1
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Mateus P, Delgado R. Zinc(ii) and copper(ii) complexes as tools to monitor/inhibit protein phosphorylation events. Dalton Trans 2020; 49:17076-17092. [DOI: 10.1039/d0dt03503c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A perspective on the advance of copper(ii) and zinc(ii) complexes of varied ligand architectures as binders of phosphorylated peptides/proteins and as sensors of phosphorylation reactions is presented.
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Affiliation(s)
- Pedro Mateus
- Laboratorio Associado para a Química Verde (LAQV)
- Rede de Química e Tecnologia (REQUIMTE)
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
| | - Rita Delgado
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa (ITQB NOVA)
- 2780-157 Oeiras
- Portugal
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2
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Zhou Y, Yin H, Li X, Li Z, Ai S, Lin H. Electrochemical biosensor for protein kinase A activity assay based on gold nanoparticles-carbon nanospheres, phos-tag-biotin and β-galactosidase. Biosens Bioelectron 2016; 86:508-515. [DOI: 10.1016/j.bios.2016.07.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/30/2016] [Accepted: 07/03/2016] [Indexed: 12/19/2022]
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3
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Abstract
On a past volume of this monograph we have reviewed general aspects of the varied technologies available to generate peptide arrays. Hallmarks in the development of the technology and a main sketch of preparative steps and applications in binding assays were used to walk the reader through details of peptide arrays. In this occasion, we resume from that work and bring in some considerations on quantitative evaluation of measurements as well as on selected reports applying the technology.
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Affiliation(s)
| | - Rudolf Volkmer
- Institute of Medical Immunology, Charité-Universitätsmedizin zu Berlin, Hessische Str. 3-4, Berlin, 10115, Germany
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4
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Ikeda H, Yayama Y, Hata A, Kamimoto J, Yamamoto T, Mori T, Katayama Y. PNA-tagged peptide microarrays for ratiometric activity detection of cellular protein kinases. ANAL SCI 2015; 30:631-5. [PMID: 24919666 DOI: 10.2116/analsci.30.631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Peptide microarrays can be used to measure the activity of multiple protein kinases (PKs), which can be used to elucidate kinomics for drug discovery and diagnosis. Here we demonstrated a new microarray for ratiometric detection of the activity of PKs using peptide nucleic acid (PNA)-tagged peptides labeled with two different fluorophores, Cy3 and Cy5. We successfully detected cellular PK activities based on ratiometry, and applied the system for evaluation of an inhibitory drug.
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Affiliation(s)
- Hiromu Ikeda
- Department of Applied Chemistry, Kyushu University
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5
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Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015; 115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Emil Paleček
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Tkáč
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Martin Bartošík
- Regional
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomáš Bertók
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Veronika Ostatná
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Paleček
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, 625 00 Brno, Czech Republic
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6
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Livnat Levanon N, Vigonsky E, Lewinson O. Real time measurements of membrane protein:receptor interactions using Surface Plasmon Resonance (SPR). J Vis Exp 2014:e51937. [PMID: 25489923 DOI: 10.3791/51937] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Protein-protein interactions are pivotal to most, if not all, physiological processes, and understanding the nature of such interactions is a central step in biological research. Surface Plasmon Resonance (SPR) is a sensitive detection technique for label-free study of bio-molecular interactions in real time. In a typical SPR experiment, one component (usually a protein, termed 'ligand') is immobilized onto a sensor chip surface, while the other (the 'analyte') is free in solution and is injected over the surface. Association and dissociation of the analyte from the ligand are measured and plotted in real time on a graph called a sensogram, from which pre-equilibrium and equilibrium data is derived. Being label-free, consuming low amounts of material, and providing pre-equilibrium kinetic data, often makes SPR the method of choice when studying dynamics of protein interactions. However, one has to keep in mind that due to the method's high sensitivity, the data obtained needs to be carefully analyzed, and supported by other biochemical methods. SPR is particularly suitable for studying membrane proteins since it consumes small amounts of purified material, and is compatible with lipids and detergents. This protocol describes an SPR experiment characterizing the kinetic properties of the interaction between a membrane protein (an ABC transporter) and a soluble protein (the transporter's cognate substrate binding protein).
