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Liu J, Ren J, Li S, He H, Wang Y. Protein Interface Regulating the Inserting Process of Imidazole Ionic Liquids into the Cell Membrane. J Phys Chem B 2024. [PMID: 38691101 DOI: 10.1021/acs.jpcb.3c08451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Ionic liquids (ILs) have shown promising potential in membrane protein extraction; however, the underlying mechanism remains unclear. Herein, we employed GPU-accelerated molecular dynamics (MD) simulations to investigate the dynamic insertion process of ILs into cell membranes containing membrane proteins. Our findings reveal that ILs spontaneously insert into the membrane, and the presence of membrane proteins significantly decelerates the rate of IL insertion into the membrane. Specifically, the relationship between the insertion rate and inserting free energy exhibits non-monotonic changes, which can be attributed to interfacial effects. The protein-water interface acts as trap for free ions and ionic clusters, while free ions preferentially insert into the membrane from the protein-lipid interface, which limits the insertion rate due to its narrowness. Thus, the insertion rate is governed by a combination of the free energy and interfacial effects. These findings provide valuable insights into the interfacial effects of protein-lipid bilayers and have implications for various biochemical-related applications.
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Affiliation(s)
- Ju Liu
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Ren
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Simin Li
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongyan He
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanlei Wang
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Jiang Q, Wang H, Qiao Z, Hou Y, Sui Z, Zhao B, Liang Z, Jiang B, Zhang Y, Zhang L. Metal organic layers enabled cell surface engineering coupling biomembrane fusion for dynamic membrane proteome profiling. Chem Sci 2023; 14:11727-11736. [PMID: 37920345 PMCID: PMC10619618 DOI: 10.1039/d3sc03725h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/30/2023] [Indexed: 11/04/2023] Open
Abstract
Systematically dissecting the highly dynamic and tightly communicating membrane proteome of living cells is essential for the system-level understanding of fundamental cellular processes and intricate relationship between membrane-bound organelles constructed through membrane traffic. While extensive efforts have been made to enrich membrane proteins, their comprehensive analysis with high selectivity and deep coverage remains a challenge, especially at the living cell state. To address this problem, we developed the cell surface engineering coupling biomembrane fusion method to map the whole membrane proteome from the plasma membrane to various organelle membranes taking advantage of the exquisite interaction between two-dimensional metal-organic layers and phospholipid bilayers on the membrane. This approach, which bypassed conventional biochemical fractionation and ultracentrifugation, facilitated the enrichment of membrane proteins in their native phospholipid bilayer environment, helping to map the membrane proteome with a specificity of 77% and realizing the deep coverage of the HeLa membrane proteome (5087 membrane proteins). Furthermore, membrane N-phosphoproteome was profiled by integrating the N-phosphoproteome analysis strategy, and the dynamic membrane proteome during apoptosis was deciphered in combination with quantitative proteomics. The features of membrane protein N-phosphorylation modifications and many differential proteins during apoptosis associated with mitochondrial dynamics and ER homeostasis were found. The method provided a simple and robust strategy for efficient analysis of membrane proteome, offered a reliable platform for research on membrane-related cell dynamic events and expanded the application of metal-organic layers.
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Affiliation(s)
- Qianqian Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - He Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zichun Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Yutong Hou
- Dalian Medical University Dalian 116044 China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Bo Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
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3
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Deep coverage proteome analysis of hair shaft for forensic individual identification. Forensic Sci Int Genet 2022; 60:102742. [DOI: 10.1016/j.fsigen.2022.102742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022]
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4
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Chen L, Guo P, Li W, Jiang X, Zhao Q, Li D, Wang Q, Xiao Y, Xing X, Pang Y, Aschner M, Zhang L, Chen W. Protein phosphatase 2A regulates cytotoxicity and drug resistance by dephosphorylating xenobiotic metabolism enzymes AHR and MDR1. J Biol Chem 2022; 298:101918. [PMID: 35405096 PMCID: PMC9118923 DOI: 10.1016/j.jbc.2022.101918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 11/20/2022] Open
Abstract
Protein phosphatase 2A (PP2A) is a serine/threonine dephosphorylating enzyme complex that plays numerous roles in biological processes, including cell growth and metabolism. However, its specific actions in many of these critical pathways are unclear. To explore mechanisms underlying metabolic enzyme regulation in the liver, we investigated the key pathways involved in regulation of xenobiotic-metabolizing enzymes in a mouse model with hepatocyte-specific deletion of Ppp2r1a, encoding the Aα subunit of PP2A. We performed transcriptome and phosphoproteome analysis in mouse livers at the age of 3 months and identified 2695 differentially expressed genes and 549 upregulated phosphoproteins in homozygous knockout mouse livers compared with WT littermates. In particular, the expression of metabolic enzymes Cyp2e1, Cyp1a1, Cyp1a2, Mdr1a, and Abcg2 was dramatically altered in homozygous knockout mouse livers. We also demonstrated that activation of PP2A reversed the decline of metabolic enzyme expression in primary mouse hepatocytes. We found that specific PP2A holoenzymes were involved in metabolic enzyme induction through dephosphorylation of transcription factors, nuclear receptors, or the target enzymes themselves, leading to dysregulation of xenobiotic metabolism or drug-induced hepatotoxicity. Notably, we confirmed that a regulatory axis, PP2A B56α–aryl hydrocarbon receptor–Cyp1a1, was involved in benzo(a)pyrene-induced cytotoxicity through dephosphorylation of the metabolic nuclear receptor, aryl hydrocarbon receptor, at serine 36. In addition, we showed that PP2A B56δ complexes directly dephosphorylated the multidrug efflux pump MDR1 (encoded by multi-drug resistance gene 1), contributing to drug resistance against the chemotherapeutic 5-fluorouracil. Taken together, these novel findings demonstrate the involvement of PP2A in the regulation of liver metabolism.
