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Khatun MS, Shoombuatong W, Hasan MM, Kurata H. Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction. Curr Genomics 2020; 21:454-463. [PMID: 33093807 PMCID: PMC7536797 DOI: 10.2174/1389202921999200625103936] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/19/2020] [Accepted: 05/27/2020] [Indexed: 12/22/2022] Open
Abstract
Protein-protein interactions (PPIs) are the physical connections between two or more proteins via electrostatic forces or hydrophobic effects. Identification of the PPIs is pivotal, which contributes to many biological processes including protein function, disease incidence, and therapy design. The experimental identification of PPIs via high-throughput technology is time-consuming and expensive. Bioinformatics approaches are expected to solve such restrictions. In this review, our main goal is to provide an inclusive view of the existing sequence-based computational prediction of PPIs. Initially, we briefly introduce the currently available PPI databases and then review the state-of-the-art bioinformatics approaches, working principles, and their performances. Finally, we discuss the caveats and future perspective of the next generation algorithms for the prediction of PPIs.
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Affiliation(s)
| | | | - Md. Mehedi Hasan
- Address correspondence to these authors at the Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan; Tel: +81-948-297-828; E-mail: and Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Tel: +81-948-297-828; E-mail:
| | - Hiroyuki Kurata
- Address correspondence to these authors at the Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan; Tel: +81-948-297-828; E-mail: and Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Tel: +81-948-297-828; E-mail:
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2
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The specific seroreactivity to ∆Np73 isoforms shows higher diagnostic ability in colorectal cancer patients than the canonical p73 protein. Sci Rep 2019; 9:13547. [PMID: 31537884 PMCID: PMC6753153 DOI: 10.1038/s41598-019-49960-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/31/2019] [Indexed: 02/05/2023] Open
Abstract
The p53-family is tightly regulated at transcriptional level. Due to alternative splicing, up to 40 different theoretical proteoforms have been described for p73 and at least 20 and 10 for p53 and p63, respectively. However, only the canonical proteins have been evaluated as autoantibody targets in cancer patients for diagnosis. In this study, we have cloned and expressed in vitro the most upregulated proteoforms of p73, ΔNp73α and ΔNp73β, for the analysis of their seroreactivity by a developed luminescence based immunoassay test using 145 individual plasma from colorectal cancer, premalignant individuals and healthy controls. ∆Np73α seroreactivity showed the highest diagnostic ability to discriminate between groups. The combination of ∆Np73α, ∆Np73β and p73 proteoforms seroreactivity were able to improve their individual diagnostic ability. Competitive inhibition experiments further demonstrated the presence of unique specific epitopes in ΔNp73 isoforms not present in p73, with several colorectal patients showing unique and specific seroreactivity to the ΔNp73 proteoforms. Overall, we have increased the complexity of the humoral immune response to the p53-family in cancer patients, showing that the proteoforms derived from the alternative splicing of p73 possess a higher diagnostic ability than the canonical protein, which might be extensive for p53 and p63 proteins.
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3
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Pick E. Using Synthetic Peptides for Exploring Protein-Protein Interactions in the Assembly of the NADPH Oxidase Complex. Methods Mol Biol 2019; 1982:377-415. [PMID: 31172485 DOI: 10.1007/978-1-4939-9424-3_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The NADPH oxidase complex, responsible for reactive oxygen species (ROS) generation by phagocytes, consists of a membrane-associated flavocytochrome b 558 (a heterodimer of NOX2 and p22phox) and the cytosolic components p47phox, p67phox, Rac(1 or 2), and p40phox. NOX2 carries all redox stations through which electrons flow from NADPH to molecular oxygen, to generate the primary ROS, superoxide. For the electron flow to start, a conformational change in NOX2 is required. The dominant hypothesis is that this change is the result of the interaction of NOX2 with one or more of the cytosolic components (NADPH oxidase assembly). At the most basic level, assembly is the sum of several protein-protein interactions among oxidase components. This chapter describes a reductionist approach to the identification of regions in oxidase components involved in assembly. This approach consists of "transforming" one component in an array of overlapping synthetic peptides and assessing binding to the peptides of another component, represented by a recombinant protein. The peptides are tagged with biotin, at the N- or C-terminus, and immobilized on streptavidin-coated 96-well plates. The protein partners are expressed with a 6His tag and added to the plates in the fluid phase. Binding of the protein to the peptides is quantified by a kinetic ELISA , using a peroxidase-conjugated anti-polyhistidine antibody. Protein-peptide binding assays were applied successfully to (a) identifying the binding site on one component (represented by peptides) for another component (proteins), (b) precisely defining the "binding sequence," (c) acquiring information on the binding site in the partner protein, (d) investigating the effect of conformational changes in proteins on binding to peptides, (e) determining the effect of physicochemical modification of peptides on binding of proteins, and (f) identifying epitopes recognized by anti-oxidase component antibodies by binding of antibody to peptide arrays derived from the component.
