydrogen/deuterium and 16O/18O-exchange approaches. The number of labile atoms (those from -OH, -NH, ═O, and -COOH groups) can be predicted from SMILES patterns and serves as an additional structural descriptor when performing a database search. In addition, distribution of isotope labels among MS/MS fragments can be roughly predicted by software such as MetFrag or CFM-ID. Here, we present an approach utilizing the selection of structural candidates from a database on the basis of the number of functional groups and analysis of isotope labels distribution among fragments. It was found that our approach allows reduction of the search space by a factor of 10 and considerably increases the reliability of the compound identification.
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Affiliation(s)
- Yury Kostyukevich
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Alexander Zherebker
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Alexey Orlov
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Oxana Kovaleva
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
| | - Tatyana Burykina
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 8-2 Trubetskaya St., Moscow 119048, Russian Federation
| | - Boris Isotov
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 8-2 Trubetskaya St., Moscow 119048, Russian Federation
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology Novaya St., 100, Skolkovo 143025, Russian Federation
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48
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Puglisi R, Boeri Erba E, Pastore A. A Guide to Native Mass Spectrometry to determine complex interactomes of molecular machines. FEBS J 2020; 287:2428-2439. [PMID: 32142206 PMCID: PMC8647915 DOI: 10.1111/febs.15281] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/01/2020] [Accepted: 03/04/2020] [Indexed: 01/17/2023]
Abstract
Native mass spectrometry is an emerging technique in biology that gives the possibility to study noncovalently bound complexes with high sensitivity and accuracy. It thus allows the characterization of macromolecular assemblies, assessing their mass and stoichiometries and mapping the interacting surfaces. In this review, we discuss the application of native mass spectrometry to dynamic molecular machines based on multiple weak interactions. In the study of these machines, it is crucial to understand which and under which conditions various complexes form at any time point. We focus on the specific example of the iron-sulfur cluster biogenesis machine because this is an archetype of a dynamic machine that requires very specific and demanding experimental conditions, such as anaerobicity and the need of retaining the fold of marginally folded proteins. We describe the advantages, challenges and current limitations of the technique by providing examples from our own experience and suggesting possible future solutions.
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Affiliation(s)
- Rita Puglisi
- UK Dementia Research Institute at the Wohl Institute of King's College London, UK
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Annalisa Pastore
- UK Dementia Research Institute at the Wohl Institute of King's College London, UK
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49
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Zherebker A, Shirshin E, Rubekina A, Kharybin O, Kononikhin A, Kulikova NA, Zaitsev KV, Roznyatovsky VA, Grishin YK, Perminova IV, Nikolaev EN. Optical Properties of Soil Dissolved Organic Matter Are Related to Acidic Functions of Its Components as Revealed by Fractionation, Selective Deuteromethylation, and Ultrahigh Resolution Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2667-2677. [PMID: 32045519 DOI: 10.1021/acs.est.9b05298] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The goal of this study was to establish a relationship between the optical properties of soil dissolved organic matter (DOM) and acidic functions carried out by its individual constituents. We obtained 12 fractions of DOM samples using sequential solid phase extraction on nonionic sorbent at steadily lowered pH values: 7, 5, 3, 2, which correspond to low bounds of pKa values of phenols, aliphatic, and aromatic carboxylic acids, and ketoacids. The structural studies were conducted with the use of NMR and selective deuteromethylation of isolated fractions coupled to ultrahigh resolution mass spectrometry. First, a gradual shift of molecular compositions was observed from reduced components to aromatic oxidized compounds isolated at pH 7 and 2, respectively. Changes in molecular compositions were accompanied by a red shift of fluorescence spectra. Further application of deuteromethylation enabled us to distinguish DOM constituents with different amounts of carboxylic groups. Moreover, identification of structural isomers in a single DOM sample was achieved. Statistical analysis revealed that red shift of fluorescence is facilitated by the increase of a contribution of aromatic poly(carboxylic acid)s with high conjugation lengths. Additionally, analysis of the labeled fractionated permafrost thaw DOM directly showed carboxyl-rich alicyclic molecules, while the same components from lower-latitude DOM were assigned to lignin-like species.
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Affiliation(s)
- Alexander Zherebker
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143025, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Evgeny Shirshin
- Department of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna Rubekina
- Department of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Oleg Kharybin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143025, Russia
| | - Alexey Kononikhin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143025, Russia
| | - Natalia A Kulikova
- Department of Soil Science, Lomonosov Moscow State University, Moscow, 119991, Russia
- Federal Research Center "Fundamentals of Biotechnology", Bakh Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Kirill V Zaitsev
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | | | - Yuri K Grishin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Irina V Perminova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143025, Russia
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50
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Largy E, Gabelica V. Native Hydrogen/Deuterium Exchange Mass Spectrometry of Structured DNA Oligonucleotides. Anal Chem 2020; 92:4402-4410. [PMID: 32039580 DOI: 10.1021/acs.analchem.9b05298] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although solution hydrogen-deuterium exchange mass spectrometry (HDX/MS) is well-established for the analysis of the structure and dynamics of proteins, it is currently not exploited for nucleic acids. Here we used DNA G-quadruplex structures as model systems to demonstrate that DNA oligonucleotides are amenable to in-solution HDX/MS in native conditions. In trimethylammonium acetate solutions and in soft source conditions, the protonated phosphate groups are fully back-exchanged in the source, while the exchanged nucleobases remain labeled without detectable back-exchange. As a result, the exchange rates depend strongly on the secondary structure (hydrogen bonding status) of the oligonucleotides, but neither on their charge state nor on the presence of nonspecific adducts. We show that native mass spectrometry methods can measure these exchange rates on the second to the day time scale with high precision. Such combination of HDX with native MS opens promising avenues for the analysis of the structural and biophysical properties of oligonucleotides and their complexes.
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Affiliation(s)
- Eric Largy
- University of Bordeaux, INSERM and CNRS, Laboratoires Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, Laboratoires Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33600 Pessac, France
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