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Affiliation(s)
- Nurit Livnat Levanon
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology
| | - Elena Vigonsky
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology
| | - Oded Lewinson
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology;
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7
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Tyagi D, Perez JB, Nand A, Zhiqiang C, Wang P, Na J, Zhu J. Detection of embryonic stem cell lysate biomarkers by surface plasmon resonance with reduced nonspecific adsorption. Anal Biochem 2014; 471:29-37. [PMID: 25447493 DOI: 10.1016/j.ab.2014.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/29/2014] [Accepted: 11/01/2014] [Indexed: 12/11/2022]
Abstract
Surface plasmon resonance imaging (SPRi) has emerged as a versatile biosensor to detect a wide range of biomolecular interactions with divergent potential applications. However, the use of this advanced-level technology for stem cell lysate study is still not much explored. Cell lysates are significant biological analytes used for disease diagnostics and proteomic studies, but their complex nature limits their use as an analyte for SPRi biosensors. Here, we review the problems associated with the use of SPRi for stem cell lysate study and examine the role of surface chemistry, running buffer, and blocking solution in order to minimize nonspecific adsorption (NSA). We detect the expression of Oct4, Sox2, Nanog, Rex1, and Lin28 biomarkers present in mouse embryonic stem cell (mESC) lysate against their corresponding antibodies immobilized on the sensor surface with reduced NSA. The current study shows that the conjunction of SPRi and microarray can be used as a label-free, high-throughput, and rapid technique for detection of biomarkers and their relative abundance in stem cell lysate study.
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Affiliation(s)
- Deependra Tyagi
- National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Javier Batista Perez
- National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Amita Nand
- National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Zhiqiang
- National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Peizhe Wang
- Centre for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jie Na
- Centre for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jingsong Zhu
- National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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8
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Amplified electrochemical detection of protein kinase activity based on gold nanoparticles/multi-walled carbon nanotubes nanohybrids. Talanta 2014; 129:328-35. [DOI: 10.1016/j.talanta.2014.05.043] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 05/05/2014] [Accepted: 05/07/2014] [Indexed: 11/19/2022]
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9
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Diculescu VC, Enache TA. Electrochemical evaluation of Abelson tyrosine-protein kinase 1 activity and inhibition by imatinib mesylate and danusertib. Anal Chim Acta 2014; 845:23-9. [DOI: 10.1016/j.aca.2014.06.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/12/2014] [Accepted: 06/15/2014] [Indexed: 01/17/2023]
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10
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Gray CJ, Weissenborn MJ, Eyers CE, Flitsch SL. Enzymatic reactions on immobilised substrates. Chem Soc Rev 2014; 42:6378-405. [PMID: 23579870 DOI: 10.1039/c3cs60018a] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.
