51
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Kim J, Kim BC, Lopez-Ferrer D, Petritis K, Smith RD. Nanobiocatalysis for protein digestion in proteomic analysis. Proteomics 2010; 10:687-99. [PMID: 19953546 DOI: 10.1002/pmic.200900519] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The process of protein digestion is a critical step for successful protein identification in bottom-up proteomic analyses. To substitute the present practice of in-solution protein digestion, which is long, tedious, and difficult to automate, many efforts have been dedicated for the development of a rapid, recyclable and automated digestion system. Recent advances of nanobiocatalytic approaches have improved the performance of protein digestion by using various nanomaterials such as nanoporous materials, magnetic nanoparticles, and polymer nanofibers. Especially, the unprecedented success of trypsin stabilization in the form of trypsin-coated nanofibers, showing no activity decrease under repeated uses for 1 year and retaining good resistance to proteolysis, has demonstrated its great potential to be employed in the development of automated, high-throughput, and on-line digestion systems. This review discusses recent developments of nanobiocatalytic approaches for the improved performance of protein digestion in speed, detection sensitivity, recyclability, and trypsin stability. In addition, we also introduce approaches for protein digestion under unconventional energy input for protein denaturation and the development of microfluidic enzyme reactors that can benefit from recent successes of these nanobiocatalytic approaches.
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Affiliation(s)
- Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Anam-dong, Seongbuk-gu, Seoul, Republic of Korea.
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52
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Yamaguchi H, Miyazaki M, Maeda H. Proteolysis approach without chemical modification for a simple and rapid analysis of disulfide bonds using thermostable protease-immobilized microreactors. Proteomics 2010; 10:2942-9. [DOI: 10.1002/pmic.201000166] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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53
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Dartiguenave C, Hamad H, Waldron KC. Immobilization of trypsin onto 1,4-diisothiocyanatobenzene-activated porous glass for microreactor-based peptide mapping by capillary electrophoresis: Effect of calcium ions on the immobilization procedure. Anal Chim Acta 2010; 663:198-205. [DOI: 10.1016/j.aca.2010.01.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 01/20/2010] [Accepted: 01/22/2010] [Indexed: 10/19/2022]
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54
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Bellino MG, Regazzoni AE, Soler-Illia GJAA. Amylase-functionalized mesoporous silica thin films as robust biocatalyst platforms. ACS APPLIED MATERIALS & INTERFACES 2010; 2:360-365. [PMID: 20356181 DOI: 10.1021/am900645b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A robust biocatalyst was produced by immobilization of alpha-amylase into mesoporous silica thin films with local order pore structure and 11 nm pore diameter, supported on glass stripes. The activity of this novel catalyst was evaluated for direct starch degradation. The catalyst films show excellent activity, and enhanced stability with respect to free enzyme at extreme conditions of pH and temperature. In addition, they can be easily separated from the reaction media and reused several times.
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Affiliation(s)
- Martín G Bellino
- Comision Nacional de Energia Atomica, Centro Atomico Constituyentes, B1650KNA-San Martin, Argentina.
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55
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Abele S, Smejkal P, Yavorska O, Foret F, Macka M. Evanescent wave-initiated photopolymerisation as a new way to create monolithic open-tubular capillary columns: use as enzymatic microreactor for on-line protein digestion. Analyst 2010; 135:477-81. [DOI: 10.1039/b920789a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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56
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Rapid online proteolytic mapping of PEGylated rhGH for identity confirmation, quantitation of methionine oxidation and quantitation of UnPEGylated N-terminus using HPLC with UV detection. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:4065-70. [DOI: 10.1016/j.jchromb.2009.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 10/12/2009] [Accepted: 10/13/2009] [Indexed: 11/23/2022]
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57
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Liu X, Lo RC, Gomez FA. Fabrication of a microfluidic enzyme reactor utilizing magnetic beads. Electrophoresis 2009; 30:2129-33. [PMID: 19582716 DOI: 10.1002/elps.200900041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An enzyme-catalyzed microfluidic assay using magnetic micro-beads is described. Here, diaphorase (DI) (E.C. 1.6.99) is covalently attached to the magnetic micro-beads (2.7 mum) and integrated into a short section of a microchip fabricated from PDMS. DI converts non-fluorescent resazurin to fluorescent resorufin in the presence of nicotinamide adenine dinucleotide phosphate (NADH). In this work, an embedded magnet holds the micro-beads in place within the microchannel while a solution of resazurin and NADH in buffer is flowed through the beads. Incorporation of the micro-beads into the microchannel requires only a few minutes and offers well-defined spatial resolution and reproducibility. At a flow rate of 41.2 microL/h, a stable state for the enzyme reaction in the microfluidic format was achieved within 50 s. The maximum conversion of the reaction was obtained at a concentration of 1.25 mM NADH. The reaction yield is affected by ZnCl(2) and at concentrations in excess of 90.0 mM, the activity of DI was almost double without ZnCl(2). At 5.2 mM potassium chloride, the activity of DI reached its maximum value. Overall, the conversion of resazurin in microfluidic format was more than twice than that in a batch assay.