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Affiliation(s)
- Liping Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Ping Guo
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Wenxue Li
- Department of Toxicology, Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - Xinhang Jiang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Qun Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian 116023, China
| | - Daochuan Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Qing Wang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yongmei Xiao
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiumei Xing
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yaqin Pang
- Faculty of Toxicology, School of Public Health, Youjiang Medical College for Nationalities, Guangxi 533000, China
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Forchheimer 209, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian 116023, China.
| | - Wen Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
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Chu H, Zhao Q, Liu J, Yang K, Wang Y, Liu J, Zhang K, Zhao B, He H, Zheng Y, Zhong S, Liang Z, Zhang L, Zhang Y. Ionic Liquid-Based Extraction System for In-Depth Analysis of Membrane Protein Complexes. Anal Chem 2021; 94:758-767. [PMID: 34932315 DOI: 10.1021/acs.analchem.1c03195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Limited by the rare efficient extraction system in extracting hydrophobic membrane protein complexes (MPCs) without compromising the stability of protein-protein interactions (PPIs), the in-depth functional study of MPCs has lagged far behind. In this study, the first systematic screening of ionic liquids (ILs) was performed and showed that triethylammonium acetate (TEAA) IL exhibited excellent performance in stabilizing PPIs, which was further confirmed by molecular docking simulations. By combining TEAA with the conventional detergent Nonidet P-40 (NP-40), a novel IL-based extraction system, i-TAN (TEAA IL with 1% NP-40), was proposed, which demonstrated superior performance in extracting and stabilizing MPCs, attributed to its larger size, more uniform distribution, and closer-to-neutral microenvironment of micelles. Extraction of MPCs with i-TAN allowed the confident identification of more hydrophobic EGFR-interacting proteins that are easily dissociated during the extraction process. Quantitative analysis of the difference in EGFR complexes between trastuzumab-sensitive and trastuzumab-resistant breast cancer cells provided comprehensive insights to understand the drug resistance mechanism, suggesting that i-TAN has great potential in interactomics and functional analysis of MPCs. This study provides a novel strategy for MPC extraction and downstream processing.
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Affiliation(s)
- Hongwei Chu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,Dalian University of Technology, Dalian 116024, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Ju Liu
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yanlei Wang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianhui Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Kun Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Hongyan He
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Yong Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Shijun Zhong
- Dalian University of Technology, Dalian 116024, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,Dalian University of Technology, Dalian 116024, China
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6
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Chen L, Guo P, Li W, Fang F, Zhu W, Fan J, Wang F, Gao Y, Zhao Q, Wang Q, Xiao Y, Xing X, Li D, Shi T, Yu D, Aschner M, Zhang L, Chen W. Perturbation of Specific Signaling Pathways Is Involved in Initiation of Mouse Liver Fibrosis. Hepatology 2021; 73:1551-1569. [PMID: 32654205 DOI: 10.1002/hep.31457] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIMS To identify the regulatory role of protein phosphatase 2A (PP2A) in the development of liver disease, we generated a mouse model with hepatocyte-specific deletion of Ppp2r1a gene (encoding PP2A Aα subunit). APPROACH AND RESULTS Homozygote (HO) mice and matched wild-type littermates were investigated at 3, 6, 9, 12, 15, and 18 months of age. Pathological examination showed that PP2A Aα deficiency in hepatocytes resulted in progressive liver fibrosis phenotype from 9 months of age. No hepatocyte death was observed in HO mice. However, perturbation of pathways including epidermal growth factor receptor 1 (EGFR1), amino acid metabolism, and translation factors as well as leptin and adiponectin led to pronounced hepatic fibrosis. In vitro studies demonstrated the involvement of specific B subunit complexes in the regulation of EGFR1 signaling pathway and cross talk between defected hepatocytes and stimulation of interstitial hyperplasia. It is noteworthy that HO mice failed to develop hepatocellular carcinoma for as long as 22 months of age. We further demonstrate that PP2A Aβ-containing holoenzymes played a critical role in preventing hepatocyte apoptosis and antagonizing tumorigenesis through specific pathways on Aα loss. Furthermore, PP2A Aα and Aβ were functionally distinct, and the Aβ isoform failed to substitute for Aα in the development of inflammation and liver fibrosis. CONCLUSIONS These observations identify pathways that contribute to the pathogenesis of liver fibrosis and provide putative therapeutic targets for its treatment.
