1
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Swinnen S, de Azambuja F, Parac-Vogt TN. From Nanozymes to Multi-Purpose Nanomaterials: The Potential of Metal-Organic Frameworks for Proteomics Applications. Adv Healthc Mater 2025; 14:e2401547. [PMID: 39246191 DOI: 10.1002/adhm.202401547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/14/2024] [Indexed: 09/10/2024]
Abstract
Metal-organic frameworks (MOFs) have the potential to revolutionize the biotechnological and medical landscapes due to their easily tunable crystalline porous structure. Herein, the study presents MOFs' potential impact on proteomics, unveiling the diverse roles MOFs can play to boost it. Although MOFs are excellent catalysts in other scientific disciplines, their role as catalysts in proteomics applications remains largely underexplored, despite protein cleavage being of crucial importance in proteomics protocols. Additionally, the study discusses evolving MOF materials that are tailored for proteomics, showcasing their structural diversity and functional advantages compared to other types of materials used for similar applications. MOFs can be developed to seamlessly integrate into proteomics workflows due to their tunable features, contributing to protein separation, peptide enrichment, and ionization for mass spectrometry. This review is meant as a guide to help bridge the gap between material scientists, engineers, and MOF chemists and on the other side researchers in biology or bioinformatics working in proteomics.
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Affiliation(s)
- Siene Swinnen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven, 3001, Belgium
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2
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Chen M, Li B, Wei W, Zhang Z, Zhang L, Li C, Huang Q. Ultrafast protein digestion using an immobilized enzyme reactor following high-resolution mass spectrometry analysis for rapid identification of abrin toxin. Analyst 2024; 149:3783-3792. [PMID: 38845587 DOI: 10.1039/d4an00406j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Abrin toxin, highly dangerous with an estimated human lethal dose of 0.1-1 μg per kg body weight, has attracted much attention regarding criminal and terroristic misuse over the past decade. Therefore, developing a rapid detection method for abrin toxin is of great significance in the field of biosecurity. In this study, based on the specific dissociation method of an immobilized enzyme reactor, the trypsin immobilized reactor Fe3O4@CTS-GA-Try was prepared to replace free trypsin, and the immobilized enzyme digestion process was systematically investigated and optimized by using bovine serum albumin as the simulant of abrin. After 5 min one-step denaturation and reduction, a satisfactory peptide number and coverage were yielded with only 15 s assisted by an ultrasound probe to identify model proteins. Subsequently, abrin was rapidly digested using the established method, resulting in a stable and highly reproducible characteristic peptide number of 39, which can be analyzed by nanoelectrospray ionization coupled with high-resolution mass spectrometry. With the acquisition mode of full MS scan coupled with PRM, not only MS spectroscopy of total abrin peptides but also the corresponding MS/MS spectroscopy of specific abrin peptides can achieve the characteristic detection of abrin toxin and its different isoforms in less than 10 minutes, with high repeatability. This assay provides a universal platform and has great potential for the development of on-site detection and rapid mass spectrometric analysis techniques for macromolecular protein toxins and can further be applied to the integrated detection of chemical and biological agents.
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Affiliation(s)
- Meng Chen
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Baoqiang Li
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Wenlu Wei
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Zhongyao Zhang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Lin Zhang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Cuiping Li
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Qibin Huang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
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3
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Shui T, Li A, Chae M, Xu CC, Bressler DC. Valorization strategies for hazardous proteinaceous waste from rendering production - Recent advances in specified risk materials (SRMs) conversion. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131339. [PMID: 37058938 DOI: 10.1016/j.jhazmat.2023.131339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
Strict bans on specific risk materials (SRMs) are in place to prevent the spread of bovine spongiform encephalopathy (BSE). SRMs are characterized as tissues in cattle where misfolded proteins, the potential source of BSE infection, are concentrated. As a result of these bans, SRMs must be strictly isolated and disposed of, resulting in great costs for rendering companies. The increasing yield and the landfill of SRMs also exacerbated the burden on the environment. To cope with the emergence of SRMs, novel disposal methods and feasible value-added conversion routes are needed. The focus of this review is on the valorization progress achieved in the conversion of peptides derived from SRMs via an alternative disposal method, thermal hydrolysis. Promising value-added conversion of SRM-derived peptides into tackifiers, wood adhesives, flocculants, and bioplastics, is introduced. The potential conjugation strategies that can be adapted to SRM-derived peptides for desired properties are also critically reviewed. The purpose of this review is to discover a technical platform through which other hazardous proteinaceous waste, SRMs, can be treated as a high-demand feedstock for the production of renewable materials.
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Affiliation(s)
- Tao Shui
- School of Materials Science and Engineering, Southeast University, Nanjing, China; Biorefining Conversions and Fermentation Laboratory, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - An Li
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Michael Chae
- Biorefining Conversions and Fermentation Laboratory, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Chunbao Charles Xu
- Department of Chemical and Biochemical Engineering, Western University, London, Ontario N6A 5B9, Canada
| | - David C Bressler
- Biorefining Conversions and Fermentation Laboratory, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada.
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4
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Verma NK, Raghav N. In-silico identification of lysine residue for lysozyme immobilization on dialdehyde cellulose. Int J Biol Macromol 2023:125367. [PMID: 37327935 DOI: 10.1016/j.ijbiomac.2023.125367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/07/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
In the realm of enzymes, the Enzyme Immobilization technique can be extremely beneficial. More research into computational approaches could lead to a better understanding as well as lead us in the direction of a more environmentally friendly and greener path. In this study, molecular modelling techniques were used to collect information regarding the immobilization of Lysozyme (EC 3.2.1.17) on Dialdehyde Cellulose (CDA). Lysine, being the most nucleophilic, is most likely to interact with dialdehyde cellulose. Enzyme substrate interactions have been studied with and without the refinement of modified lysozyme molecules. A total of six CDA-modified lysine residues were selected for the study. The docking process for all modified lysozymes was carried out using four distinct docking programs: Autodock Vina, GOLD, Swissdock, and iGemdock. The binding affinity (-7.8 & -8.0 kcal mol-1 in case of non-refinement and -4.7 & -5.0 kcal mol-1 in case of refinement), calculated from Autodock vina, as well as the interaction similarity of Lys116 immobilized lysozyme with its substrate, were found to be 75 % (W/o simulation) & 66.7 % (With simulation) identical with the reference case (unmodified lysozyme) if Lys116 is bound to Dialdehyde Cellulose. The approach described here is utilized to identify amino acid residues that are used in the immobilization of lysozyme.