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Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Road, Manchester, M1 7DN, UK
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11
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Li T, Liu X, Liu D, Wang Z. Sensitive detection of protein kinase A activity in cell lysates by peptide microarray-based assay. Anal Chem 2013; 85:7033-7. [PMID: 23855559 DOI: 10.1021/ac4010502] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In the present work, the activities of protein kinase A (PKA) in cell lysates have been detected by a peptide microarray-based resonance light scattering assay with gold nanoparticle probes. Highly sensitive detection of PKA activity in 0.1 μg total cell proteins of SHG-44 cell lysate (corresponding to 200 cells) is achieved by a selected peptide substrate. The experimental results also demonstrate that the assay can be employed to evaluate expression levels of PKA activity in different cell lines and chemical (e.g., Forskolin )-mediated PKA activity fluctuation in living cells. In addition, PKA inhibition by the inhibitor (H89) is shown, suggesting the potential for screening PKA inhibitors at the living cell level.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P R China
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12
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Li B, Shi X, Gu W, Zhao K, Chen N, Xian Y. Graphene based electrochemical biosensor for label-free measurement of the activity and inhibition of protein tyrosine kinase. Analyst 2013; 138:7212-7. [DOI: 10.1039/c3an01483e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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13
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Knight JDR, Pawson T, Gingras AC. Profiling the kinome: current capabilities and future challenges. J Proteomics 2012; 81:43-55. [PMID: 23099349 DOI: 10.1016/j.jprot.2012.10.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 10/09/2012] [Accepted: 10/14/2012] [Indexed: 01/08/2023]
Abstract
Protein kinases are the second largest human protein family, but in terms of research interest, both basic and applied, they are surely the most popular. Over the past decade, many techniques and approaches for studying the kinome have been described and the pace of development is ever increasing. Presently, a molecular biologist can approach the kinome from many different angles: what kinases are active during a specific cell state of interest or become activated in response to a specific stimulus? What are the effects of controlling the activation status of an individual kinase? What substrates are targeted by a particular kinase, either in general or under particular conditions? And what kinase is responsible for targeting a specific phosphorylation site of interest? These are some of the more commonly asked questions during any kinase-centric research project and different strategies have been devised for answering such queries. In this review, we outline the most promising of these approaches, particularly those with a capacity for high-throughput studies. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Affiliation(s)
- James D R Knight
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
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14
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Electrocatalytic oxidation of tyrosines shows signal enhancement in label-free protein biosensors. Trends Analyt Chem 2012. [DOI: 10.1016/j.trac.2012.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Jung SH, Lee K, Kong DH, Kim WJ, Kim YM, Ha KS. Integrative proteomic profiling of protein activity and interactions using protein arrays. Mol Cell Proteomics 2012; 11:1167-76. [PMID: 22843993 DOI: 10.1074/mcp.m112.016964] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Proteomic studies based on abundance, activity, or interactions have been used to investigate protein functions in normal and pathological processes, but their combinatory approach has not been attempted. We present an integrative proteomic profiling method to measure protein activity and interaction using fluorescence-based protein arrays. We used an on-chip assay to simultaneously monitor the transamidating activity and binding affinity of transglutaminase 2 (TG2) for 16 TG2-related proteins. The results of this assay were compared with confidential scores provided by the STRING database to analyze the functional interactions of TG2 with these proteins. We further created a quantitative activity-interaction map of TG2 with these 16 proteins, categorizing them into seven groups based upon TG2 activity and interaction. This integrative proteomic profiling method can be applied to quantitative validation of previously known protein interactions, and in understanding the functions and regulation of target proteins in biological processes of interest.
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Affiliation(s)
- Se-Hui Jung
- Department of Molecular and Cellular Biochemistry, Kangwon National University School of Medicine, Kangwon-Do, Korea
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16
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Abstract
Enzymes are key molecules in signal-transduction pathways. However, only a small fraction of more than 500 human kinases, 300 human proteases and 200 human phosphatases is characterised so far. Peptide microarray based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimisation of enzyme substrates. Focus of this review is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimisation for kinases. Additionally, several examples for reliable identification of substrates for lysine methyl-transferases, histone deacetylases and SUMO-transferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological samples like cell lysates or lysates of complete organisms is described. All published examples of peptide arrays used for enzyme profiling are summarised comprehensively.
