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Rejeeth C, Sharma A. Label-free designed nanomaterials enrichment and separation techniques for phosphoproteomics based on mass spectrometry. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.1047055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The surface chemical characteristics of nanomaterials have a substantial impact on the affinity probe used to enrich proteins and peptides for MALDI-MS analysis of a real human sample. Detecting phosphoproteins involved in signalling is always difficult, even with recent developments in mass spectrometry, because protein phosphorylation is often temporary from complicated mixtures. This review summarizes current research on the successful enrichment of various intriguing glycoproteins and glycol peptides using surface affinity materials with distinctive qualities such as low cost, excellent structural stability, diversity, and multifunction. As a consequence, this review will provide a quick overview of the scholars from various backgrounds who are working in this intriguing interdisciplinary field. Label-free cancer biomarkers and other diseases will benefit from future challenges.
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2
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Designing robust nano-biocatalysts using nanomaterials as multifunctional carriers - expanding the application scope of bio-enzymes. Top Catal 2022. [DOI: 10.1007/s11244-022-01657-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Cluster-Assembled Nanoporous Super-Hydrophilic Smart Surfaces for On-Target Capturing and Processing of Biological Samples for Multi-Dimensional MALDI-MS. Molecules 2022; 27:molecules27134237. [PMID: 35807482 PMCID: PMC9268371 DOI: 10.3390/molecules27134237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/21/2022] [Accepted: 06/26/2022] [Indexed: 12/10/2022] Open
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) on cluster-assembled super-hydrophilic nanoporous titania films deposited on hydrophobic conductive-polymer substrates feature a unique combination of surface properties that significantly improve the possibilities of capturing and processing biological samples before and during the MALDI-MS analysis without changing the selected sample target (multi-dimensional MALDI-MS). In contrast to pure hydrophobic surfaces, such films promote a remarkable biologically active film porosity at the nanoscale due to the soft assembling of ultrafine atomic clusters. This unique combination of nanoscale porosity and super-hydrophilicity provides room for effective sample capturing, while the hydrophilic-hydrophobic discontinuity at the border of the dot-patterned film acts as a wettability-driven containment for sample/reagent droplets. In the present work, we evaluate the performance of such advanced surface engineered reactive containments for their benefit in protein sample processing and characterization. We shortly discuss the advantages resulting from the introduction of the described chips in the MALDI-MS workflow in the healthcare/clinical context and in MALDI-MS bioimaging (MALDI-MSI).
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Amalia S, Angga SC, Iftitah ED, Septiana D, Anggraeny BOD, Warsito, Hasanah AN, Sabarudin A. Immobilization of trypsin onto porous methacrylate-based monolith for flow-through protein digestion and its potential application to chiral separation using liquid chromatography. Heliyon 2021; 7:e07707. [PMID: 34401587 PMCID: PMC8350527 DOI: 10.1016/j.heliyon.2021.e07707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/11/2021] [Accepted: 07/26/2021] [Indexed: 10/27/2022] Open
Abstract
Monolithic columns for analytical applications have attracted the researcher's attention. In this work, the laboratory-made organic-polymer monolithic column is modified with trypsin and further applied as a nanobiocatalyst microreactor and a stationary phase for separating chiral compounds by liquid chromatography. The monolith was synthesized by in-situ copolymerization of glycidyl methacrylate (GMA) and ethylene glycol dimethacrylate (EDMA) or trimethylolpropane trimethacrylate (TRIM) as a crosslinking agent, with porogen of 1,4-butanediol/propanol/water (4:7:1 v/v) and AIBN as the radical polymerization initiator inside PEEK and silicosteel tubings (1.0 mm i.d × 100 mm) at 60 °C for 12 h. A total monomer ratio (%T) and crosslinking agent (%C) of 40:25 and 28:12 were applied to prepare poly-(GMA-co-EDMA) and poly-(GMA-co-TRIM), respectively. The produced monoliths were further modified by introducing trypsin (10 mg/L) through the ring-opening reaction of the epoxide group existing in the monolithic column. The trypsin-immobilized poly-(GMA-co-EDMA) monolithic column was applied as the nanobiocatalyst microreactor for online/flow-through and rapid digestion of β-casein sample into its peptide fragments. The trypsin-immobilized poly-(GMA-co-TRIM) column has potential application to be used as the HPLC stationary phase for the separation of R/S-citronellal enantiomers.
