1
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Zhu P, Nguyen KT, Estelle AB, Sluchanko NN, Mehl RA, Cooley RB. Genetic encoding of 3-nitro-tyrosine reveals the impacts of 14-3-3 nitration on client binding and dephosphorylation. Protein Sci 2023; 32:e4574. [PMID: 36691781 PMCID: PMC9926477 DOI: 10.1002/pro.4574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023]
Abstract
14-3-3 proteins are central hub regulators of hundreds of phosphorylated "client" proteins. They are subject to over 60 post-translational modifications (PTMs), yet little is known how these PTMs alter 14-3-3 function and its ability to regulate downstream signaling pathways. An often neglected, but well-documented 14-3-3 PTM found under physiological and immune-stimulatory conditions is the conversion of tyrosine to 3-nitro-tyrosine at several Tyr sites, two of which are located at sites considered important for 14-3-3 function: Y130 (β-isoform numbering) is located in the primary phospho-client peptide-binding groove, while Y213 is found on a secondary binding site that engages with clients for full 14-3-3/client complex formation and client regulation. By genetically encoding 3-nitro-tyrosine, we sought to understand if nitration at Y130 and Y213 effectively modulated 14-3-3 structure, function, and client complexation. The 1.5 Å resolution crystal structure of 14-3-3 nitrated at Y130 showed the nitro group altered the conformation of key residues in the primary binding site, while functional studies confirmed client proteins failed to bind this variant of 14-3-3. But, in contrast to other client-binding deficient variants, it did not localize to the nucleus. The 1.9 Å resolution structure of 14-3-3 nitrated at Y213 revealed unusual flexibility of its C-terminal α-helix resulting in domain swapping, suggesting additional structural plasticity though its relevance is not clear as this nitrated form retained its ability to bind clients. Collectively, our data suggest that nitration of 14-3-3 will alter downstream signaling systems, and if uncontrolled could result in global dysregulation of the 14-3-3 interactome.
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Affiliation(s)
- Phillip Zhu
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Kyle T. Nguyen
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Aidan B. Estelle
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of SciencesA.N. Bach Institute of BiochemistryMoscowRussia
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Richard B. Cooley
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
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2
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Dong N, Spencer DM, Quan Q, Le Blanc JCY, Feng J, Li M, Siu KWM, Chu IK. rPTMDetermine: A Fully Automated Methodology for Endogenous Tyrosine Nitration Validation, Site-Localization, and Beyond. Anal Chem 2020; 92:10768-10776. [DOI: 10.1021/acs.analchem.0c02148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Naiping Dong
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Daniel M. Spencer
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Quan Quan
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | | | - Jinwen Feng
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Mengzhu Li
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - K. W. Michael Siu
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Ivan K. Chu
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
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3
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Zhang W, Liu J, Li P, Wang X, Bi S, Zhang J, Zhang W, Wang H, Tang B. In situ and real-time imaging of superoxide anion and peroxynitrite elucidating arginase 1 nitration aggravating hepatic ischemia-reperfusion injury. Biomaterials 2019; 225:119499. [PMID: 31561087 DOI: 10.1016/j.biomaterials.2019.119499] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/26/2019] [Accepted: 09/15/2019] [Indexed: 02/02/2023]
Abstract
Hepatic ischemia-reperfusion (IR) injury is dynamically regulated by intertwined superoxide anion (O2-)-peroxynitrite (ONOO-) cascaded molecules. Arginase 1 involves in O2-/ONOO- fluctuations and is strongly connected to IR injury. A few probes have been innovated to measure intracellular O2- or ONOO- by fluorescent imaging separately, but revealing the definite link of O2-, ONOO- and arginase 1 in situ remains unidentified in hepatic IR. Thus, a well-designed dual-color two-photon fluorescence probe (CyCA) was created for the in situ real-time detection of O2--ONOO-. Surprisingly, CyCA exhibited a suitable combination of high specificity, preeminent sensitivity, exclusive mitochondria-targeting and fast-response. On the basis of remarkable advantages, we successfully applied CyCA to visualize endogenous O2- and ONOO- in living cells and mice. The synergistic elevation of mitochondrial O2--ONOO- in IR mice was observed for the first time. Furthermore, three tyrosine nitration-sites in arginase 1 caused by ONOO- were identified in proteomic analysis, which was never reported previously. Attractively, nitro-modified arginase 1 could further promote ONOO- formation, ultimately exacerbating the intracellular redox imbalance and IR injury. These new findings decipher direct molecular links of O2--ONOO--arginase 1, and suggest effective strategies for the prevention and treatment of IR injury.
