1
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Morellon-Sterling R, Tavano O, Bolivar JM, Berenguer-Murcia Á, Vela-Gutiérrez G, Sabir JSM, Tacias-Pascacio VG, Fernandez-Lafuente R. A review on the immobilization of pepsin: A Lys-poor enzyme that is unstable at alkaline pH values. Int J Biol Macromol 2022; 210:682-702. [PMID: 35508226 DOI: 10.1016/j.ijbiomac.2022.04.224] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 11/05/2022]
Abstract
Pepsin is a protease used in many different applications, and in many instances, it is utilized in an immobilized form to prevent contamination of the reaction product. This enzyme has two peculiarities that make its immobilization complex. The first one is related to the poor presence of primary amino groups on its surface (just one Lys and the terminal amino group). The second one is its poor stability at alkaline pH values. Both features make the immobilization of this enzyme to be considered a complicated goal, as most of the immobilization protocols utilize primary amino groups for immobilization. This review presents some of the attempts to get immobilized pepsin biocatalyst and their applications. The high density of anionic groups (Asp and Glu) make the anion exchange of the enzyme simpler, but this makes many of the strategies utilized to immobilize the enzyme (e.g., amino-glutaraldehyde supports) more related to a mixed ion exchange/hydrophobic adsorption than to real covalent immobilization. Finally, we propose some possibilities that can permit not only the covalent immobilization of this enzyme, but also their stabilization via multipoint covalent attachment.
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Affiliation(s)
- Roberto Morellon-Sterling
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Student of Departamento de Biología Molecular, Universidad Autónoma de Madrid, Darwin 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Olga Tavano
- Faculty of Nutrition, Alfenas Federal Univ., 700 Gabriel Monteiro da Silva St, Alfenas, MG 37130-000, Brazil
| | - Juan M Bolivar
- Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Complutense Ave., Madrid 28040, Spain
| | - Ángel Berenguer-Murcia
- Departamento de Química Inorgánica e Instituto Universitario de Materiales, Universidad de Alicante, Alicante, Spain
| | - Gilber Vela-Gutiérrez
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico
| | - Jamal S M Sabir
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Veymar G Tacias-Pascacio
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico; Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana Km. 1080, 29050 Tuxtla Gutiérrez, Chiapas, Mexico.
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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2
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Ye X, Tang J, Mao Y, Lu X, Yang Y, Chen W, Zhang X, Xu R, Tian R. Integrated proteomics sample preparation and fractionation: Method development and applications. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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3
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Meller K, Pomastowski P, Szumski M, Buszewski B. Preparation of an improved hydrophilic monolith to make trypsin-immobilized microreactors. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1043:128-137. [DOI: 10.1016/j.jchromb.2016.08.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/17/2016] [Accepted: 08/20/2016] [Indexed: 11/24/2022]
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4
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Vit O, Petrak J. Integral membrane proteins in proteomics. How to break open the black box? J Proteomics 2016; 153:8-20. [PMID: 27530594 DOI: 10.1016/j.jprot.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]
Abstract
Integral membrane proteins (IMPs) are coded by 20-30% of human genes and execute important functions - transmembrane transport, signal transduction, cell-cell communication, cell adhesion to the extracellular matrix, and many other processes. Due to their hydrophobicity, low expression and lack of trypsin cleavage sites in their transmembrane segments, IMPs have been generally under-represented in routine proteomic analyses. However, the field of membrane proteomics has changed markedly in the past decade, namely due to the introduction of filter assisted sample preparation (FASP), the establishment of cell surface capture (CSC) protocols, and the development of methods that enable analysis of the hydrophobic transmembrane segments. This review will summarize the recent developments in the field and outline the most successful strategies for the analysis of integral membrane proteins. SIGNIFICANCE Integral membrane proteins (IMPs) are attractive therapeutic targets mostly due to their many important functions. However, our knowledge of the membrane proteome is severely limited to effectively exploit their potential. This is mostly due to the lack of appropriate techniques or methods compatible with the typical features of IMPs, namely hydrophobicity, low expression and lack of trypsin cleavage sites. This review summarizes the most recent development in membrane proteomics and outlines the most successful strategies for their large-scale analysis.