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Affiliation(s)
- Suci Amalia
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia.,Department of Chemistry, Faculty of Science and Technology, Maulana Malik Ibrahim Islamic State University, Malang, 65144, Indonesia
| | - Stevin Carolius Angga
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia
| | - Elvina Dhiaul Iftitah
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia
| | - Dias Septiana
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia
| | | | - Warsito
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia
| | - Aliya Nur Hasanah
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Akhmad Sabarudin
- Department of Chemistry, Faculty of Science, Brawijaya University, Malang, 65154, Indonesia.,Research Center for Advanced System and Material Technology (ASMAT), Brawijaya University, Malang, 65145, Indonesia
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5
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Darren Tan CW, Forsthuber A, Ehmoser EK. Functional proteoliposome-like structure derived from simultaneous evisceration and enucleation of T-lymphoblastoid A3R5.7 cells: A top-down story. Exp Cell Res 2021; 400:112487. [PMID: 33476652 DOI: 10.1016/j.yexcr.2021.112487] [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: 09/16/2020] [Revised: 01/08/2021] [Accepted: 01/10/2021] [Indexed: 10/22/2022]
Abstract
Structurally-reduced cells and cell-derived structures are powerful tools for membrane studies. Using this approach, we probed whether a cell, without its nucleus and cytoplasm, is still capable of undergoing CD4-mediated membrane fusion. For this, we needed a cell-derived structure, akin to a giant liposome functionalised with CD4 and chemokine receptors. We present a method for the simultaneous removal of cytoplasmic and nuclear material from cells presenting CD4, CCR5, and CXCR4, using Colcemid treatment followed by hypotonic cytolysis, and then enriched using preparative flow cytometry. We show that the resultant cell membrane remains intact, retains presentation of CD4, CCR5, and CXCR4, and is still capable of CD4-mediated membrane fusion with a target cell. Finally, we detail how this protocol was developed, as well as how such samples should be handled for storage and assays. We envision the use of such systems for host-pathogen interaction studies, and the development of targeted delivery vehicles.
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Affiliation(s)
- Cherng-Wen Darren Tan
- University of Natural Resources and Life Sciences Vienna, Department of Nanobiotechnology, Institute for Synthetic Bioarchitectures, Muthgasse 11, 1190, Vienna, Austria.
| | - Andreas Forsthuber
- University of Natural Resources and Life Sciences Vienna, Department of Nanobiotechnology, Institute for Synthetic Bioarchitectures, Muthgasse 11, 1190, Vienna, Austria
| | - Eva-Kathrin Ehmoser
- University of Natural Resources and Life Sciences Vienna, Department of Nanobiotechnology, Institute for Synthetic Bioarchitectures, Muthgasse 11, 1190, Vienna, Austria
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6
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Jun SH, Yang J, Jeon H, Kim HS, Pack SP, Jin E, Kim J. Stabilized and Immobilized Carbonic Anhydrase on Electrospun Nanofibers for Enzymatic CO 2 Conversion and Utilization in Expedited Microalgal Growth. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:1223-1231. [PMID: 31899628 DOI: 10.1021/acs.est.9b05284] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Carbonic anhydrases convert CO2 to bicarbonate at a high turnover rate up to 106 s-1, but their actual applications in CO2 conversion processes are hampered by their poor stability. This study reports highly loaded and stabilized bovine carbonic anhydrase (bCA) upon being immobilized onto electrospun polymer nanofibers in the form of enzyme precipitate coating (EPC). The EPC protocol, consisting of enzyme covalent attachment, precipitation, and cross-linking, maintained 65.3% of initial activity even after being incubated in aqueous solution at room temperature under shaking at 200 rpm for 868 days. EPC also showed strong resistance to the treatment of the metal chelation agent, ethylenediaminetetraacetic acid, and molecular dynamic simulation was carried out to elucidate the prevention of metal leaching from the active site of bCA upon being cross-linked in the form of EPC. Highly stable EPC with high bCA loading was employed for the conversion of bubbling CO2 to bicarbonate, and the bicarbonate solution was utilized as a carbon source for expedited microalgae growth in a separate bioreactor. The addition of EPC in the bubbling CO2 reactor resulted in 134 and 231% accelerated microalgae growths compared to the controls with and without 25 mM sodium bicarbonate, respectively. EPC with high enzyme loading and unprecedentedly successful stabilization of enzyme stability has a great potential to be used for the development of various enzyme-mediated CO2 conversion and utilization technologies.
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Affiliation(s)
- Seung-Hyun Jun
- Department of Chemical and Biological Engineering , Korea University , Seoul 02841 , Republic of Korea
| | - Jusang Yang
- Department of Chemical and Biological Engineering , Korea University , Seoul 02841 , Republic of Korea
| | - Hancheol Jeon
- Department of Genetic Resources Research , National Marine Biodiversity Institute of Korea , Seocheon 33662 , Republic of Korea
| | - Han Sol Kim
- Department of Chemical and Biological Engineering , Korea University , Seoul 02841 , Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics , Korea University , Sejong 30019 , Republic of Korea
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Republic of Korea
| | - Jungbae Kim
- Department of Chemical and Biological Engineering , Korea University , Seoul 02841 , Republic of Korea
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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: 6.6] [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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Kim H, Kim HS, Lee D, Shin D, Shin D, Kim J, Kim J. Microwave-Assisted Protein Digestion in a Plate Well for Facile Sampling and Rapid Digestion. Anal Chem 2017; 89:10655-10660. [PMID: 28945068 DOI: 10.1021/acs.analchem.7b02169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein digestion is one of the most important processes in proteomic analysis. Here, we report microwave-assisted protein digestion in a plate well, which allows for facile sampling as well as rapid protein digestion based on the combination of highly stable enzyme immobilization and 3D printing technologies. Trypsin (TR) was immobilized on polystyrene-based nanofibers via an enzyme coating (EC) approach. The EC with stabilized TR activity was assembled with the 3D-printed structure in the plate well (EC/3D), which provides two separated compartments for the solution sampling and the TR-catalyzed protein digestion, respectively. EC/3D can effectively prevent the interference of sampling by accommodating EC in the separated compartment from the sampling hole in the middle. EC/3D in the plate well maintained its protein digestion performance under shaking over 160 days. Microwave irradiation enabled the digestion of bovine serum albumin within 10 min, generating the MALDI-TOF MS results of 75.0% sequence coverage and 61 identified peptides. EC/3D maintained its protein digestion performance under microwave irradiation after 30 times of recycled uses. EC/3D in the plate well has demonstrated its potential as a robust and facile tool for the development of an automated protein digestion platform. The combination of stable immobilized enzymes and 3D-printed structures can be potentially utilized not only for the protein digestion, but also for many other enzyme applications, including bioconversion and biosensors.