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17
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Jung SH, Kong DH, Park SW, Kim YM, Ha KS. Quantitative kinetics of proteolytic enzymes determined by a surface concentration-based assay using peptide arrays. Analyst 2012; 137:3814-20. [DOI: 10.1039/c2an35080g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Label-free electrochemical measurement of protein tyrosine kinase activity and inhibition based on electro-catalyzed tyrosine signaling. Biosens Bioelectron 2011; 28:284-90. [DOI: 10.1016/j.bios.2011.07.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/29/2011] [Accepted: 07/14/2011] [Indexed: 12/16/2022]
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19
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Coppé JP, Xu Z, Chen Y, Liu GL. Metallic nanocone array photonic substrate for high-uniformity surface deposition and optical detection of small molecules. NANOTECHNOLOGY 2011; 22:245710. [PMID: 21543836 DOI: 10.1088/0957-4484/22/24/245710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Molecular probe arrays printed on solid surfaces such as DNA, peptide, and protein microarrays are widely used in chemical and biomedical applications especially genomic and proteomic studies (Pollack et al 1999 Nat. Genet. 23 41-6, Houseman et al 2002 Nat. Biotechnol. 20 270-4, Sauer et al 2005 Nat. Rev. Genet. 6 465-76) as well as surface imaging and spectroscopy (Mori et al 2008 Anal. Biochem. 375 223-31, Liu et al 2006 Nat. Nanotechnol. 1 47-52, Liu 2010 IEEE J. Sel. Top. Quantum Electron. 16 662-71). Unfortunately the printed molecular spots on solid surfaces often suffer low distribution uniformity due to the lingering 'coffee stain' (Deegan et al 1997 Nature 389 827-9) problem of molecular accumulations and blotches, especially around the edge of deposition spots caused by solvent evaporation and convection processes. Here we present, without any surface chemistry modification, a unique solid surface of high-aspect-ratio silver-coated silicon nanocone arrays that allows highly uniform molecular deposition and thus subsequent uniform optical imaging and spectroscopic molecular detection. Both fluorescent Rhodamine dye molecules and unlabeled oligopeptides are printed on the metallic nanocone photonic substrate surface as circular spot arrays. In comparison with the printed results on ordinary glass slides and silver-coated glass slides, not only high printing density but uniform molecular distribution in every deposited spot is achieved. The high-uniformity and repeatability of molecular depositions on the 'coffee stain'-free nanocone surface is confirmed by laser scanning fluorescence imaging and surface enhanced Raman imaging experiments. The physical mechanism for the uniform molecular deposition is attributed to the superhydrophobicity and localized pinned liquid-solid-air interface on the silver-coated silicon nanocone surface. The unique surface properties of the presented nanocone surface enabled high-density, high-uniformity probe spotting beneficial for genomic and proteomic microarrays and surface molecular imaging.
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20
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SHIMOMURA T, HAN X, HATA A, NIIDOME T, MORI T, KATAYAMA Y. Optimization of Peptide Density on Microarray Surface for Quantitative Phosphoproteomics. ANAL SCI 2011; 27:13-7. [DOI: 10.2116/analsci.27.13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | - Xiaoming HAN
- Department of Applied Chemistry, Kyushu University
| | - Akito HATA
- Department of Applied Chemistry, Kyushu University
| | - Takuro NIIDOME
- Department of Applied Chemistry, Kyushu University
- Center for Future Chemistry, Kyushu University
| | - Takeshi MORI
- Department of Applied Chemistry, Kyushu University
- Center for Future Chemistry, Kyushu University
| | - Yoshiki KATAYAMA
- Department of Applied Chemistry, Kyushu University
- Center for Future Chemistry, Kyushu University
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21
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Zhou G, Sylvester JE, Wu D, Veach DR, Kron SJ. A magnetic bead-based protein kinase assay with dual detection techniques. Anal Biochem 2010; 408:5-11. [PMID: 20807497 DOI: 10.1016/j.ab.2010.08.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 08/17/2010] [Accepted: 08/26/2010] [Indexed: 01/08/2023]
Abstract
A novel magnetic bead-based protein kinase assay was developed using MALDI-TOF mass spectrometry (MALDI-TOF MS) and immunochemifluorescence as two independent detection techniques. Abltide substrate was immobilized onto magnetic beads via noncovalent biotin-streptavidin interactions. This noncovalent immobilization strategy facilitated peptide release and allowed MALDI-TOF MS analysis of substrate phosphorylation. The use of magnetic beads provided rapid sample handling and allowed secondary analysis by immunochemifluorescence to determine the degree of substrate phosphorylation. This dual detection technique was used to evaluate the inhibition of c-Abl kinase by imatinib and dasatinib. For each inhibitor, IC₅₀ (half-maximal inhibitory concentration) values determined by these two different detection methods were consistent and close to values reported in the literature. The high-throughput potential of this new approach to kinase assays was preliminarily demonstrated by screening a chemical library consisting of 31 compounds against c-Abl kinase using a 96-well plate. In this proof-of-principle experiment, both MALDI-TOF MS and immunochemifluorescence were able to compare inhibitor potencies with consistent values. Dual detection may significantly enhance the reliability of chemical library screening and identify false positives and negatives. Formatted for 96-well plates and with high-throughput potential, this dual detection kinase assay may provide a rapid, reliable, and inexpensive route to the discovery of small-molecule drug leads.