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Affiliation(s)
- Liping Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ping Guo
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wenxue Li
- Department of Toxicology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Fei Fang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Wei Zhu
- Department of Toxicology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Junling Fan
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Fangping Wang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yuanyuan Gao
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Qun Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Qing Wang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yongmei Xiao
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiumei Xing
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Daochuan Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Wen Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
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7
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Zhao Q, Chu H, Zhao B, Liang Z, Zhang L, Zhang Y. Advances of ionic liquids-based methods for protein analysis. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.09.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Han S, Yang K, Zhu H, Liu J, Zhang L, Zhao J. Proteomics investigation of the changes in serum proteins after high- and low-flux hemodialysis. Ren Fail 2018; 40:506-513. [PMID: 30284957 PMCID: PMC6179064 DOI: 10.1080/0886022x.2018.1491406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/10/2018] [Accepted: 06/14/2018] [Indexed: 01/09/2023] Open
Abstract
PURPOSE This study aimed to use proteomics methods to investigate the changes in serum protein levels after high- and low-flux hemodialysis (HD). METHODS Before and after HD, serum samples were obtained from two selected patients who were treated with a Polyflux 140 H high-flux dialyzer and a Polyflux 14 L low-flux dialyzer during two continuous therapy sessions. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to identify the proteins. RESULTS A total of 212 and 203 serum proteins were identified after high-flux and low-flux HD, respectively. After high-flux HD, 21 proteins increased, and 132 proteins decreased. After low-flux HD, 87 proteins increased, and 45 proteins decreased. High-flux HD led to a significantly greater reduction in protein levels than low-flux HD (0.73 ± 0.13 vs. 0.84 ± 0.18, p = .00). Among the increased and decreased proteins, the isoelectric point (pI) values mainly ranged from 5 to 7, and the molecular weights (Mws) were mostly smaller than 30 kDa. The serum proteins showed no difference in pI or Mw for high- and low-flux HD. Gene ontology (GO) analysis showed that the detected proteins were related to immune system processes and complement activation. CONCLUSIONS Serum protein levels differentially changed after high- and low-flux HD. Long-term effects should be observed in future studies.
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Affiliation(s)
- Shuai Han
- Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Kaiguang Yang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Hong Zhu
- Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Jianhui Liu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Jiuyang Zhao
- Department of Nephritic Medicine, Second Affiliated Hospital of Dalian Medical University, Dalian, China
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Cheng H, Zhao H, Yang T, Ruan S, Wang H, Xiang N, Zhou H, Li QX, Diao X. Comparative evaluation of five protocols for protein extraction from stony corals (Scleractinia) for proteomics. Electrophoresis 2018; 39:1062-1070. [DOI: 10.1002/elps.201700436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/04/2018] [Accepted: 01/16/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Huamin Cheng
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Hongwei Zhao
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Tinghan Yang
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Sunlan Ruan
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Haihua Wang
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Nan Xiang
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Hailong Zhou
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering; University of Hawaii at Manoa; Honolulu USA
| | - Xiaoping Diao
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Ministry of Eduction Key Laboratory of Tropical Island Ecology; Hainan Normal University; Haikou P. R. China
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Wang S, Xiao C, Jiang L, Ling L, Chen X, Guo X. A high sensitive and contaminant tolerant matrix for facile detection of membrane proteins by matrix-assisted laser desorption/ionization mass spectrometry. Anal Chim Acta 2017; 999:114-122. [PMID: 29254561 DOI: 10.1016/j.aca.2017.11.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 11/05/2017] [Accepted: 11/09/2017] [Indexed: 02/07/2023]
Abstract