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Affiliation(s)
- Nitin Kumar Verma
- Chemistry Department, Kurukshetra University, Kurukshetra 136119, Haryana, India
| | - Neera Raghav
- Chemistry Department, Kurukshetra University, Kurukshetra 136119, Haryana, India.
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5
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Ryan KA, Bruening ML. Online protein digestion in membranes between capillary electrophoresis and mass spectrometry. Analyst 2023; 148:1611-1619. [PMID: 36912593 DOI: 10.1039/d3an00106g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
This research employs pepsin-containing membranes to digest proteins online after a capillary electrophoresis (CE) separation and prior to tandem mass spectrometry. Proteolysis after the separation allows the peptides from a given protein to enter the mass spectrometer in a single plug. Thus, migration time can serve as an additional criterion for confirming the identification of a peptide. The membrane resides in a sheath-flow electrospray ionization (ESI) source to enable digestion immediately before spray into the mass spectrometer, thus limiting separation of the digested peptides. Using the same membrane, digestion occurred reproducibly during 20 consecutive CE analyses performed over a 10 h period. Additionally, after separating a mixture of six unreduced proteins with CE, online digestion facilitated protein identification with at least 2 identifiable peptides for all the proteins. Sequence coverages were >75% for myoglobin and carbonic anhydrase II but much lower for proteins containing disulfide bonds. Development of methods for efficient separation of reduced proteins or identification of cross-linked peptides should enhance sequence coverages for proteins with disulfide bonds. Migration times for the peptides identified from a specific protein differed by <∼30 s, which allows for rejection of some spurious peptide identifications.
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Affiliation(s)
- Kendall A Ryan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Merlin L Bruening
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. .,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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6
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Kašička V. Peptide mapping of proteins by capillary electromigration methods. J Sep Sci 2022; 45:4245-4279. [PMID: 36200755 DOI: 10.1002/jssc.202200664] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 12/13/2022]
Abstract
This review article provides a wide overview of important developments and applications of capillary electromigration methods in the area of peptide mapping of proteins in the period 1997-mid-2022, including review articles on this topic. It deals with all major aspects of peptide mapping by capillary electromigration methods: i) precleavage sample preparation involving purification, preconcentration, denaturation, reduction and alkylation of protein(s) to be analyzed, ii) generation of peptide fragments by off-line or on-line enzymatic and/or chemical cleavage of protein(s), iii) postcleavage preparation of the generated peptide mixture for capillary electromigration separation, iv) separation of the complex peptide mixtures by one-, two- and multidimensional capillary electromigration methods coupled with mass spectrometry detection, and v) a large application of peptide mapping for variable purposes, such as qualitative analysis of monoclonal antibodies and other protein biopharmaceuticals, monitoring of posttranslational modifications, determination of primary structure and investigation of function of proteins in biochemical and clinical research, characterization of proteins of variable origin as well as for protein and peptide identification in proteomic and peptidomic studies.
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Affiliation(s)
- Václav Kašička
- Electromigration Methods, The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia
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7
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Rainer T, Egger AS, Zeindl R, Tollinger M, Kwiatkowski M, Müller T. 3D-Printed High-Pressure-Resistant Immobilized Enzyme Microreactor (μIMER) for Protein Analysis. Anal Chem 2022; 94:8580-8587. [PMID: 35678765 PMCID: PMC9218953 DOI: 10.1021/acs.analchem.1c05232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Additive manufacturing
(3D printing) has greatly revolutionized
the way researchers approach certain technical challenges. Despite
its outstanding print quality and resolution, stereolithography (SLA)
printing is cost-effective and relatively accessible. However, applications
involving mass spectrometry (MS) are few due to residual oligomers
and additives leaching from SLA-printed devices that interfere with
MS analyses. We identified the crosslinking agent urethane dimethacrylate
as the main contaminant derived from SLA prints. A stringent washing
and post-curing protocol mitigated sample contamination and rendered
SLA prints suitable for MS hyphenation. Thereafter, SLA printing was
used to produce 360 μm I.D. microcolumn chips with excellent
structural properties. By packing the column with polystyrene microspheres
and covalently immobilizing pepsin, an exceptionally effective microscale
immobilized enzyme reactor (μIMER) was created. Implemented
in an online liquid chromatography-MS/MS setup, the protease microcolumn
enabled reproducible protein digestion and peptide mapping with 100%
sequence coverage obtained for three different recombinant proteins.
Additionally, when assessing the μIMER digestion efficiency
for complex proteome samples, it delivered a 144-fold faster and significantly
more efficient protein digestion compared to 24 h for bulk digestion.
The 3D-printed μIMER withstands remarkably high pressures above
130 bar and retains its activity for several weeks. This versatile
platform will enable researchers to produce tailored polymer-based
enzyme reactors for various applications in analytical chemistry and
beyond.