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Affiliation(s)
- O Vit
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic.
| | - J Petrak
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic
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5
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Fukuyama Y, Nakajima C, Izumi S, Tanaka K. Membrane Protein Analyses Using Alkylated Trihydroxyacetophenone (ATHAP) as a MALDI Matrix. Anal Chem 2016; 88:1688-95. [DOI: 10.1021/acs.analchem.5b03700] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuko Fukuyama
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
- Koichi
Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Chihiro Nakajima
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shunsuke Izumi
- Department
of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Koichi Tanaka
- Koichi
Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
- Koichi
Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
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6
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Zhang Z, Sun L, Zhu G, Cox OF, Huber PW, Dovichi NJ. Nearly 1000 Protein Identifications from 50 ng of Xenopus laevis Zygote Homogenate Using Online Sample Preparation on a Strong Cation Exchange Monolith Based Microreactor Coupled with Capillary Zone Electrophoresis. Anal Chem 2015; 88:877-82. [PMID: 26670623 DOI: 10.1021/acs.analchem.5b03496] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A sulfonate-silica hybrid strong cation exchange monolith microreactor was synthesized and coupled to a linear polyacrylamide coated capillary for online sample preparation and capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) bottom-up proteomic analysis. The protein sample was loaded onto the microreactor in an acidic buffer. After online reduction, alkylation, and digestion with trypsin, the digests were eluted with 200 mM ammonium bicarbonate at pH 8.2 for CZE-MS/MS analysis using 1 M acetic acid as the background electrolyte. This combination of basic elution and acidic background electrolytes results in both sample stacking and formation of a dynamic pH junction. 369 protein groups and 1274 peptides were identified from 50 ng of Xenopus laevis zygote homogenate, which is comparable with an offline sample preparation method, but the time required for sample preparation was decreased from over 24 h to less than 40 min. Dramatically improved performance was produced by coupling the reactor to a longer separation capillary (∼100 cm) and a Q Exactive HF mass spectrometer. 975 protein groups and 3749 peptides were identified from 50 ng of Xenopus protein using the online sample preparation method.
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Affiliation(s)
- Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Olivia F Cox
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Paul W Huber
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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7
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An effective and in-situ method based tresyl-functionalized porous polymer material for enrichment and digestion of membrane proteins and its application in extraction tips. Anal Chim Acta 2015; 880:77-83. [DOI: 10.1016/j.aca.2015.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 03/25/2015] [Accepted: 04/16/2015] [Indexed: 11/21/2022]
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8
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Investigation of bi-enzymatic reactor based on hybrid monolith with nanoparticles embedded and its proteolytic characteristics. J Chromatogr A 2015; 1388:158-66. [DOI: 10.1016/j.chroma.2015.02.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 12/11/2022]
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9
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Li J, Zhou L, Wang H, Yan H, Li N, Zhai R, Jiao F, Hao F, Jin Z, Tian F, Peng B, Zhang Y, Qian X. A new sample preparation method for the absolute quantitation of a target proteome using 18O labeling combined with multiple reaction monitoring mass spectrometry. Analyst 2015; 140:1281-90. [DOI: 10.1039/c4an02092h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new sample preparation method for target proteome absolute quantitation using 18O labeling-MRM MS.