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Affiliation(s)
- Wen Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan, 250014, PR China
| | - Jihong Liu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan, 250014, PR China
| | - Ping Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan, 250014, PR China.
| | - Xin Wang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan, 250014, PR China
| | - Simin Bi
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan, 250014, PR China
| | - Jiao Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan, 250014, PR China
| | - Wei Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan, 250014, PR China
| | - Hui Wang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan, 250014, PR China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institutes of Biomedical Sciences, Shandong Normal University, Jinan, 250014, PR China.
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4
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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5
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Quan Q, Feng J, Lui LT, Shi T, Chu IK. Phosphoproteome of crab-eating macaque cerebral cortex characterized through multidimensional reversed-phase liquid chromatography/mass spectrometry with tandem anion/cation exchange columns. J Chromatogr A 2017; 1498:196-206. [DOI: 10.1016/j.chroma.2017.01.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 01/13/2017] [Accepted: 01/21/2017] [Indexed: 02/06/2023]
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6
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Wang Y, Hu L, Xu F, Quan Q, Lai YT, Xia W, Yang Y, Chang YY, Yang X, Chai Z, Wang J, Chu IK, Li H, Sun H. Integrative approach for the analysis of the proteome-wide response to bismuth drugs in Helicobacter pylori. Chem Sci 2017. [PMID: 28626571 PMCID: PMC5471454 DOI: 10.1039/c7sc00766c] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
An integrative metalloproteomic approach to unveil the role of antimicrobial metals in general using bismuth as an example.
Bismuth drugs, despite being clinically used for decades, surprisingly remain in use and effective for the treatment of Helicobacter pylori infection, even for resistant strains when co-administrated with antibiotics. However, the molecular mechanisms underlying the clinically sustained susceptibility of H. pylori to bismuth drugs remain elusive. Herein, we report that integration of in-house metalloproteomics and quantitative proteomics allows comprehensive uncovering of the bismuth-associated proteomes, including 63 bismuth-binding and 119 bismuth-regulated proteins from Helicobacter pylori, with over 60% being annotated with catalytic functions. Through bioinformatics analysis in combination with bioassays, we demonstrated that bismuth drugs disrupted multiple essential pathways in the pathogen, including ROS defence and pH buffering, by binding and functional perturbation of a number of key enzymes. Moreover, we discovered that HpDnaK may serve as a new target of bismuth drugs to inhibit bacterium-host cell adhesion. The integrative approach we report, herein, provides a novel strategy to unveil the molecular mechanisms of antimicrobial metals against pathogens in general. This study sheds light on the design of new types of antimicrobial agents with multiple targets to tackle the current crisis of antimicrobial resistance.