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Affiliation(s)
- Hyeonil Kim
- Department of Chemical and Biological Engineering, Korea University , Seoul 02841, Republic of Korea
| | - Han Sol Kim
- Department of Chemical and Biological Engineering, Korea University , Seoul 02841, Republic of Korea
| | - Dabin Lee
- Department of Chemistry, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Dongwon Shin
- Department of Chemistry, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Daeho Shin
- Bio Medical Technologies Co., Ltd., Seoul 04598, Republic of Korea
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University , Seoul 02841, Republic of Korea
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9
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Yan L, Qiao L, Ji J, Li Y, Yin X, Lin L, Liu X, Yao J, Wang Y, Liu B, Qian K, Liu B, Yang P. In-tip nanoreactors for cancer cells proteome profiling. Anal Chim Acta 2017; 949:43-52. [DOI: 10.1016/j.aca.2016.11.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 09/29/2016] [Accepted: 11/02/2016] [Indexed: 12/31/2022]
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10
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Deng J, Lazar IM. Proteolytic Digestion and TiO2 Phosphopeptide Enrichment Microreactor for Fast MS Identification of Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:686-698. [PMID: 26883530 DOI: 10.1007/s13361-015-1332-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/20/2015] [Accepted: 12/27/2015] [Indexed: 06/05/2023]
Abstract
The characterization of phosphorylation state(s) of a protein is best accomplished by using isolated or enriched phosphoprotein samples or their corresponding phosphopeptides. The process is typically time-consuming as, often, a combination of analytical approaches must be used. To facilitate throughput in the study of phosphoproteins, a microreactor that enables a novel strategy for performing fast proteolytic digestion and selective phosphopeptide enrichment was developed. The microreactor was fabricated using 100 μm i.d. fused-silica capillaries packed with 1-2 mm beds of C18 and/or TiO2 particles. Proteolytic digestion-only, phosphopeptide enrichment-only, and sequential proteolytic digestion/phosphopeptide enrichment microreactors were developed and tested with standard protein mixtures. The protein samples were adsorbed on the C18 particles, quickly digested with a proteolytic enzyme infused over the adsorbed proteins, and further eluted onto the TiO2 microreactor for enrichment in phosphopeptides. A number of parameters were optimized to speed up the digestion and enrichments processes, including microreactor dimensions, sample concentrations, digestion time, flow rates, buffer compositions, and pH. The effective time for the steps of proteolytic digestion and enrichment was less than 5 min. For simple samples, such as standard protein mixtures, this approach provided equivalent or better results than conventional bench-top methods, in terms of both enzymatic digestion and selectivity. Analysis times and reagent costs were reduced ~10- to 15-fold. Preliminary analysis of cell extracts and recombinant proteins indicated the feasibility of integration of these microreactors in more advanced workflows amenable for handling real-world biological samples. Graphical Abstract ᅟ.
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Affiliation(s)
- Jingren Deng
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA, 24061, USA
| | - Iulia M Lazar
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA, 24061, USA.
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11
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Lai E, Wang Y, Wei Y, Li G, Ma G. Covalent immobilization of trypsin onto thermo-sensitive poly(N-isopropylacrylamide-co-acrylic acid) microspheres with high activity and stability. J Appl Polym Sci 2016. [DOI: 10.1002/app.43343] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Enping Lai
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering; Donghua University; Shanghai 201620 People's Republic of China
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
| | - Yuxia Wang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
| | - Yi Wei
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
| | - Guang Li
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering; Donghua University; Shanghai 201620 People's Republic of China
| | - Guanghui Ma
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
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12
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Silva TR, Rodrigues DP, Rocha JM, Gil MH, Pinto SC, Lopes-da-Silva JA, Guiomar AJ. Immobilization of trypsin onto poly(ethylene terephthalate)/poly(lactic acid) nonwoven nanofiber mats. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.04.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Misson M, Zhang H, Jin B. Nanobiocatalyst advancements and bioprocessing applications. J R Soc Interface 2015; 12:20140891. [PMID: 25392397 PMCID: PMC4277080 DOI: 10.1098/rsif.2014.0891] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/20/2014] [Indexed: 11/12/2022] Open
Abstract
The nanobiocatalyst (NBC) is an emerging innovation that synergistically integrates advanced nanotechnology with biotechnology and promises exciting advantages for improving enzyme activity, stability, capability and engineering performances in bioprocessing applications. NBCs are fabricated by immobilizing enzymes with functional nanomaterials as enzyme carriers or containers. In this paper, we review the recent developments of novel nanocarriers/nanocontainers with advanced hierarchical porous structures for retaining enzymes, such as nanofibres (NFs), mesoporous nanocarriers and nanocages. Strategies for immobilizing enzymes onto nanocarriers made from polymers, silicas, carbons and metals by physical adsorption, covalent binding, cross-linking or specific ligand spacers are discussed. The resulting NBCs are critically evaluated in terms of their bioprocessing performances. Excellent performances are demonstrated through enhanced NBC catalytic activity and stability due to conformational changes upon immobilization and localized nanoenvironments, and NBC reutilization by assembling magnetic nanoparticles into NBCs to defray the high operational costs associated with enzyme production and nanocarrier synthesis. We also highlight several challenges associated with the NBC-driven bioprocess applications, including the maturation of large-scale nanocarrier synthesis, design and development of bioreactors to accommodate NBCs, and long-term operations of NBCs. We suggest these challenges are to be addressed through joint collaboration of chemists, engineers and material scientists. Finally, we have demonstrated the great potential of NBCs in manufacturing bioprocesses in the near future through successful laboratory trials of NBCs in carbohydrate hydrolysis, biofuel production and biotransformation.