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Affiliation(s)
- Xiaojun Liu
- Department of Chemistry and Biochemistry, California State University, Los Angeles, CA 90032-8202, USA
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58
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59
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Ma J, Liu J, Sun L, Gao L, Liang Z, Zhang L, Zhang Y. Online Integration of Multiple Sample Pretreatment Steps Involving Denaturation, Reduction, and Digestion with Microflow Reversed-Phase Liquid Chromatography−Electrospray Ionization Tandem Mass Spectrometry for High-Throughput Proteome Profiling. Anal Chem 2009; 81:6534-40. [DOI: 10.1021/ac900971w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junfeng Ma
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinxiang Liu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Liangliang Sun
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Liang Gao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of Chinese Academy of Sciences, Beijing 100039, China
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60
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Temporini C, Calleri E, Cabrera K, Felix G, Massolini G. On-line multi-enzymatic approach for improved sequence coverage in protein analysis. J Sep Sci 2009; 32:1120-8. [PMID: 19301325 DOI: 10.1002/jssc.200800596] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The development of a new mixed bioreactor for proteomic studies based on trypsin and chymotrypsin is described. Trypsin and chymotrypsin were simultaneously bonded to an epoxy monolithic silica column (100 mmx4.6 mm id) in a one-step reaction via epoxy-groups. In order to compare the catalytic properties of the two enzymes in the isolated and in the multi-enzymatic approach, two other single enzyme bioreactors based on trypsin and chymotrypsin were prepared following the same immobilization protocol. The kinetic parameters of the multi-enzymatic bioreactor were derived and it was demonstrated that it retains the individual catalytic activity of the two enzymes. To prove the power of this experimental approach the new mixed bioreactor was integrated in an LC-ESI-MS/MS system for digestion, enrichment, separation and identification of the test protein insulin-like growth factor binding-protein 1 (IGFBP-1). The peptide map and protein sequence coverage obtained with the three bioreactors were compared. The results clearly indicate that the proposed multi-enzyme approach can reduce both digestion and analysis time, accelerate data interpretation and increase the confidence degree in protein identification.
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Affiliation(s)
- Caterina Temporini
- Department of Pharmaceutical Chemistry, University of Pavia, Pavia, Italy.
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61
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Lin W, Skinner CD. Design and optimization of porous polymer enzymatic digestors for proteomics. J Sep Sci 2009; 32:2642-52. [DOI: 10.1002/jssc.200900221] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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62
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Kawakami K, Takahashi R, Shakeri M, Sakai S. Application of a lipase-immobilized silica monolith bioreactor to the production of fatty acid methyl esters. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2008.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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63
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Krenkova J, Svec F. Less common applications of monoliths: IV. Recent developments in immobilized enzyme reactors for proteomics and biotechnology. J Sep Sci 2009; 32:706-18. [PMID: 19194973 PMCID: PMC2766777 DOI: 10.1002/jssc.200800641] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Use of monolithic supports for enzyme immobilization has rapidly expanded since we published the preceding paper in the series of articles concerned with this topic almost three years ago. Many groups worldwide have realized the benefits of applying monoliths as support structures and used a variety of techniques to immobilize many different enzymes. Although some of these new developments are just refinements of the methods developed previously, some notable new approaches have also been reported. This review summarizes the literature published since 2006 and demonstrates the broad variability of reactive monoliths prepared from silica as well as from organic polymers in the form of disks, columns, and capillaries. All these monoliths were prepared by direct formation from reactive precursors or activation of preformed inactive structures. Interestingly, most of the applications of monolithic enzyme reactors target proteolytic digestion of proteins for proteomic analysis.
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Affiliation(s)
- Jana Krenkova
- The Molecular Foundry, E. O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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64
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Qu QS, Wang S, Mangelings D, Wang CY, Yang GJ, Hu XY, Yan C. Monolithic silica xerogel capillary column for separations in capillary LC and pressurized CEC. Electrophoresis 2009; 30:1071-6. [DOI: 10.1002/elps.200800245] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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65
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Nesbitt CA, Yeung KKC. In-capillary enrichment, proteolysis and separation using capillary electrophoresis with discontinuous buffers: application on proteins with moderately acidic and basic isoelectric points. Analyst 2009; 134:65-71. [DOI: 10.1039/b812628c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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66
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SAKAI-KATO K, ISHIKURA K. Integration of Biomolecules into Analytical Systems by Means of Silica Sol-Gel Technology. ANAL SCI 2009; 25:969-78. [DOI: 10.2116/analsci.25.969] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | - Keiko ISHIKURA
- Division of Drugs, National Institute of Health Sciences
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