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Affiliation(s)
- Edgar Pick
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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4
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Garranzo-Asensio M, Guzman-Aranguez A, Povés C, Fernández-Aceñero MJ, Torrente-Rodríguez RM, Ruiz-Valdepeñas Montiel V, Domínguez G, Frutos LS, Rodríguez N, Villalba M, Pingarrón JM, Campuzano S, Barderas R. Toward Liquid Biopsy: Determination of the Humoral Immune Response in Cancer Patients Using HaloTag Fusion Protein-Modified Electrochemical Bioplatforms. Anal Chem 2016; 88:12339-12345. [DOI: 10.1021/acs.analchem.6b03526] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- María Garranzo-Asensio
- Departamento
de Bioquímica y Biología Molecular IV, Facultad de Óptica
y Optometría, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Ana Guzman-Aranguez
- Departamento
de Bioquímica y Biología Molecular IV, Facultad de Óptica
y Optometría, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Carmen Povés
- Gastroenterology
Unit, Hospital Universitario Clínico San Carlos, E-28040 Madrid, Spain
| | | | - Rebeca M. Torrente-Rodríguez
- Departamento
de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Víctor Ruiz-Valdepeñas Montiel
- Departamento
de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Gemma Domínguez
- Departamento de Medicina, Facultad de Medicina, Instituto de Investigaciones Biomédicas “Alberto Sols”, CSIC-UAM, E-28029 Madrid, Spain
| | - Luis San Frutos
- Gynecology
and Obstetrics Department, Hospital Puerta de Hierro, E-28222 Majadahonda, Spain
| | - Nuria Rodríguez
- Medical
Oncology Department, Hospital Universitario La Paz, E-28046 Madrid, Spain
| | - Mayte Villalba
- Departamento
de Bioquímica y Biología Molecular I Facultad de Ciencias
Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - José M. Pingarrón
- Departamento
de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Susana Campuzano
- Departamento
de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Rodrigo Barderas
- Departamento
de Bioquímica y Biología Molecular I Facultad de Ciencias
Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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5
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Benink HA, Urh M. HaloTag technology for specific and covalent labeling of fusion proteins. Methods Mol Biol 2015; 1266:119-28. [PMID: 25560071 DOI: 10.1007/978-1-4939-2272-7_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Appending proteins of interest to fluorescent protein tags such as GFP has revolutionized how proteins are studied in the cellular environment. Over the last few decades many varieties of fluorescent proteins have been generated, each bringing new capability to research. However, taking full advantage of standard fluorescent proteins with advanced and differential features requires significant effort on the part of the researcher. This approach necessitates that many genetic fusions be generated and confirmed to function properly in cells with the same protein of interest. To lessen this burden, a newer category of protein fusion tags termed "self-labeling protein tags" has been developed. This approach utilizes a single protein tag, the function of which can be altered by attaching various chemical moieties (fluorescent labels, affinity handles, etc.). In this way a single genetically encoded protein fusion can easily be given functional diversity and adaptability as supplied by synthetic chemistry. Here we present protein labeling methods using HaloTag technology; comprised of HaloTag protein and the collection of small molecules designed to bind it specifically and provide it with varied functionalities. For imaging purposes these small molecules, termed HaloTag ligands, contain distinct fluorophores. Due to covalent and rapid binding between HaloTag protein and its ligands, labeling is permanent and efficient. Many of these ligands have been optimized for permeability across cellular membranes allowing for live cell labeling and imaging analysis. Nonpermeable ligands have also been developed for specific labeling of surface proteins. Overall, HaloTag is a versatile technology that empowers the end user to label a protein of interest with the choice of different fluorophores while alleviating the need for generation of multiple genetic fusions.