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10
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Wu S, Zhang H, Yang K, Ma J, Liang Z, Zhang L, Zhang Y. A rapid protein sample preparation method based on organic-aqueous microwave irradiation technique. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5163-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Direct digestion of proteins in living cells into peptides for proteomic analysis. Anal Bioanal Chem 2014; 407:1027-32. [DOI: 10.1007/s00216-014-8173-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/03/2014] [Accepted: 09/08/2014] [Indexed: 12/28/2022]
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12
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13
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Ruan G, Wei M, Chen Z, Su R, Du F, Zheng Y. Novel regenerative large-volume immobilized enzyme reactor: Preparation, characterization and application. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 967:13-20. [DOI: 10.1016/j.jchromb.2014.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/30/2014] [Accepted: 07/07/2014] [Indexed: 10/25/2022]
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14
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Zhao Q, Fang F, Liang Y, Yuan H, Yang K, Wu Q, Liang Z, Zhang L, Zhang Y. 1-Dodecyl-3-Methylimidazolium Chloride-Assisted Sample Preparation Method for Efficient Integral Membrane Proteome Analysis. Anal Chem 2014; 86:7544-50. [DOI: 10.1021/ac5013267] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Qun Zhao
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Fei Fang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yu Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Huiming Yuan
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Kaiguang Yang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Qi Wu
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
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15
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Fan C, Shi Z, Pan Y, Song Z, Zhang W, Zhao X, Tian F, Peng B, Qin W, Cai Y, Qian X. Dual Matrix-Based Immobilized Trypsin for Complementary Proteolytic Digestion and Fast Proteomics Analysis with Higher Protein Sequence Coverage. Anal Chem 2014; 86:1452-8. [DOI: 10.1021/ac402696b] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Chao Fan
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Graduate School of Anhui Medical University, Hefei, Chian
| | - Zhaomei Shi
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Graduate School of Anhui Medical University, Hefei, Chian
| | - Yiting Pan
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Zifeng Song
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Wanjun Zhang
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Xinyuan Zhao
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Fang Tian
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Bo Peng
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Weijie Qin
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yun Cai
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Xiaohong Qian
- National
Center for Protein Sciences Beijing, State Key Laboratory of Proteomics,
Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
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16
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Safdar M, Sproß J, Jänis J. Microscale immobilized enzyme reactors in proteomics: Latest developments. J Chromatogr A 2014; 1324:1-10. [DOI: 10.1016/j.chroma.2013.11.045] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 11/18/2013] [Accepted: 11/24/2013] [Indexed: 01/10/2023]
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17
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Lin Z, Xiao Y, Wang L, Yin Y, Zheng J, Yang H, Chen G. Facile synthesis of enzyme–inorganic hybrid nanoflowers and their application as an immobilized trypsin reactor for highly efficient protein digestion. RSC Adv 2014. [DOI: 10.1039/c4ra00268g] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Hybrid nanoflowers were synthesized by a novel approach. The nanoflowers exhibited an enhanced enzymatic activity and can be used as an immobilized enzyme reactor (IMER) for highly efficient protein digestion.
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Affiliation(s)
- Zian Lin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- Deparment of Chemistry
- Fuzhou University
- Fuzhou 350116, China
| | - Yun Xiao
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- Deparment of Chemistry
- Fuzhou University
- Fuzhou 350116, China
| | - Ling Wang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- Deparment of Chemistry
- Fuzhou University
- Fuzhou 350116, China
| | - Yuqing Yin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- Deparment of Chemistry
- Fuzhou University
- Fuzhou 350116, China
| | - Jiangnan Zheng
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- Deparment of Chemistry
- Fuzhou University
- Fuzhou 350116, China
| | - Huanghao Yang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- Deparment of Chemistry
- Fuzhou University
- Fuzhou 350116, China
| | - Guonan Chen
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety
- Deparment of Chemistry
- Fuzhou University
- Fuzhou 350116, China
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18
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Application of an ampholine-functionalized hybrid organic-inorganic silica material for the SPE of aromatic amines. J Sep Sci 2013; 37:143-50. [DOI: 10.1002/jssc.201300964] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/27/2013] [Accepted: 10/27/2013] [Indexed: 11/07/2022]
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19
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Zhao Q, Liang Y, Yuan H, Sui Z, Wu Q, Liang Z, Zhang L, Zhang Y. Biphasic Microreactor for Efficient Membrane Protein Pretreatment with a Combination of Formic Acid Assisted Solubilization, On-Column pH Adjustment, Reduction, Alkylation, and Tryptic Digestion. Anal Chem 2013; 85:8507-12. [DOI: 10.1021/ac402076u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Qun Zhao
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yu Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Huiming Yuan
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Zhigang Sui
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Qi Wu
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Lihua Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yukui Zhang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
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20
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Hu L, Yang L, Lipchik AM, Geahlen RL, Parker LL, Tao WA. A quantitative proteomics-based competition binding assay to characterize pITAM-protein interactions. Anal Chem 2013; 85:5071-7. [PMID: 23611696 PMCID: PMC3715304 DOI: 10.1021/ac400359t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Characterization of ligand-protein binding is of crucial importance in drug discovery. Classical competition binding assays measure the binding of a labeled ligand in the presence of various concentrations of unlabeled ligand and typically use single purified proteins. Here, we introduce a high-throughput approach to study ligand-protein interactions by coupling competition binding assays with mass spectrometry-based quantitative proteomics. With the use of a phosphorylated immunoreceptor tyrosine-based activation motif (pITAM) peptide as a model, we characterized pITAM-interacting partners in human lymphocytes. The shapes of competition binding curves of various interacting partners constructed in a single set of quantitative proteomics experiments reflect relative affinities for the pITAM peptide. This strategy can provide an efficient approach to distinguish specific interacting partners, including two signaling kinases possessing tandem SH2 domains, SYK and ZAP-70, as well as other SH2 domain-containing proteins such as CSK and PI3K, from contaminants and to measure relative binding affinities of multiple proteins in a single experiment.