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Affiliation(s)
- Tobias Rainer
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Anna-Sophia Egger
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Ricarda Zeindl
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Thomas Müller
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
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8
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Dual-function monolithic enzyme reactor based on dopamine/graphene oxide coating for simultaneous protein enzymatic hydrolysis and glycopeptide enrichment. J Chromatogr A 2022; 1666:462848. [DOI: 10.1016/j.chroma.2022.462848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/10/2022] [Accepted: 01/20/2022] [Indexed: 11/18/2022]
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10
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Hata K, Izumi Y, Hara T, Matsumoto M, Bamba T. In-Line Sample Processing System with an Immobilized Trypsin-Packed Fused-Silica Capillary Tube for the Proteomic Analysis of a Small Number of Mammalian Cells. Anal Chem 2020; 92:2997-3005. [PMID: 31961143 DOI: 10.1021/acs.analchem.9b03993] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Omics analysis at single-cell resolution has helped to demonstrate the shaping of cellular heterogeneity on the basis of the expression of various molecules. However, in-depth proteomic analysis of low-quantity samples has remained challenging because of difficulties associated with the measurement of large numbers of proteins by shotgun proteomics using nanoflow liquid chromatography tandem mass spectrometry (nano-LC/MS/MS). To meet such a demand, we developed a method called in-line sample preparation for efficient cellular proteomics (ISPEC) in which cells were captured, directly lysed, and digested with immobilized trypsin within fused-silica capillaries. ISPEC minimized sample loss during the sample preparation processes with a relatively small number of mammalian cells (<1000 cells) and improved the stability and efficiency of digestion by immobilized trypsin, compared to a conventional preparation method. Using our optimized ISPEC method with nano-LC/MS/MS analysis, we identified 1351, 351, and 60 proteins from 100 cells, 10 cells, and single cells, respectively. The linear response of the signal intensity of each peptide to the introduced cell number indicates the quantitative recovery of the proteome from a very small number of cells. Thus, our ISPEC strategy facilitates quantitative proteomic analysis of small cell populations.
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Affiliation(s)
| | | | | | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences , Niigata University , 1-757, Asahimachi-dori , Niigata , 951-8510 , Japan
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11
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Ma S, Li Y, Ma C, Wang Y, Ou J, Ye M. Challenges and Advances in the Fabrication of Monolithic Bioseparation Materials and their Applications in Proteomics Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1902023. [PMID: 31502719 DOI: 10.1002/adma.201902023] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/29/2019] [Indexed: 06/10/2023]
Abstract
High-performance liquid chromatography integrated with tandem mass spectrometry (HPLC-MS/MS) has become a powerful technique for proteomics research. Its performance heavily depends on the separation efficiency of HPLC, which in turn depends on the chromatographic material. As the "heart" of the HPLC system, the chromatographic material is required to achieve excellent column efficiency and fast analysis. Monolithic materials, fabricated as continuous supports with interconnected skeletal structure and flow-through pores, are regarded as an alternative to particle-packed columns. Such materials are featured with easy preparation, fast mass transfer, high porosity, low back pressure, and miniaturization, and are next-generation separation materials for high-throughput proteins and peptides analysis. Herein, the recent progress regarding the fabrication of various monolithic materials is reviewed. Special emphasis is placed on studies of the fabrication of monolithic capillary columns and their applications in separation of biomolecules by capillary liquid chromatography (cLC). The applications of monolithic materials in the digestion, enrichment, and separation of phosphopeptides and glycopeptides from biological samples are also considered. Finally, advances in comprehensive 2D HPLC separations using monolithic columns are also shown.
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Affiliation(s)
- Shujuan Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Ya Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Chen Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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12
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Surface modification with highly-homogeneous porous silica layer for enzyme immobilization in capillary enzyme microreactors. Talanta 2019; 197:539-547. [DOI: 10.1016/j.talanta.2019.01.080] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 12/25/2022]
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13
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Rapid proteolytic digestion and peptide separation using monolithic enzyme microreactor coupled with capillary electrophoresis. J Pharm Biomed Anal 2019; 165:129-134. [DOI: 10.1016/j.jpba.2018.11.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/22/2018] [Accepted: 11/30/2018] [Indexed: 11/21/2022]
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14
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Lam SC, Sanz Rodriguez E, Haddad PR, Paull B. Recent advances in open tubular capillary liquid chromatography. Analyst 2019; 144:3464-3482. [DOI: 10.1039/c9an00329k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review covers advances and applications of open tubular capillary liquid chromatography (OT-LC) over the period 2007–2018.
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Affiliation(s)
- Shing Chung Lam
- ASTech
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech)
- and Australian Centre for Research on Separation Science (ACROSS)
- School of Natural Sciences
- University of Tasmania
| | - Estrella Sanz Rodriguez
- ASTech
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech)
- and Australian Centre for Research on Separation Science (ACROSS)
- School of Natural Sciences
- University of Tasmania
| | - Paul R. Haddad
- ASTech
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech)
- and Australian Centre for Research on Separation Science (ACROSS)
- School of Natural Sciences
- University of Tasmania
| | - Brett Paull
- ASTech
- ARC Training Centre for Portable Analytical Separation Technologies (ASTech)
- and Australian Centre for Research on Separation Science (ACROSS)
- School of Natural Sciences
- University of Tasmania
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15
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Ulu A, Noma SAA, Koytepe S, Ates B. Chloro-Modified Magnetic Fe3O4@MCM-41 Core–Shell Nanoparticles for L-Asparaginase Immobilization with Improved Catalytic Activity, Reusability, and Storage Stability. Appl Biochem Biotechnol 2018; 187:938-956. [DOI: 10.1007/s12010-018-2853-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/30/2018] [Indexed: 12/17/2022]
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16
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Liu W, Pang Y, Tan HY, Patel N, Jokhadze G, Guthals A, Bruening ML. Enzyme-containing spin membranes for rapid digestion and characterization of single proteins. Analyst 2018; 143:3907-3917. [PMID: 30039812 DOI: 10.1039/c8an00969d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteolytic digestion is an important step in characterizing protein sequences and post-translational modifications (PTMs) using mass spectrometry (MS). This study uses pepsin- or trypsin-containing spin membranes for rapid digestion of single proteins or simple protein mixtures prior to ultrahigh-resolution Orbitrap MS analysis. Centrifugation of 100 μL of pretreated protein solutions through the functionalized membranes requires less than 1 min and conveniently digests proteins into large peptides that aid in confirming specific protein sequence variations and PTMs. Peptic and tryptic peptides from spin digestion of apomyoglobin and four commercial monoclonal antibodies (mAbs) typically cover 100% of the protein sequences in direct infusion MS analysis. Increasing the spin rate leads to a higher fraction of large peptic peptides for apomyoglobin, and MS analysis of peptic and tryptic peptides reveals mAb PTMs such as N-terminal pyroglutamate formation, C-terminal lysine clipping and glycosylation. Relative to overnight in-solution digestion of mAbs, spin digestion yields higher sequence coverages. Spin-membrane digestion followed by infusion MS readily differentiates a mAb to the Ebola virus from a related antibody that differs by addition of a single amino acid.