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Affiliation(s)
- Yuchuan Wang
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China . .,School of Chemistry , Sun Yat-sen University , Guangzhou , P. R. China
| | - Ligang Hu
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
| | - Feng Xu
- Center for Genome Sciences , The University of Hong Kong , Hong Kong , P. R. China
| | - Quan Quan
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
| | - Yau-Tsz Lai
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
| | - Wei Xia
- School of Chemistry , Sun Yat-sen University , Guangzhou , P. R. China
| | - Ya Yang
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
| | - Yuen-Yan Chang
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
| | - Xinming Yang
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
| | - Zhifang Chai
- CAS Key Laboratory of Nuclear Analytical Techniques , Institute of High Energy Physics , Chinese Academy of Sciences , Beijing , P. R. China
| | - Junwen Wang
- Center for Genome Sciences , The University of Hong Kong , Hong Kong , P. R. China.,Center for Individualized Medicine , Department of Health Sciences Research , Mayo Clinic , Scottsdale , AZ 85259 , USA.,Department of Biomedical Informatics , Arizona State University , Scottsdale , AZ 85259 , USA
| | - Ivan K Chu
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
| | - Hongyan Li
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
| | - Hongzhe Sun
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China . .,School of Chemistry , Sun Yat-sen University , Guangzhou , P. R. China
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7
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Xiao M, Yang J, Feng Y, Zhu Y, Chai X, Wang Y. Metaproteomic strategies and applications for gut microbial research. Appl Microbiol Biotechnol 2017; 101:3077-3088. [PMID: 28293710 DOI: 10.1007/s00253-017-8215-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 02/28/2017] [Accepted: 03/04/2017] [Indexed: 01/16/2023]
Abstract
The human intestine hosts various complex microbial communities that are closely associated with multiple health and disease processes. Determining the composition and function of these microbial communities is critical to unveil disease mechanisms and promote human health. Recently, meta-omic strategies have been developed that use high-throughput techniques to provide a wealth of information, thus accelerating the study of gut microbes. Metaproteomics is a newly emerged analytical approach that aims to identify proteins on a large scale in complex environmental microbial communities (e.g., the gut microbiota). This review introduces the recent analytical strategies and applications of metaproteomics, with a focus on advances in gut microbiota research, including a discussion of the limitations and challenges of these approaches.
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Affiliation(s)
- Mingming Xiao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Junjun Yang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yuxin Feng
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yan Zhu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Xin Chai
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China
| | - Yuefei Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China. .,Research and Development Center of Traditional Chinese Medicine, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, 300457, China.
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8
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Law HCH, Szeto SSW, Quan Q, Zhao Y, Zhang Z, Krakovska O, Lui LT, Zheng C, Lee SMY, Siu KWM, Wang Y, Chu IK. Characterization of the Molecular Mechanisms Underlying the Chronic Phase of Stroke in a Cynomolgus Monkey Model of Induced Cerebral Ischemia. J Proteome Res 2017; 16:1150-1166. [PMID: 28102082 DOI: 10.1021/acs.jproteome.6b00651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Stroke is one of the main causes of mortality and long-term disability worldwide. The pathophysiological mechanisms underlying this disease are not well understood, particularly in the chronic phase after the initial ischemic episode. In this study, a Macaca fascicularis stroke model consisting of two sample groups, as determined by MRI-quantified infarct volumes as a measure of the stroke severity 28 days after the ischemic episode, was evaluated using qualitative and quantitative proteomics analyses. By using multiple online multidimensional liquid chromatography platforms, 8790 nonredundant proteins were identified that condensed to 5223 protein groups at 1% global false discovery rate (FDR). After the application of a conservative criterion (5% local FDR), 4906 protein groups were identified from the analysis of cerebral cortex. Of the 2068 quantified proteins, differential proteomic analyses revealed that 31 and 23 were dysregulated in the elevated- and low-infarct-volume groups, respectively. Neurogenesis, synaptogenesis, and inflammation featured prominently as the cellular processes associated with these dysregulated proteins. Protein interaction network analysis revealed that the dysregulated proteins for inflammation and neurogenesis were highly connected, suggesting potential cross-talk between these processes in modulating the cytoskeletal structure and dynamics in the chronic phase poststroke. Elucidating the long-term consequences of brain tissue injuries from a cellular prospective, as well as the molecular mechanisms that are involved, would provide a basis for the development of new potentially neurorestorative therapies.
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Affiliation(s)
- Henry C H Law
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
| | - Samuel S W Szeto
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
| | - Quan Quan
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
| | - Yun Zhao
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
| | - Zaijun Zhang
- Institute of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University , Guangzhou 510632, China
| | - Olga Krakovska
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University , Toronto, Ontario M3J 1P3, Canada
| | - Leong Ting Lui
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
| | - Chengyou Zheng
- Institute of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University , Guangzhou 510632, China
| | - Simon M-Y Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau , Avenue Padre Tomás Pereira S.J., Taipa, Macau 999078, China
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University , Toronto, Ontario M3J 1P3, Canada.,Department of Chemistry and Biochemistry, University of Windsor , Windsor, Ontario N9B 3P4, Canada
| | - Yuqiang Wang
- Institute of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University , Guangzhou 510632, China
| | - Ivan K Chu
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
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