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Affiliation(s)
- Mailin Misson
- School of Chemical Engineering, The University of Adelaide, Adelaide, South A, ustralia 5000, Australia Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Hu Zhang
- School of Chemical Engineering, The University of Adelaide, Adelaide, South A, ustralia 5000, Australia
| | - Bo Jin
- School of Chemical Engineering, The University of Adelaide, Adelaide, South A, ustralia 5000, Australia
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14
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Yang D, Wang X, Ai Q, Shi J, Jiang Z. Performance comparison of immobilized enzyme on the titanate nanotube surfaces modified by poly(dopamine) and poly(norepinephrine). RSC Adv 2015. [DOI: 10.1039/c5ra02420j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In this study, the performance of immobilized enzyme on the titanate nanotube surfaces modified by poly(dopamine) and poly(norepinephrine) are specifically compared.
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Affiliation(s)
- Dong Yang
- Key Laboratory for Green Chemical Technology of Ministry of Education
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Xueyan Wang
- Key Laboratory for Green Chemical Technology of Ministry of Education
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Qinghong Ai
- Key Laboratory for Green Chemical Technology of Ministry of Education
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jiafu Shi
- Key Laboratory for Green Chemical Technology of Ministry of Education
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Zhongyi Jiang
- Key Laboratory for Green Chemical Technology of Ministry of Education
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
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15
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Li Y, Yan L, Liu Y, Qian K, Liu B, Yang P, Liu B. High-efficiency nano/micro-reactors for protein analysis. RSC Adv 2015. [DOI: 10.1039/c4ra12333f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This article reviews the recent advances regarding the development of nanomaterial-based nanoreactors and microfluidic droplet reactors and their applications in protein analysis.
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Affiliation(s)
- Yixin Li
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Ling Yan
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Yun Liu
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Kun Qian
- Center for Bio-Nano-Chips and Diagnostics in Translational Medicine
- School of Biomedical Engineering and Med-X Research Institute
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Bin Liu
- Center for Bio-Nano-Chips and Diagnostics in Translational Medicine
- School of Biomedical Engineering and Med-X Research Institute
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Baohong Liu
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
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16
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Dittrich J, Becker S, Hecht M, Ceglarek U. Sample preparation strategies for targeted proteomics via proteotypic peptides in human blood using liquid chromatography tandem mass spectrometry. Proteomics Clin Appl 2014; 9:5-16. [PMID: 25418444 DOI: 10.1002/prca.201400121] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/29/2014] [Accepted: 11/18/2014] [Indexed: 11/07/2022]
Abstract
The simultaneous quantification of protein concentrations via proteotypic peptides in human blood by liquid chromatography coupled to quadrupole MS/MS is an important field of bioanalytical research with a high potential for routine diagnostic applications. This review summarizes currently available sample preparation procedures and trends for absolute protein quantification in blood using LC-MS/MS. It discusses approaches of transferring established qualitative protocols to a quantitative analysis regarding their reliability and reproducibility. Techniques used to enhance method sensitivity such as the depletion of high-abundant proteins or the immunoaffinity enrichment of proteins and peptides are described. Furthermore, workflows for (i) protein denaturation, (ii) disulfide bridge reduction and (iii) thiol alkylation as well as (iv) enzymatic digestion for absolute protein quantification are presented. The main focus is on the tryptic digestion as a bottleneck of protein quantification via proteotypic peptides. Conclusively, requirements for a high-throughput application are discussed.
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Affiliation(s)
- Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
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17
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da Costa JP, Oliveira-Silva R, Daniel-da-Silva AL, Vitorino R. Bionanoconjugation for Proteomics applications — An overview. Biotechnol Adv 2014; 32:952-70. [DOI: 10.1016/j.biotechadv.2014.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/15/2014] [Accepted: 04/26/2014] [Indexed: 12/29/2022]
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18
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Xu J, Sun J, Wang Y, Sheng J, Wang F, Sun M. Application of iron magnetic nanoparticles in protein immobilization. Molecules 2014; 19:11465-86. [PMID: 25093986 PMCID: PMC6270831 DOI: 10.3390/molecules190811465] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/09/2014] [Accepted: 07/09/2014] [Indexed: 12/18/2022] Open
Abstract
Due to their properties such as superparamagnetism, high surface area, large surface-to-volume ratio, easy separation under external magnetic fields, iron magnetic nanoparticles have attracted much attention in the past few decades. Various modification methods have been developed to produce biocompatible magnetic nanoparticles for protein immobilization. This review provides an updated and integrated focus on the fabrication and characterization of suitable magnetic iron nanoparticle-based nano-active materials for protein immobilization.