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Affiliation(s)
- Weijing Liu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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17
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Guo Z, Cheng J, Sun H, Sun W. A qualitative and quantitative evaluation of the peptide characteristics of microwave- and ultrasound-assisted digestion in discovery and targeted proteomic analyses. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1353-1362. [PMID: 28557149 DOI: 10.1002/rcm.7913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Fast digestion methods can dramatically accelerate enzyme digestion and increase the throughput of proteomic analysis. However, the peptide characteristics of fast digestion methods and their performance in discovery and targeted proteomic analysis must be systematically evaluated. METHODS Three digestion methods, including overnight digestion, microwave-assisted protein enzymatic digestion (MAPED), and high-intensity focused ultrasonic-assisted enzymatic digestion (HIFUSAED), in trypsin or in trypsin/Lys-C were comprehensively compared in both discovery and targeted proteomics analysis using the HeLa cell proteome. In discovery proteomic analysis, the highest numbers of peptides and proteins were identified when the sample was digested via the MAPED method with trypsin/Lys-C. RESULTS The fast digestion methods showed a higher mis-cleavage rate and a lower semi-tryptic rate than the overnight digestion method. In both label-free quantitative analysis and targeted proteomic analysis, both fully cleaved peptides (FCPs) and mis-cleaved peptides (MCPs) from the fast digestion methods and the overnight digestion method showed good reproducibility if they showed good abundance. CONCLUSIONS When both the FCPs and MCPs were included in the analysis, the MAPED with trypsin/Lys-C method showed the best results for both discovery proteomic analysis and relative quantitative targeted proteomic analysis. These results will be beneficial for the application of fast digestion methods to proteomics.
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Affiliation(s)
- Zhengguang Guo
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jie Cheng
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Haidan Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
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18
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Chen WQ, Obermayr P, Černigoj U, Vidič J, Panić-Janković T, Mitulović G. Immobilized monolithic enzymatic reactor and its application for analysis of in-vitro fertilization media samples. Electrophoresis 2017; 38:2957-2964. [DOI: 10.1002/elps.201700197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 05/29/2017] [Accepted: 06/04/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Wei-Qiang Chen
- Clinical Institute of Laboratory Medicine; Medical University of Vienna; Vienna Austria
| | | | | | - Jana Vidič
- BIA Separations d.o.o; Ajdovščina Slovenia
| | - Tanta Panić-Janković
- Clinical Institute of Laboratory Medicine; Medical University of Vienna; Vienna Austria
| | - Goran Mitulović
- Clinical Institute of Laboratory Medicine; Medical University of Vienna; Vienna Austria
- Proteomics Core Facility; Medical University of Vienna; Vienna Austria
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19
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Šlechtová T, Gilar M, Kalíková K, Moore SM, Jorgenson JW, Tesařová E. Performance comparison of three trypsin columns used in liquid chromatography. J Chromatogr A 2017; 1490:126-132. [PMID: 28215403 DOI: 10.1016/j.chroma.2017.02.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/03/2017] [Accepted: 02/11/2017] [Indexed: 01/06/2023]
Abstract
Trypsin is the most widely used enzyme in proteomic research due to its high specificity. Although the in-solution digestion is predominantly used, it has several drawbacks, such as long digestion times, autolysis, and intolerance to high temperatures or organic solvents. To overcome these shortcomings trypsin was covalently immobilized on solid support and tested for its proteolytic activity. Trypsin was immobilized on bridge-ethyl hybrid silica sorbent with 300Å pores, packed in 2.1×30mm column and compared with Perfinity and Poroszyme trypsin columns. Catalytic efficiency of enzymatic reactors was tested using Nα-Benzoyl-l-arginine 4-nitroanilide hydrochloride as a substrate. The impact of buffer pH, mobile phase flow rate, and temperature on enzymatic activity was investigated. Digestion speed generally increased with the temperature from 20 to 37°C. Digestion speed also increased with pH from 7.0 to 9.0; the activity of prototype enzyme reactor was highest at pH 9.0, when it activity exceeded both commercial reactors. Preliminary data for fast protein digestion are presented.
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Affiliation(s)
- Tereza Šlechtová
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague, Czechia
| | - Martin Gilar
- Waters Corporation, 34 Maple Street, Milford, MA 01757, USA.
| | - Květa Kalíková
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague, Czechia
| | - Stephanie M Moore
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | - James W Jorgenson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | - Eva Tesařová
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague, Czechia
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Moore S, Hess S, Jorgenson J. Characterization of an immobilized enzyme reactor for on-line protein digestion. J Chromatogr A 2016; 1476:1-8. [PMID: 27876348 PMCID: PMC5136339 DOI: 10.1016/j.chroma.2016.11.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/29/2016] [Accepted: 11/13/2016] [Indexed: 01/05/2023]
Abstract
Despite the developments for faster liquid chromatographic and mass spectral detection techniques, the standard in-solution protein digestion for proteomic analyses has remained relatively unchanged. The typical in-solution trypsin protein digestion is usually the slowest part of the workflow, albeit one of the most important. The development of a highly efficient immobilized enzyme reactor (IMER) with rapid performance for on-line protein digestion would greatly decrease the analysis time involved in a proteomic workflow. Presented here is the development of a silica based IMER for on-line protein digestion, which produced rapid digestions in the presence of organic mobile phase for both model proteins and a complex sample consisting of the insoluble portion of a yeast cell lysate. Protein sequence coverage and identifications evaluated between the IMER and in-solution digestions were comparable. Overall, for a yeast cell lysate with only a 10s volumetric residence time on-column, the IMER identified 507 proteins while the in-solution digestion identified 490. There were no significant differences observed based on identified protein's molecular weight or isoelectric point between the two digestion methods. Implementation of the IMER into the proteomic workflow provided similar protein identification results, automation for sample analysis, and reduced the analysis time by 15h.