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Affiliation(s)
- Guangchang Zhou
- Ludwig Center for Metastasis Research, The University of Chicago, IL 60637, USA
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22
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Bai Y, Liu X, Cook P, Abbott NL, Himpsel F. Characterization of surfaces presenting covalently immobilized oligopeptides using near-edge X-ray absorption fine structure spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:6464-6470. [PMID: 20387822 PMCID: PMC2862363 DOI: 10.1021/la101101a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This study addresses the need for methods that validate the surface chemistry leading to the immobilization of biomolecules and provide information about the resulting structural configurations. We report on the use of near-edge X-ray absorption fine structure spectroscopy (NEXAFS) to characterize a widely employed immobilization chemistry that leads to the covalent attachment of a biologically relevant oligopeptide to a surface. The oligopeptide used in this study is a kinase substrate of the epidermal growth factor receptor (EGFR), a protein that is a common target for cancer therapeutics. By observing changes in the pi* and sigma* orbitals of specific nitrogen and carbon atoms (amide, imide, carbonyl), we are able to follow the sequential reactions leading to immobilization of the oligopeptide. We also show that it is possible to use NEXAFS to extend this characterization method to submonolayer densities that are relevant to biological assays. Such an element-specific chemical characterization of small peptides on surfaces fills an unmet need and establishes NEXAFS as useful technique for characterizing the immobilization of small biomolecules on surfaces.
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Affiliation(s)
- Yiqun Bai
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706
| | - Xiaosong Liu
- Department of Physics, 1150 University Avenue, Madison WI 53706
| | - Peter Cook
- Department of Physics, 1150 University Avenue, Madison WI 53706
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706
| | - F.J. Himpsel
- Department of Physics, 1150 University Avenue, Madison WI 53706
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23
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Rich RL, Myszka DG. Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'. J Mol Recognit 2010; 23:1-64. [PMID: 20017116 DOI: 10.1002/jmr.1004] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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24
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Jung SH, Kong DH, Park JH, Lee ST, Hyun J, Kim YM, Ha KS. Rapid analysis of matrix metalloproteinase-3 activity by gelatin arrays using a spectral surface plasmon resonance biosensor. Analyst 2010; 135:1050-7. [DOI: 10.1039/b919857a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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25
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Robertus J, Browne WR, Feringa BL. Dynamic control over cell adhesive properties using molecular-based surface engineering strategies. Chem Soc Rev 2010; 39:354-78. [DOI: 10.1039/b906608j] [Citation(s) in RCA: 194] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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26
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Han A, Hosokawa K, Maeda M. Phosphate-affinity electrophoresis on a microchip for determination of protein kinase activity. Electrophoresis 2009; 30:3507-13. [DOI: 10.1002/elps.200900142] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Inamori K, Kyo M, Matsukawa K, Inoue Y, Sonoda T, Mori T, Niidome T, Katayama Y. Establishment of screening system toward discovery of kinase inhibitors using label-free on-chip phosphorylation assays. Biosystems 2009; 97:179-85. [DOI: 10.1016/j.biosystems.2009.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 04/16/2009] [Accepted: 04/29/2009] [Indexed: 12/15/2022]
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A Phos-tag-based fluorescence resonance energy transfer system for the analysis of the dephosphorylation of phosphopeptides. Anal Biochem 2009; 388:235-41. [DOI: 10.1016/j.ab.2009.02.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 01/27/2009] [Accepted: 02/28/2009] [Indexed: 11/19/2022]