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Affiliation(s)
- Jiakun Xu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
| | - Jingjing Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
| | - Yuejun Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
| | - Jun Sheng
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
| | - Fang Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
| | - Mi Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
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Graphene-based nanobiocatalytic systems: recent advances and future prospects. Trends Biotechnol 2014; 32:312-20. [PMID: 24794165 DOI: 10.1016/j.tibtech.2014.04.004] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/29/2014] [Accepted: 04/02/2014] [Indexed: 01/06/2023]
Abstract
Graphene-based nanomaterials are particularly useful nanostructured materials that show great promise in biotechnology and biomedicine. Owing to their unique structural features, exceptional chemical, electrical, and mechanical properties, and their ability to affect the microenvironment of biomolecules, graphene-based nanomaterials are suitable for use in various applications, such as immobilization of enzymes. We present the current advances in research on graphene-based nanomaterials used as novel scaffolds to build robust nanobiocatalytic systems. Their catalytic behavior is affected by the nature of enzyme-nanomaterial interactions and, thus, the availability of methods to couple enzymes with nanomaterials is an important issue. We discuss the implications of such interactions along with future prospects and possible challenges in this rapidly developing area.
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20
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Wu HJ, Li Y, Fan J, Deng Z, Hu Z, Liu X, Graviss EA, Ferrari M, Ma X, Hu Y. Antibody-free detection of Mycobacterium tuberculosis antigen using customized nanotraps. Anal Chem 2014; 86:1988-96. [PMID: 24446580 PMCID: PMC3983014 DOI: 10.1021/ac4027669] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Rapid
screening and diagnosis of tuberculosis disease (TB) is still
challenging and critically needed for global TB control efforts. In
this study, we present a rapid and streamlined technology, using precisely
engineered silica nanopore thin films, which are optimized for pore
size, structure, capillary force, and film thickness, to isolate Mycobacterium tuberculosis (MTB) antigens in laboratory
and clinical samples for rapid TB screening. This technology, referred
to here as on-chip fractionation, is integrated with high-throughput
matrix-assisted laser desorption/ionization time-of flight mass spectrometry
to screen and identify fragments of the MTB antigen, CFP-10, from
complex biological samples, without use of immunoaffinity agents.
With the use of this comprehensive approach, we were able to clearly
distinguish a clinical isolate of MTB from a nonTB species of the
genus Mycobacterium avium grown in
liquid culture media. This assay can reach a detection limit of 10
fmol and an isolation rate of 90% for the antigen CFP-10. Our strategy
has significant potential to fill the conceptual and technical gaps
in rapid diagnosis of active TB disease.
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Affiliation(s)
- Hung-Jen Wu
- Department of Nanomedicine, Houston Methodist Research Institute , 6670 Bertner Avenue R8-213, Houston, TX 77030, United States
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21
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Eum JY, Hwang SY, Ju Y, Shim JM, Piao Y, Lee J, Kim HS, Kim J. A highly sensitive immunoassay using antibody-conjugated spherical mesoporous silica with immobilized enzymes. Chem Commun (Camb) 2014; 50:3546-8. [DOI: 10.1039/c3cc48044e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Walmsley SJ, Rudnick PA, Liang Y, Dong Q, Stein SE, Nesvizhskii AI. Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics. J Proteome Res 2013; 12:5666-80. [PMID: 24116745 DOI: 10.1021/pr400611h] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Trypsin is an endoprotease commonly used for sample preparation in proteomics experiments. Importantly, protein digestion is dependent on multiple factors, including the trypsin origin and digestion conditions. In-depth characterization of trypsin activity could lead to improved reliability of peptide detection and quantitation in both targeted and discovery proteomics studies. To this end, we assembled a data analysis pipeline and suite of visualization tools for quality control and comprehensive characterization of preanalytical variability in proteomics experiments. Using these tools, we evaluated six available proteomics-grade trypsins and their digestion of a single purified protein, human serum albumin (HSA). HSA was aliquoted and then digested for 2 or 18 h for each trypsin, and the resulting digests were desalted and analyzed in triplicate by reversed-phase liquid chromatography-tandem mass spectrometry. Peptides were identified and quantified using the NIST MSQC pipeline and a comprehensive HSA mass spectral library. We performed a statistical analysis of peptide abundances from different digests and further visualized the data using the principal component analysis and quantitative protein "sequence maps". While the performance of individual trypsins across repeat digests was reproducible, significant differences were observed depending on the origin of the trypsin (i.e., bovine vs porcine). Bovine trypsins produced a higher number of peptides containing missed cleavages, whereas porcine trypsins produced more semitryptic peptides. In addition, many cleavage sites showed variable digestion kinetics patterns, evident from the comparison of peptide abundances in 2 h vs 18 h digests. Overall, this work illustrates effects of an often neglected source of variability in proteomics experiments: the origin of the trypsin.