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Affiliation(s)
- Stephanie Moore
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States
| | - Stephanie Hess
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States
| | - James Jorgenson
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States.
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21
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Yin J, Xu T, Zhang N, Wang H. Three-Enzyme Cascade Bioreactor for Rapid Digestion of Genomic DNA into Single Nucleosides. Anal Chem 2016; 88:7730-7. [DOI: 10.1021/acs.analchem.6b01682] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Junfa Yin
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Tian Xu
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Zhang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hailin Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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22
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Ruan G, Wu Z, Huang Y, Wei M, Su R, Du F. An easily regenerable enzyme reactor prepared from polymerized high internal phase emulsions. Biochem Biophys Res Commun 2016; 473:54-60. [DOI: 10.1016/j.bbrc.2016.03.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/11/2016] [Indexed: 12/15/2022]
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23
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Wen L, Gao A, Cao Y, Svec F, Tan T, Lv Y. Layer-by-Layer Assembly of Metal-Organic Frameworks in Macroporous Polymer Monolith and Their Use for Enzyme Immobilization. Macromol Rapid Commun 2016; 37:551-7. [DOI: 10.1002/marc.201500705] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 12/30/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Liyin Wen
- Beijing Key Laboratory of Bioprocess; College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
| | - Aicong Gao
- Beijing Key Laboratory of Bioprocess; College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
| | - Yao Cao
- Beijing Key Laboratory of Bioprocess; College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
| | - Frantisek Svec
- International Research Center for Soft Matter; Beijing University of Chemical Technology; Beijing 100029 China
| | - Tianwei Tan
- Beijing Key Laboratory of Bioprocess; College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
| | - Yongqin Lv
- Beijing Key Laboratory of Bioprocess; College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
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24
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Moridi N, Corvini PF, Shahgaldian P. Reversible Supramolecular Surface Attachment of Enzyme–Polymer Conjugates for the Design of Biocatalytic Filtration Membranes. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Negar Moridi
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
| | - Philippe F.‐X. Corvini
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
- School of the Environment, Nanjing University, 210093 Nanjing (China)
| | - Patrick Shahgaldian
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
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25
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Álvarez Porebski PW, Gyssels E, Madder A, Lynen F. Hyphenation of a Deoxyribonuclease I immobilized enzyme reactor with liquid chromatography for the online stability evaluation of oligonucleotides. J Chromatogr A 2015; 1422:18-26. [PMID: 26515385 DOI: 10.1016/j.chroma.2015.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 10/05/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
The stability of antisense oligonucleotides (ONs) toward nucleases is a key aspect for their possible implementation as therapeutic agents. Typically, ON stability studies are performed off-line, where the ONs are incubated with nucleases in solution, followed by their analysis. The problematics of off-line processing render the detailed comparison of relative ON stability quite challenging. Therefore, the development of an online platform based on an immobilized enzyme reactor (IMER) coupled to liquid chromatography (LC) was developed as an alternative for improved ON stability testing. More in detail, Deoxyribonuclease I (DNase I) was immobilized on epoxy-silica particles of different pore sizes and packed into a column for the construction of an IMER. Subsequently, the hyphenation of the IMER with ion-pair chromatography (IPC) and ion-exchange chromatography (IEC) was evaluated, leading to the successful development of two online methodologies: IMER-IPC and IMER-IEC. More specifically, natural and modified DNA and RNA oligonucleotides were used for testing the performance of the methodologies. Both methodologies proved to be simple, automatable, fast and highly reproducible for the quantitative and qualitative evaluation of ON degradation. In addition, the extended IMER life time in combination with a more straightforward control of the reaction kinetics substantiate the applicability of the IMER-LC platform for ON stability tests and its implementation in routine and research laboratories.
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Affiliation(s)
- Piotr Wiktor Álvarez Porebski
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
| | - Ellen Gyssels
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
| | - Frederic Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Universiteit Gent, Krijgslaan 281 S4-bis, 9000 Gent, Belgium.
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26
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Moridi N, Corvini PF, Shahgaldian P. Reversible Supramolecular Surface Attachment of Enzyme–Polymer Conjugates for the Design of Biocatalytic Filtration Membranes. Angew Chem Int Ed Engl 2015; 54:14800-4. [DOI: 10.1002/anie.201507020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Negar Moridi
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
| | - Philippe F.‐X. Corvini
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
- School of the Environment, Nanjing University, 210093 Nanjing (China)
| | - Patrick Shahgaldian
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, Muttenz CH‐4132 (Switzerland)
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27
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Rodríguez Gastón JA, Costa H, Ferrarotti SA. Continuous production of cyclodextrins in an ultrafiltration membrane reactor, catalyzed by cyclodextrin glycosyltransferase from Bacillus circulans DF 9R. Biotechnol Prog 2015; 31:695-9. [PMID: 25583301 DOI: 10.1002/btpr.2053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/11/2014] [Indexed: 11/07/2022]
Abstract
Cyclodextrins (CDs) are cyclic oligosaccharides of wide industrial application, whose synthesis is catalyzed by Cyclodextrin glycosyltransferase (CGTase) from starch. Here, CDs were produced using CGTase from Bacillus circulans DF 9R in continuous process and an ultrafiltration membrane reactor. The batch process was conducted as a control. This method allowed increasing the yield from 40 to 55.6% and the productivity from 26.1 to 99.5 mg of CD per unit of enzyme. The method also allowed obtaining a high-purity product. The flow rate remained at 50% of its initial value after 24 h of process, improving the results described in the literature for starch hydrolysis processes. CGTase remained active throughout the process, which could be explained by the protective effect of the substrate and reaction products on CGTase stability. In addition, batch processes were developed using starches from different sources. We concluded that any of the starches studied could be used as substrate for CD production with similar yields and product specificity.