Despite the significance of membrane proteins (MPs) in biological system is indisputable, their specific natures make them notoriously difficult to be analyzed. Particularly, the widely used Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) prefers analyses of hydrophilic cytosolic proteins and has a limited ionization efficiency towards hydrophobic MPs. Herein, a hydrophobic compound (E)-propyl α-Cyano-4-Hydroxyl Cinnamylate (CHCA-C3), a propyl-esterified derivative of α-cyano-4-hydroxycinnamic acid (CHCA), was applied as a contaminant tolerant matrix for high sensitivity MALDI-MS analyses of MPs. With CHCA-C3, the detection limits of hydrophobic peptides were 10- to 100-fold better than those using CHCA. Furthermore, high quality of spectra could be achieved in the presence of high concentration of chaotropes, salts and detergents, as well as human urinary and serum environment. Also, CHCA-C3 could generate uniform sample distribution even in the presence of contaminants. This high contaminant-resistance was revealed to be ascribed to the enhanced hydrophobicity of CHCA-C3 with a lower affinity towards hydrophilic contaminants. The application of CHCA-C3 is further demonstrated by the analysis of trypsin/CNBr digests of bacteriorhodopsin containing seven transmembrane domains (TMDs), which dramatically increased numbers of identified hydrophobic peptides in TMDs and sequence coverage (∼100%). Besides, a combined method by using CHCA-C3 with fluoride solvent and a patterned paraffin plate was established for analysis of integral MPs. We achieved a low detection limit of 10 fmol for integral bacteriorhodopsin, which could not be detected using traditional matrices such as 3,5-dimethoxy-4-hydroxycinamic acid, 2,5-dihydroxyacetophenone even at sample concentration of 10 pmol.
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Affiliation(s)
- Sheng Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Chunsheng Xiao
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Liyan Jiang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, China
| | - Ling Ling
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, China.
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Han S, Yang K, Sun J, Liu J, Zhang L, Zhao J. Proteomics Investigations into Serum Proteins Adsorbed by High-Flux and Low-Flux Dialysis Membranes. Proteomics Clin Appl 2017; 11. [PMID: 28795537 DOI: 10.1002/prca.201700079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/06/2017] [Indexed: 01/05/2023]
Abstract
Hemodialysis is one of the most important therapies for patients with uremia, and the dialysis membrane is the predominant factor that impacts the efficiency of dialysis. Here, a protein adsorption on two different membranes is investigated to provide a basis for improving dialysis materials. Two cases treated with the Polyflux 14L low-flux dialyzer and the Polyflux 140H high-flux dialyzers during two continuous therapies are selected. Four used dialyzers from selected patients are infused with C12Im-Cl to elute the adsorbed proteins. Then labeled digested proteins adsorb by Polyflux 140H and Polyflux 14L with 13 CD2 O and NaCNBD3 (light labeling, L) and CD2 O and NaCNBH3 (heavy labeling, H), respectively. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is used to identify the proteins. According to the ratio (Light labeling/Heavy labeling), the eluted proteins are divided into three groups: significantly higher, significantly lower, and no significant differences with a ratio of >2, <0.5, and 0.5-2, respectively. A total of 668 proteins are identified by LC-MS/MS, among which 177 proteins are retained more by the Polyflux 140H membrane (ratio >2), 320 proteins are retained more by the Polyflux 14L membrane (ratio <0.5), and 171 proteins show no significant difference (ratio 0.5-2) between the two types of membranes. Statistical significance is shown in the percentage of adsorbed proteins with an isoelectric point (pI) ranging from 9 to 10 (19.08 versus 7.69%; χ2 = 11.87, p = 0.0006). Proteins with a molecular weight (MW) of 10-15 kDa tend to deposit on Polyflux 140H compared with Polyflux 14L (25 versus 9.23%; χ2 = 18.66, p = 0.0000) and proteins with a MW of 30-60 kDa tend to deposit on Polyflux 14L compared with Polyflux 140H (36.54 versus 22.37%; χ2 = 8.96, p = 0.0028). According to gene ontology analysis, the proteins adsorbed by dialysis membranes are closely related to activation of complement system and the coagulation cascade. The proteins adsorbed by Polyflux 140H and Polyflux 14L show significant differences in PI, MW, and protein class. Proteomic techniques are an effective approach for studying hemodialysis membranes.
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Affiliation(s)
- Shuai Han
- The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Kaiguang Yang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Jingdi Sun
- The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jianhui Liu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Jiuyang Zhao
- The Second Affiliated Hospital of Dalian Medical University, Dalian, China
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