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Affiliation(s)
- Scott J Walmsley
- Department of Pathology, University of Michigan , 4237 Medical Science I, 1301 Catherine Road, Ann Arbor, Michigan 48109, United States
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23
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Liu S, Bao H, Zhang L, Chen G. Efficient proteolysis strategies based on microchip bioreactors. J Proteomics 2013; 82:1-13. [DOI: 10.1016/j.jprot.2013.02.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 02/09/2013] [Accepted: 02/13/2013] [Indexed: 01/19/2023]
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24
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Wang MF, Mu YY, Qi W, Su RX, He ZM. Intensive Protein Digestion Using Cross-Linked Trypsin Aggregates in Proteomics Analysis. Chempluschem 2013. [DOI: 10.1002/cplu.201200323] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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25
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Switzar L, Giera M, Niessen WMA. Protein Digestion: An Overview of the Available Techniques and Recent Developments. J Proteome Res 2013; 12:1067-77. [DOI: 10.1021/pr301201x] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Switzar
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Martin Giera
- Division of Molecular Cell Physiology,
Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilfried M. A. Niessen
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
- hyphen MassSpec, de Wetstraat 8, 2332 XT Leiden, The Netherlands
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26
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Wang LB, Wang YC, He R, Zhuang A, Wang X, Zeng J, Hou JG. A new nanobiocatalytic system based on allosteric effect with dramatically enhanced enzymatic performance. J Am Chem Soc 2013; 135:1272-5. [PMID: 23317038 DOI: 10.1021/ja3120136] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report a rational design of CaHPO(4)-α-amylase hybrid nanobiocatalytic system based on allosteric effect and an explanation of the increase in catalytic activity when certain enzymes are immobilized in specific nanomaterials. Employing a calcification approach in aqueous solutions, we acquired such new nanobiocatalytic systems with three different morphologies, i.e., nanoflowers, nanoplates, and parallel hexahedrons. Through studying enzymatic performance of these systems and free α-amylase with/without Ca(2+), we demonstrated how two factors, allosteric regulation and morphology of the as-synthesized nanostructures, predominantly influence enzymatic activity. Benefiting from both the allosteric modulation and its hierarchical structure, CaHPO(4)-α-amylase hybrid nanoflowers exhibited dramatically enhanced enzymatic activity. As a bonus, the new system we devised was found to enjoy higher stability and durability than free α-amylase plus Ca(2+).
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Affiliation(s)
- Liang-Bing Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, PR China
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27
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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: 3.8] [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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28
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Shen Y, Guo W, Qi L, Qiao J, Wang F, Mao L. Immobilization of trypsin via reactive polymer grafting from magnetic nanoparticles for microwave-assisted digestion. J Mater Chem B 2013; 1:2260-2267. [DOI: 10.1039/c3tb20116c] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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29
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Jiao J, Miao A, Zhang X, Cai Y, Lu Y, Zhang Y, Lu H. Realization of on-tissue protein identification by highly efficient in situ digestion with graphene-immobilized trypsin for MALDI imaging analysis. Analyst 2013; 138:1645-8. [DOI: 10.1039/c3an36391k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Li Y, Zhang X, Deng C. Functionalized magnetic nanoparticles for sample preparation in proteomics and peptidomics analysis. Chem Soc Rev 2013; 42:8517-39. [DOI: 10.1039/c3cs60156k] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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31
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Mogil’naya OA, Bondar VS. Comparative study of antibacterial properties of Lysozyme upon its adsorption and covalent binding to nanodiamonds. ACTA ACUST UNITED AC 2012. [DOI: 10.1134/s1995078012060080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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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: 1.7] [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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33
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Ahn J, Jung MC, Wyndham K, Yu YQ, Engen JR. Pepsin immobilized on high-strength hybrid particles for continuous flow online digestion at 10,000 psi. Anal Chem 2012; 84:7256-62. [PMID: 22856522 DOI: 10.1021/ac301749h] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Pepsin was immobilized on ethyl-bridged hybrid (BEH) particles, and digestion performance was evaluated in a completely online format, with the specific intent of using the particles for hydrogen-deuterium exchange mass spectrometry (HDX MS) experiments. Because the BEH particles are mechanically strong, they could withstand prolonged, continuous high-pressure at 10,000 psi. Online digestion was performed under isobaric conditions with continuous solvent flow, in contrast to other approaches where the pressure or flow is cycled. As expected, digestion efficiency at 10,000 psi was increased and reproducibly produced more peptic peptides versus digestion at 1000 psi. Prototype columns made with the BEH pepsin particles exhibited robust performance, and deuterium back-exchange was similar to that of other immobilized pepsin particles. These particles can be easily incorporated in existing HDX MS workflows to provide more peptide coverage in experiments where fast, efficient, and reproducible online pepsin digestion is desired.