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Affiliation(s)
- Lianghai Hu
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907
- College of Life Science, Jilin University, Changchun 130012, PR China
| | - Li Yang
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907
| | - Andrew M. Lipchik
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907
| | - Robert L. Geahlen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907
- Purdue Center for Cancer Research, West Lafayette, IN, 47907
| | - Laurie L. Parker
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907
- Purdue Center for Cancer Research, West Lafayette, IN, 47907
| | - W. Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907
- Purdue Center for Cancer Research, West Lafayette, IN, 47907
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
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21
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Vuckovic D, Dagley LF, Purcell AW, Emili A. Membrane proteomics by high performance liquid chromatography-tandem mass spectrometry: Analytical approaches and challenges. Proteomics 2013; 13:404-23. [DOI: 10.1002/pmic.201200340] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/24/2012] [Accepted: 10/09/2012] [Indexed: 01/01/2023]
Affiliation(s)
- Dajana Vuckovic
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto ON Canada
| | - Laura F. Dagley
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto ON Canada
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Victoria Australia
| | - Andrew Emili
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto ON Canada
- Department of Molecular Genetics; University of Toronto; Toronto ON Canada
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Wang F, Wei X, Zhou H, Liu J, Figeys D, Zou H. Combination of online enzyme digestion with stable isotope labeling for high-throughput quantitative proteome analysis. Proteomics 2012; 12:3129-37. [DOI: 10.1002/pmic.201200162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/15/2012] [Accepted: 08/14/2012] [Indexed: 12/31/2022]
Affiliation(s)
- Fangjun Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Xiaoluan Wei
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Hu Zhou
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
- Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Jing Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
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Tan YJ, Wang WH, Zheng Y, Dong J, Stefano G, Brandizzi F, Garavito RM, Reid GE, Bruening ML. Limited proteolysis via millisecond digestions in protease-modified membranes. Anal Chem 2012; 84:8357-63. [PMID: 22950601 DOI: 10.1021/ac3019153] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sequential adsorption of poly(styrene sulfonate) (PSS) and proteases in porous nylon yields enzymatic membrane reactors for limited protein digestion. Although a high local enzyme density (~30 mg/cm(3)) and small pore diameters in the membrane lead to digestion in <1 s, the low membrane thickness (170 μm) affords control over residence times at the millisecond level to limit digestion. Apomyoglobin digestion demonstrates that peptide lengths increase as the residence time in the membrane decreases. Moreover, electron transfer dissociation (ETD) tandem mass spectrometry (MS/MS) on a large myoglobin proteolytic peptide (8 kDa) provides a resolution of 1-2 amino acids. Under denaturing conditions, limited membrane digestion of bovine serum albumin (BSA) and subsequent ESI-Orbitrap MS analysis reveal large peptides (3-10 kDa) that increase the sequence coverage from 53% (2 s digestion) to 82% (0.05 s digestion). With this approach, we also performed membrane-based limited proteolysis of a large Arabidopsis GTPase, Root Hair Defective 3 (RHD3) and showed suitable probing for labile regions near the C-terminus to suggest what protein reconstruction might make RHD3 more suitable for crystallization.