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Affiliation(s)
| | - Hernán Costa
- Dept. de Ciencias Básicas, Universidad Nacional de Luján, Luján (6700), Buenos Aires, República Argentina
| | - Susana A Ferrarotti
- Dept. de Ciencias Básicas, Universidad Nacional de Luján, Luján (6700), Buenos Aires, República Argentina
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28
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Mu X, Qiao J, Qi L, Dong P, Ma H. Poly(2-vinyl-4,4-dimethylazlactone)-functionalized magnetic nanoparticles as carriers for enzyme immobilization and its application. ACS APPLIED MATERIALS & INTERFACES 2014; 6:21346-54. [PMID: 25360545 DOI: 10.1021/am5063025] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fabrication of various efficient enzyme reactors has triggered increasing interests for its extensive applications in biological and clinical research. In this study, magnetic nanoparticles were functionalized by a biocompatible reactive polymer, poly(2-vinyl-4,4-dimethylazlactone), which was synthesized by reversible addition-fragmentation chain transfer polymerization. Then, the prepared polymer-modified magnetic nanoparticles were employed as favorable carriers for enzyme immobilization. l-Asparaginase was selected as the model enzyme to fabricate the enzyme reactor, and the prepared enzyme reactor exhibited high loading capacity of 318.0 μg mg(-1) magnetic nanoparticle. Interestingly, it has been observed that the enzymolysis efficiency increased slightly with the lengthened polymer chain, resulting from the increased immobilization amount of enzyme. Meanwhile, the immobilized enzyme could retain more than 95.7% activity after 10 repeated uses and maintain more than 72.6% activity after 10 weeks storage. Moreover, an extracorporeal shunt system was simulated to estimate the potential application capability of the prepared l-asparaginase reactor in acute lymphoblastic leukemia treatment.
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Affiliation(s)
- Xiaoyu Mu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P.R. China
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29
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Nakagawa K, Tamura A, Chaiya C. Preparation of proteolytic microreactors by freeze-drying immobilization. Chem Eng Sci 2014. [DOI: 10.1016/j.ces.2014.07.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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31
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Capillary electrophoresis-based immobilized enzyme reactor using particle-packing technique. J Chromatogr A 2014; 1352:80-6. [DOI: 10.1016/j.chroma.2014.05.058] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 01/26/2023]
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32
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Zhang Z, Zhang L, Zhang C, Zhang W. Hybrid organic–inorganic monolithic enzymatic reactor with SBA-15 nanoparticles incorporated. Talanta 2014; 119:485-91. [DOI: 10.1016/j.talanta.2013.11.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 11/11/2013] [Accepted: 11/13/2013] [Indexed: 10/26/2022]
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33
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Fu R, Liu L, Guo Y, Guo L, Yang L. Sequential micellar electrokinetic chromatography analysis of racemization reaction of alanine enantiomers. J Chromatogr A 2014; 1331:123-8. [DOI: 10.1016/j.chroma.2014.01.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Revised: 01/16/2014] [Accepted: 01/19/2014] [Indexed: 12/13/2022]
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34
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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: 5.5] [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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35
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Matsuura SI, Chiba M, Tomon E, Tsunoda T. Synthesis of amino acid using a flow-type microreactor containing enzyme–mesoporous silica microsphere composites. RSC Adv 2014. [DOI: 10.1039/c3ra45315d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A flow-type microreactor containing composites of the enzyme (glutaminase) and mesoporous silica microspheres with a 23.6 nm pore diameter (SBA23.6) exhibited precise, efficient, and continuous synthesis of theanine.
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Affiliation(s)
- Shun-ichi Matsuura
- Research Center for Compact Chemical System
- National Institute of Advanced Industrial Science and Technology (AIST)
- Sendai 983-8551, Japan
| | - Manami Chiba
- Research Center for Compact Chemical System
- National Institute of Advanced Industrial Science and Technology (AIST)
- Sendai 983-8551, Japan
| | - Emiko Tomon
- Research Center for Compact Chemical System
- National Institute of Advanced Industrial Science and Technology (AIST)
- Sendai 983-8551, Japan
| | - Tatsuo Tsunoda
- Research Center for Compact Chemical System
- National Institute of Advanced Industrial Science and Technology (AIST)
- Sendai 983-8551, Japan
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36
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Hustoft HK, Brandtzaeg OK, Rogeberg M, Misaghian D, Torsetnes SB, Greibrokk T, Reubsaet L, Wilson SR, Lundanes E. Integrated enzyme reactor and high resolving chromatography in "sub-chip" dimensions for sensitive protein mass spectrometry. Sci Rep 2013; 3:3511. [PMID: 24336509 PMCID: PMC3863811 DOI: 10.1038/srep03511] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 11/28/2013] [Indexed: 12/29/2022] Open
Abstract
Reliable, sensitive and automatable analytical methodology is of great value in e.g. cancer diagnostics. In this context, an on-line system for enzymatic cleavage of proteins, subsequent peptide separation by liquid chromatography (LC) with mass spectrometric detection has been developed using "sub-chip" columns (10-20 μm inner diameter, ID). The system could detect attomole amounts of isolated cancer biomarker progastrin-releasing peptide (ProGRP), in a more automatable fashion compared to previous methods. The workflow combines protein digestion using an 20 μm ID immobilized trypsin reactor with a polymeric layer of 2-hydroxyethyl methacrylate-vinyl azlactone (HEMA-VDM), desalting on a polystyrene-divinylbenzene (PS-DVB) monolithic trap column, and subsequent separation of resulting peptides on a 10 μm ID (PS-DVB) porous layer open tubular (PLOT) column. The high resolution of the PLOT columns was maintained in the on-line system, resulting in narrow chromatographic peaks of 3-5 seconds. The trypsin reactors provided repeatable performance and were compatible with long-term storage.