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Affiliation(s)
- Joomi Ahn
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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34
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Abstract
A newcomer to the -omics era, proteomics, is a broad instrument-intensive research area that has advanced rapidly since its inception less than 20 years ago. Although the 'wet-bench' aspects of proteomics have undergone a renaissance with the improvement in protein and peptide separation techniques, including various improvements in two-dimensional gel electrophoresis and gel-free or off-gel protein focusing, it has been the seminal advances in MS that have led to the ascension of this field. Recent improvements in sensitivity, mass accuracy and fragmentation have led to achievements previously only dreamed of, including whole-proteome identification, and quantification and extensive mapping of specific PTMs (post-translational modifications). With such capabilities at present, one might conclude that proteomics has already reached its zenith; however, 'capability' indicates that the envisioned goals have not yet been achieved. In the present review we focus on what we perceive as the areas requiring more attention to achieve the improvements in workflow and instrumentation that will bridge the gap between capability and achievement for at least most proteomes and PTMs. Additionally, it is essential that we extend our ability to understand protein structures, interactions and localizations. Towards these ends, we briefly focus on selected methods and research areas where we anticipate the next wave of proteomic advances.
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35
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Ansari SA, Husain Q. Potential applications of enzymes immobilized on/in nano materials: A review. Biotechnol Adv 2012; 30:512-23. [DOI: 10.1016/j.biotechadv.2011.09.005] [Citation(s) in RCA: 834] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 08/26/2011] [Accepted: 09/12/2011] [Indexed: 12/15/2022]
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36
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Nanomaterials for Sensing Applications: Introduction and Perspective. SPRINGER SERIES ON CHEMICAL SENSORS AND BIOSENSORS 2012. [DOI: 10.1007/5346_2012_41] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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37
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Li Z, Ruan W, Song W, Xue X, Mao Z, Ji W, Zhao B. SERS detection of protein biochip fabricated by etching polystyrene template. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 82:456-460. [PMID: 21852186 DOI: 10.1016/j.saa.2011.07.077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 07/21/2011] [Indexed: 05/31/2023]
Abstract
In this study, a nanoscale protein chip is prepared by using an etched polystyrene (PS) template. This protein chip can be directly used for immunoassay, with the help of Surface Enhanced Raman Scattering (SERS) spectra. Some glass slides submerged in aldehyde is initially prepared, modified with antibodies, human immunoglobulin G (IgG). Then PS arrays are self-assembled on these slides with the Langmuir-Blodgett method. The PS template pattern is transferred to the human IgG substrate using an etching process-slides are exposed to O(2) plasma for 90s. The PS nanoparticles are then washed away using phosphate buffered saline solution. Next, the slides are dipped into bovine serum albumin solution to ensure that the anti IgG would bond only to the human IgG. At this moment, a patterned protein chip is obtained. When used for protein detection, the protein chip could be immersed into labeled specificity antigen solution. Here we chose fluorescein isothiocyanate anti-human IgG. After washing, only bonded antigens remain. Fluorescence microscopy and SERS is used to characterize the samples. The SERS spectra intensity shows liner correlation with the concentration of anti-human IgG. All the experiments are conducted in a phosphate buffered saline solution at 37°C for 2 h.
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Affiliation(s)
- Zhishi Li
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
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38
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Abstract
The completion of the human genome project has led to intensified efforts toward comprehensive analysis of proteomes. New possibilities exist for efficient proteomic technologies. However, primary attention is given to the discovery of new predictive biomarker patterns. Understanding proteomes and, in particular, protein-mediated interactions underlying their complexity and diversity, is critical for the development of more reliable and robust diagnostic platforms, which are anticipated to enable personalized medicine. Of immediate relevance in this respect are those approaches that capitalize on the application of nanotechnology, which is seen as a powerful tool for the diagnosis of early-stage diseases. Here we highlight the current state of the field exemplified by recent nano-enabled technologies for biomarker discovery.
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Savino R, Casadonte F, Terracciano R. In mesopore protein digestion: a new forthcoming strategy in proteomics. Molecules 2011; 16:5938-62. [PMID: 21765391 PMCID: PMC6264412 DOI: 10.3390/molecules16075938] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 07/07/2011] [Accepted: 07/13/2011] [Indexed: 01/11/2023] Open
Abstract
The conventional protocols for in solution or in gel protein digestion require many steps and long reaction times. The use of trypsin immobilized onto solid supports has recently captured the attention of many research groups, because these systems can speed-up protein digestion significantly. The utilization of new materials such as mesoporous silica as supports, in which enzyme and substrate are dramatically concentrated and confined in the nanospace, offers new opportunities to reduce the complexity of proteomics workflows. An overview of the procedures for in situ proteolysis of single proteins or complex protein mixtures is reported, with a special focus on porous materials used as catalysts. The challenging efforts for designing such systems aimed at mimicking the biochemistry of living cells are reviewed. Potentials, limitations and challenges of this branch of enzyme catalysis, which we indicate as in mesopore digestion, are discussed, in relation to its suitability for high-speed and high-throughput proteomics.