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Affiliation(s)
- Yu-Jing Tan
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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24
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Valveless gated injection for microfluidic chip-based liquid chromatography system with polymer monolithic column. J Chromatogr A 2012; 1246:123-8. [DOI: 10.1016/j.chroma.2012.03.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 03/13/2012] [Accepted: 03/16/2012] [Indexed: 11/24/2022]
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25
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Wu Q, Yuan H, Zhang L, Zhang Y. Recent advances on multidimensional liquid chromatography-mass spectrometry for proteomics: from qualitative to quantitative analysis--a review. Anal Chim Acta 2012; 731:1-10. [PMID: 22652259 DOI: 10.1016/j.aca.2012.04.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 04/09/2012] [Accepted: 04/09/2012] [Indexed: 02/08/2023]
Abstract
With the acceleration of proteome research, increasing attention has been paid to multidimensional liquid chromatography-mass spectrometry (MDLC-MS) due to its high peak capacity and separation efficiency. Recently, many efforts have been put to improve MDLC-based strategies including "top-down" and "bottom-up" to enable highly sensitive qualitative and quantitative analysis of proteins, as well as accelerate the whole analytical procedure. Integrated platforms with combination of sample pretreatment, multidimensional separations and identification were also developed to achieve high throughput and sensitive detection of proteomes, facilitating highly accurate and reproducible quantification. This review summarized the recent advances of such techniques and their applications in qualitative and quantitative analysis of proteomes.
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Affiliation(s)
- Qi Wu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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26
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Prefractionation and separation by C8 stationary phase: Effective strategies for integral membrane proteins analysis. Talanta 2012; 88:567-72. [DOI: 10.1016/j.talanta.2011.11.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 11/10/2011] [Accepted: 11/13/2011] [Indexed: 11/18/2022]
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27
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Preparing a metal-ion chelated immobilized enzyme reactor based on the polyacrylamide monolith grafted with polyethylenimine for a facile regeneration and high throughput tryptic digestion in proteomics. Anal Bioanal Chem 2011; 402:703-10. [DOI: 10.1007/s00216-011-5501-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 10/11/2011] [Accepted: 10/11/2011] [Indexed: 11/26/2022]
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28
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Abstract
Proteomic analysis requires the combination of an extensive suite of technologies including protein processing and separation, micro-flow HPLC, MS and bioinformatics. Although proteomic technologies are still in flux, approaches that bypass gel electrophoresis (gel-free approaches) are dominating the field of proteomics. Along with the development of gel-free proteomics, came the development of devices for the processing of proteomic samples termed proteomic reactors. These microfluidic devices provide rapid, robust and efficient pre-MS sample procession by performing protein sample preparation/concentration, digestion and peptide fractionation. The proteomic reactor has advanced in two major directions: immobilized enzyme reactor and ion exchange-based proteomic reactor. This review summarizes the technical developments and biological applications of the proteomic reactor over the last decade.
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Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, ON, Canada
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29
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Zhou H, Wang F, Wang Y, Ning Z, Hou W, Wright TG, Sundaram M, Zhong S, Yao Z, Figeys D. Improved recovery and identification of membrane proteins from rat hepatic cells using a centrifugal proteomic reactor. Mol Cell Proteomics 2011; 10:O111.008425. [PMID: 21749988 DOI: 10.1074/mcp.o111.008425] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite their importance in many biological processes, membrane proteins are underrepresented in proteomic analysis because of their poor solubility (hydrophobicity) and often low abundance. We describe a novel approach for the identification of plasma membrane proteins and intracellular microsomal proteins that combines membrane fractionation, a centrifugal proteomic reactor for streamlined protein extraction, protein digestion and fractionation by centrifugation, and high performance liquid chromatography-electrospray ionization-tandem MS. The performance of this approach was illustrated for the study of the proteome of ER and Golgi microsomal membranes in rat hepatic cells. The centrifugal proteomic reactor identified 945 plasma membrane proteins and 955 microsomal membrane proteins, of which 63 and 47% were predicted as bona fide membrane proteins, respectively. Among these proteins, >800 proteins were undetectable by the conventional in-gel digestion approach. The majority of the membrane proteins only identified by the centrifugal proteomic reactor were proteins with ≥ 2 transmembrane segments or proteins with high molecular mass (e.g. >150 kDa) and hydrophobicity. The improved proteomic reactor allowed the detection of a group of endocytic and/or signaling receptor proteins on the plasma membrane, as well as apolipoproteins and glycerolipid synthesis enzymes that play a role in the assembly and secretion of apolipoprotein B100-containing very low density lipoproteins. Thus, the centrifugal proteomic reactor offers a new analytical tool for structure and function studies of membrane proteins involved in lipid and lipoprotein metabolism.
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Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Canada
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30
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31
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Ning Z, Zhou H, Wang F, Abu-Farha M, Figeys D. Analytical Aspects of Proteomics: 2009–2010. Anal Chem 2011; 83:4407-26. [DOI: 10.1021/ac200857t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Hu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Fangjun Wang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China 116023
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