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Affiliation(s)
- Hanne Kolsrud Hustoft
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | | | - Magnus Rogeberg
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
- Department of Neurology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Dorna Misaghian
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Silje Bøen Torsetnes
- School of Pharmacy, University of Oslo, Post Box 1068 Blindern, NO-0316 Oslo, Norway
| | - Tyge Greibrokk
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Léon Reubsaet
- School of Pharmacy, University of Oslo, Post Box 1068 Blindern, NO-0316 Oslo, Norway
| | - Steven Ray Wilson
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Elsa Lundanes
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
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37
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Screening α-glucosidase inhibitor from natural products by capillary electrophoresis with immobilised enzyme onto polymer monolith modified by gold nanoparticles. Food Chem 2013; 141:1854-9. [DOI: 10.1016/j.foodchem.2013.04.100] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 04/18/2012] [Accepted: 04/23/2013] [Indexed: 12/22/2022]
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38
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Xu Y, Xu L, Qi S, Dong Y, ur Rahman Z, Chen H, Chen X. In situ synthesis of MIL-100(Fe) in the capillary column for capillary electrochromatographic separation of small organic molecules. Anal Chem 2013; 85:11369-75. [PMID: 24187953 DOI: 10.1021/ac402254u] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Because of the unusual properties of the structure, the metal organic frameworks (MOFs) have received great interest in separation science. However, the most existing methods for the applications of MOFs in separation science require an off-line procedure to prepare the materials. Here, we report an in situ, layer-by-layer self-assembly approach to fabricate MIL-100(Fe) coated open tubular (OT) capillary columns for capillary electrochromatography. By a controllable manner, the OT capillary columns with a tailored MIL-100(Fe) coating have been successfully synthesized. The results of SEM, XRD, FT-IR, and ICP-AES indicated that MIL-100(Fe) was successfully grafted on the inner wall of the capillary. Some neutral, acidic and basic analytes were used to evaluate the performance of the MIL-100(Fe) coating OT capillary column. Because of the size selectivity of lattice aperture and hydrophobicity of the organic ligands, three types of analytes were well separated with this novel MIL-100(Fe) coating OT capillary column. For three consecutive runs, the intraday relative standard deviations (RSDs) of migration time and peak areas were 0.4-4.6% and 1.2-6.6%, respectively. The interday RSDs of migration time and peak areas were 0.6-8.0% and 2.2-9.5%, respectively. The column-to-column reproducibility of retention time was in range of 0.6-9.2%. Additionally, the 10 cycles OT capillary column (10-LC) could be used for more than 150 runs with no observable changes on the separation efficiency.
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Affiliation(s)
- Yinyin Xu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University , Lanzhou 730000, China
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39
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Li X, Zhang Z, Tao L, Li Y, Li Y. Development a novel approach of chemiluminescent probe array. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:67-71. [PMID: 24177871 DOI: 10.1016/j.saa.2013.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 10/01/2013] [Accepted: 10/05/2013] [Indexed: 06/02/2023]
Abstract
A new chemiluminescent (CL) probe array assay approach was first developed. The new CL probe array was based on Co3O4-SiO2 mesoporous nanocomposite material, which not only has an excellent catalytic effect on the luminol-H2O2 CL reaction in alkaline medium but also can be used for the immobilization of enzymes. As a model, the novel bifunctional CL probe array has been applied to the high-throughput determination of glucose in human. The linear range of the glucose concentration was 3-90 μM and the detection limit was 0.36 μM. It breaks traditional development view in solid phase supports and provides new insights into the application of mesoporous material.
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Affiliation(s)
- Xiaohua Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, China
| | - Zhujun Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, China.
| | - Liang Tao
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, China
| | - Yongbo Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, China
| | - Yunyun Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, China
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40
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Ghafourifar G, Fleitz A, Waldron KC. Development of glutaraldehyde-crosslinked chymotrypsin and an in situ immobilized enzyme microreactor with peptide mapping by capillary electrophoresis. Electrophoresis 2013; 34:1804-11. [PMID: 23686566 DOI: 10.1002/elps.201200663] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/10/2013] [Accepted: 02/19/2013] [Indexed: 11/06/2022]
Abstract
Immobilized proteolytic enzymes present several advantages over their soluble form, not the least of which is suppression of autoproteolysis peaks even at high enzyme-to-substrate ratios. We have made immobilized chymotrypsin by directly crosslinking it with glutaraldehyde to produce polymeric particles. Digestion of two model substrates using the particles was followed by CE peptide mapping with detection by UV absorbance or LIF. Results showed that autoproteolysis was highly suppressed and that different storage conditions of the particles in the short term (24 h) did not affect digestion of denatured BSA. As well, the chymotrypsin particles were indifferent to the presence of fluorescein groups on a casein substrate. Glutaraldehyde crosslinking of chymotrypsin inside a fused silica capillary column to make an immobilized enzyme reactor (IMER) was achieved in a series of reagent addition and washing steps, entirely automated using a commercial CE instrument. Digestion of myoglobin in the IMER for 30 min at 37°C followed by peptide mapping by CE-MS of the collected digest allowed identification of 17 chymotryptic peptides of myoglobin, or 83% primary sequence coverage.