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Affiliation(s)
| | | | - Rosa Terracciano
- Author to whom correspondence should be addressed; ; Tel.: +39-0961-3694085; Fax: +39-0961-3694090
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40
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Zheng M, Zhang S, Ma G, Wang P. Effect of molecular mobility on coupled enzymatic reactions involving cofactor regeneration using nanoparticle-attached enzymes. J Biotechnol 2011; 154:274-80. [PMID: 21684312 DOI: 10.1016/j.jbiotec.2011.04.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 04/06/2011] [Accepted: 04/18/2011] [Indexed: 10/18/2022]
Abstract
Cofactor-dependent multi-step enzymatic reactions generally require dynamic interactions among cofactor, enzyme and substrate molecules. Maintaining such molecular interactions can be quite challenging especially when the catalysts are tethered to solid state supports for heterogeneous catalysis for either biosynthesis or biosensing. The current work examines the effects of the pattern of immobilization, which presumably impacts molecular interactions on the surface of solid supports, on the reaction kinetics of a multienzymic system including glutamate dehydrogenase, glucose dehydrogenase and cofactor NAD(H). Interestingly, particle collision due to Brownian motion of nanoparticles successfully enabled the coupled reactions involving a regeneration cycle of NAD(H) even when the enzymes and cofactor were immobilized separately onto superparamagnetic nanoparticles (124 nm). The impact of particle motion and collision was evident in that the overall reaction rate was increased by over 100% by applying a moderate alternating magnetic field (500 Hz, 17 Gs), or using additional spacers, both of which could improve the mobility of the immobilized catalysts. We further observed that integrated immobilization, which allowed the cofactor to be placed in the molecular vicinity of enzymes on the same nanoparticles, could enhance the reaction rate by 1.8 fold. These results demonstrated the feasibility in manipulating molecular interactions among immobilized catalyst components by using nanoscale fabrication for efficient multienzymic biosynthesis.
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Affiliation(s)
- Muqing Zheng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
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41
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42
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Novel nanotechnology approaches to diagnosis and therapy of ovarian cancer. Gynecol Oncol 2011; 120:393-403. [DOI: 10.1016/j.ygyno.2010.11.029] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 11/17/2010] [Accepted: 11/17/2010] [Indexed: 12/22/2022]
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43
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Jun SH, Chang MS, Kim BC, An HJ, Lopez-Ferrer D, Zhao R, Smith RD, Lee SW, Kim J. Trypsin coatings on electrospun and alcohol-dispersed polymer nanofibers for a trypsin digestion column. Anal Chem 2011; 82:7828-34. [PMID: 20718428 DOI: 10.1021/ac101633e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The construction of a trypsin column for rapid and efficient protein digestion in proteomics is described. Electrospun and alcohol-dispersed polymer nanofibers were used for the fabrication of highly stable trypsin coatings, which were prepared by a two-step process of covalent attachment and enzyme cross-linking. In a comparative study with the trypsin coatings on as-spun and nondispersed nanofibers, it has been observed that a simple step of alcohol dispersion improved not only the enzyme loading but also the performance of protein digestion. In-column digestion of enolase was successfully performed in less than 20 min. By applying the alcohol dispersion of polymer nanofibers, the bypass of samples was reduced by filling up the column with well-dispersed nanofibers, and subsequently, interactions between the protein and the trypsin coatings were improved, yielding more complete and reproducible digestions. Regardless of alcohol dispersion or not, trypsin coatings showed better digestion performance and improved performance stability under recycled uses than covalently attached trypsin, in-solution digestion, and commercial trypsin beads. The combination of highly stable trypsin coatings and alcohol dispersion of polymer nanofibers has opened up a new potential to develop a trypsin column for online and automated protein digestion.
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Affiliation(s)
- Seung-Hyun Jun
- Department of Chemical and Biological Engineering, Korea University, 1, 5-ka, Anam-dong, Seongbuk-gu, Seoul 136-701, Republic of Korea
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44
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Xu F, Wang WH, Tan YJ, Bruening ML. Facile trypsin immobilization in polymeric membranes for rapid, efficient protein digestion. Anal Chem 2010; 82:10045-51. [PMID: 21087034 PMCID: PMC3052767 DOI: 10.1021/ac101857j] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sequential adsorption of poly(styrene sulfonate) and trypsin in nylon membranes provides a simple, inexpensive method to create stable, microporous reactors for fast protein digestion. The high local trypsin concentration and short radial diffusion distances in membrane pores facilitate proteolysis in residence times of a few seconds, and the minimal pressure drop across the thin membranes allows their use in syringe filters. Membrane digestion and subsequent MS analysis of bovine serum albumin provide 84% sequence coverage, which is higher than the 71% coverage obtained with in-solution digestion for 16 h or the <50% sequence coverages of other methods that employ immobilized trypsin. Moreover, trypsin-modified membranes digest protein in the presence of 0.05 wt % sodium dodecyl sulfate (SDS), whereas in-solution digestion under similar conditions yields no peptide signals in mass spectra even after removal of SDS. These membrane reactors, which can be easily prepared in any laboratory, have a shelf life of several months and continuously digest protein for at least 33 h without significant loss of activity.
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Affiliation(s)
| | | | - Yu-Jing Tan
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
| | - Merlin L. Bruening
- Department of Chemistry, Michigan State University, East Lansing, MI 48824
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45
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Lee SM, Nair S, Ahn HK, Kim BS, Jun SH, An HJ, Hsiao E, Kim SH, Koo YM, Kim J. Property control of enzyme coatings on polymer nanofibers by varying the conjugation site concentration. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2010.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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