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Syahir A, Tomizaki KY, Kajikawa K, Mihara H. Poly(amidoamine)-dendrimer-modified gold surfaces for anomalous reflection of gold to detect biomolecular interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:3667-3674. [PMID: 19227984 DOI: 10.1021/la8028275] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Label-free protein detecting chip technology has encouraged a number of discoveries, as it is a powerful analytical tool in the postgenomic era. In particular, we have focused on a unique characteristic of anomalous reflection of gold (AR) as a new class of label-free detection method for a protein chip system. In this paper, in order to improve the sensitivity of detection of biomolecular interactions by the AR method, we have constructed three-dimensional (3D) nanostructures on gold surfaces with a series of well-defined structures of poly(amidoamine) dendrimers (PAMAMs) from generation 2 to 4 (G2, G3, and G4) tethering biotin moieties as capturing agents for avidin and antibiotin IgG. Comparison of features of such 3D nanostructured surfaces with a diamine-modified flat-like surface revealed a 2-fold increase in the amount of avidin for 3D surfaces relative to the flat surface, and surface-assisted nonspecific interactions were significantly suppressed. We thus obtained 91% coverage for avidin detection on the PAMAM G4-modified surface, indicating a theoretically maximum attainable absorption considering a hexagonal-packed arrangement as a saturated monomolecular layer. In the antibiotin IgG assay, the PAMAM G4-modified surface clearly improved the amount of proteins captured compared to that for the flat surface, indicating that an appropriate density of capturing agents played a more important role in the interaction of larger molecular-sized proteins such as antibiotin IgG, which requires more space for interaction than the medium-sized avidin. These findings should assist in the development of a simple and practical tool for high-throughput protein detection, particularly with the AR method.
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Affiliation(s)
- Amir Syahir
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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Peptide microarrays for detailed, high-throughput substrate identification, kinetic characterization, and inhibition studies on protein kinase A. Anal Biochem 2009; 387:150-61. [DOI: 10.1016/j.ab.2009.01.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 01/09/2009] [Accepted: 01/14/2009] [Indexed: 11/22/2022]
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Abstract
Enzymes are key molecules in signal transduction pathways. However, only a small fraction of more than 500 predicted human kinases, 250 proteases and 250 phosphatases is characterized so far. Peptide microarray-based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. Additionally, patterns of enzymatic activities could be used to fingerprint the status of cells or organisms. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimization of enzyme substrates. A comprehensive overview regarding enzyme profiling using peptide microarrays is presented with special focus on assay principles.
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Affiliation(s)
- Alexandra Thiele
- Max Planck Research Unit for Enzymology of Protein Folding, Halle, Germany
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Nakkach M, Lecaruyer P, Bardin F, Sakly J, Ben Lakhdar Z, Canva M. Absorption and related optical dispersion effects on the spectral response of a surface plasmon resonance sensor. APPLIED OPTICS 2008; 47:6177-82. [PMID: 19023380 DOI: 10.1364/ao.47.006177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Surface plasmon resonance (SPR) sensing is an optical technique that allows real time detection of small changes in the physical properties, in particular in the refractive index, of a dielectric medium near a metal film surface. One way to increase the SPR signal shift is then to incorporate a substance possessing a strong dispersive refractive index in the range of the plasmon resonance band. In this paper, we investigate the impact of materials possessing a strong dispersive index integrated to the dielectric medium on the SPR reflectivity profile. We present theoretical results based on chromophore absorption spectra and on their associated refractive index obtained from the Lorentz approach and Kramers-Krönig equations. As predicted by the theory, the experimental results show an enhancement of the SPR response, maximized when the chromophore absorption band coincides with the plasmon resonant wavelength. This shows that chromophores labeling can provide a potential way for SPR response enhancement.
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Affiliation(s)
- Mohamed Nakkach
- Laboratoire Charles Fabry de l'Institut d'Optique, Institut d'Optique Graduate School, Univ Paris-Sud, CNRS, Campus Polytechnique, RD 128, 91127 Palaiseau Cedex, France.
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