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Prikryl P, Ticha M, Kucerova Z. Immobilized endoproteinase Glu-C to magnetic bead cellulose as a tool in proteomic analysis. J Sep Sci 2013; 36:2043-8. [DOI: 10.1002/jssc.201300118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/01/2013] [Accepted: 04/01/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Petr Prikryl
- Institute of Pathological Physiology; First Faculty of Medicine; Charles University; Prague Czech Republic
| | - Marie Ticha
- Institute of Pathological Physiology; First Faculty of Medicine; Charles University; Prague Czech Republic
- Department of Biochemistry; Faculty of Science; Charles University; Prague Czech Republic
| | - Zdenka Kucerova
- Institute of Pathological Physiology; First Faculty of Medicine; Charles University; Prague Czech Republic
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Xiao P, Lv X, Man Y, Qing H, Li Q, Deng Y. Rapid and Efficient Proteolysis for Protein Analysis by an Aptamer-Based Immobilized Chymotrypsin Microreactor. ANAL LETT 2013. [DOI: 10.1080/00032719.2012.733902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Vlakh EG, Tennikova TB. Flow-through immobilized enzyme reactors based on monoliths: II. Kinetics study and application. J Sep Sci 2013; 36:1149-67. [DOI: 10.1002/jssc.201201090] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 12/17/2012] [Accepted: 12/17/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Evgenia G. Vlakh
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
| | - Tatiana B. Tennikova
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
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Yamaguchi H, Miyazaki M. Enzyme-immobilized reactors for rapid and efficient sample preparation in MS-based proteomic studies. Proteomics 2013; 13:457-66. [DOI: 10.1002/pmic.201200272] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 11/03/2012] [Accepted: 11/14/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Hiroshi Yamaguchi
- Liberal Arts Education Center; Tokai University; Minamiaso Kumamoto Japan
| | - Masaya Miyazaki
- Measurement Solution Research Center; National Institute of Advanced Industrial Science and Technology; Tosu Saga Japan
- Interdisciplinary Graduate School of Engineering Science; Kyushu University; Kasuga Fukuoka Japan
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Vlakh EG, Tennikova TB. Flow-through immobilized enzyme reactors based on monoliths: I. Preparation of heterogeneous biocatalysts. J Sep Sci 2013; 36:110-27. [DOI: 10.1002/jssc.201200594] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/13/2012] [Accepted: 08/13/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Evgenia G. Vlakh
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
| | - Tatiana B. Tennikova
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
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Abstract
In the past years, capillary electrophoresis has become a frequently used technique for enzyme assays due to the high separation efficiency and versatility as well as small sample size and low consumption of chemicals. The capillary electrophoresis assays can be divided into two general categories: pre-capillary (or offline) assays and in-capillary (or online) assays. In pre-capillary assays, the incubation is performed offline and substrate(s) and product(s) are subsequently analyzed by capillary electrophoresis. In in-capillary assays enzyme reaction and separation of the analytes are performed inside the same capillary. In such assays the enzyme is either immobilized or in solution. The latter techniques is also referred to as electrophoretically mediated microanalysis (EMMA) indicating that the individual steps of the incubation as well as analysis are performed via electrophoretic phenomena. This chapter describes both techniques using the deacetylation of acetyl-lysine residues in model peptides by sirtuin enzymes as well as the hydrolysis of acetylthiocholine by acetylcholinesterase as examples.
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Affiliation(s)
- Gerhard K E Scriba
- Department of Pharmaceutical Chemistry, School of Pharmacy, Friedrich Schiller University, Jena, Germany.
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Rigobello-Masini M, Penteado JCP, Masini JC. Monolithic columns in plant proteomics and metabolomics. Anal Bioanal Chem 2012; 405:2107-22. [DOI: 10.1007/s00216-012-6574-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 11/02/2012] [Accepted: 11/13/2012] [Indexed: 12/16/2022]
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Rodríguez Gastón JA, Costa H, Rossi AL, Krymkiewicz N, Ferrarotti SA. Maltooligosaccharides production catalysed by cyclodextrin glycosyltransferase from Bacillus circulans DF 9R in batch and continuous operation. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Guedidi S, Portugal CA, Innocent C, Janot JM, Deratani A, Crespo JG. Fluorescence monitoring of trypsin adsorption in layer-by-layer membrane systems. Enzyme Microb Technol 2012; 51:325-33. [DOI: 10.1016/j.enzmictec.2012.07.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/21/2012] [Accepted: 07/27/2012] [Indexed: 01/06/2023]
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Shi J, Zhao W, Chen Y, Guo L, Yang L. A replaceable dual-enzyme capillary microreactor using magnetic beads and its application for simultaneous detection of acetaldehyde and pyruvate. Electrophoresis 2012; 33:2145-51. [PMID: 22821491 DOI: 10.1002/elps.201200090] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A novel replaceable dual-enzyme capillary microreactor was developed and evaluated using magnetic fields to immobilize the alcohol dehydrogenase (ADH)- and lactate dehydrogenase (LDH)-coated magnetic beads at desired positions in the capillary. The dual-enzyme assay was achieved by measuring the two consumption peaks of the coenzyme β-nicotinamide adenine dinucleotide (NADH), which were related to the ADH reaction and LDH reaction. The dual-enzyme capillary microreactor was constructed using magnetic beads without any modification of the inner surface of the capillary, and showed great stability and reproducibility. The electrophoretic resolution for different analytes can be easily controlled by altering the relative distance of different enzyme-coated magnetic beads. The apparent K(m) values for acetaldehyde with ADH-catalyzed reaction and for pyruvate with LDH-catalyzed reaction were determined. The detection limits for acetaldehyde and pyruvate determination are 0.01 and 0.016 mM (S/N = 3), respectively. The proposed method was successfully applied to simultaneously determine the acetaldehyde and pyruvate contents in beer samples. The results indicated that combing magnetic beads with CE is of great value to perform replaceable and controllable multienzyme capillary microreactor for investigation of a series of enzyme reactions and determination of multisubstrates.
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Affiliation(s)
- Jing Shi
- Faculty of Chemistry, Northeast Normal University, Changchun, Jilin, P. R. China
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