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Affiliation(s)
- Hélène A Benink
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA
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6
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Abstract
![]()
Exploration of protein function and
interaction is critical for
discovering links among genomics, proteomics, and disease state; yet,
the immense complexity of proteomics found in biological systems currently
limits our investigational capacity. Although affinity and autofluorescent
tags are widely employed for protein analysis, these methods have
been met with limited success because they lack specificity and require
multiple fusion tags and genetic constructs. As an alternative approach,
the innovative HaloTag protein fusion platform allows protein function
and interaction to be comprehensively analyzed using a single genetic
construct with multiple capabilities. This is accomplished using a
simplified process, in which a variable HaloTag ligand binds rapidly
to the HaloTag protein (usually linked to the protein of interest)
with high affinity and specificity. In this review, we examine all
current applications of the HaloTag technology platform for biomedical
applications, such as the study of protein isolation and purification,
protein function, protein–protein and protein–DNA interactions,
biological assays, in vitro cellular imaging, and in vivo molecular imaging. In addition, novel uses of the
HaloTag platform are briefly discussed along with potential future
applications.
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Affiliation(s)
- Christopher G England
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Haiming Luo
- ‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weibo Cai
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,§University of Wisconsin Carbone Cancer Center, Madison, Wisconsin 53705, United States
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7
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Päkkilä H, Peltomaa R, Lamminmäki U, Soukka T. Precise construction of oligonucleotide-Fab fragment conjugate for homogeneous immunoassay using HaloTag technology. Anal Biochem 2014; 472:37-44. [PMID: 25481738 DOI: 10.1016/j.ab.2014.11.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/19/2014] [Accepted: 11/24/2014] [Indexed: 10/24/2022]
Abstract
The use of oligonucleotide-protein conjugates enables the development of novel types of bioanalytical assays. However, convenient methods for producing covalent and stoichiometric oligonucleotide-protein conjugates are still rare. Here we demonstrate, for the first time, covalent conjugation of DNA oligonucleotide to Fab fragments with a 1:1 ratio using HaloTag self-labeling technology. The oligonucleotide coupling was carried out while the Fab was attached to protein G matrix, thereby enabling straightforward production of covalent conjugates. Furthermore, it allowed convenient purification of the product because the unreacted components were easily removed before the elution of the high-purity conjugate. The prepared conjugate was employed in a homogeneous immunoassay where prostate-specific antigen was used as a model analyte. Switchable lanthanide luminescence was used for detection, and the obtained limit of detection was 0.27 ng/ml. In the future, the developed method for covalent conjugation and successive purification in protein G column could also be applied for introducing other kinds of modifications to Fab fragments in a simple and site-specific manner.
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Affiliation(s)
- Henna Päkkilä
- Department of Biochemistry/Biotechnology, University of Turku, FI-20014 Turun yliopisto, Finland.
| | - Riikka Peltomaa
- Department of Biochemistry/Biotechnology, University of Turku, FI-20014 Turun yliopisto, Finland
| | - Urpo Lamminmäki
- Department of Biochemistry/Biotechnology, University of Turku, FI-20014 Turun yliopisto, Finland
| | - Tero Soukka
- Department of Biochemistry/Biotechnology, University of Turku, FI-20014 Turun yliopisto, Finland
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8
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Gahoi N, Ray S, Srivastava S. Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges. Proteomics 2014; 15:218-31. [PMID: 25266292 DOI: 10.1002/pmic.201400261] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 09/17/2014] [Accepted: 09/25/2014] [Indexed: 01/17/2023]
Abstract
Very often dysfunctional aspects of various signalling networks are found to be associated with human diseases and disorders. The major characteristics of signal transduction pathways are specificity, amplification of the signal, desensitisation and integration, which is accomplished not solely, but majorly by proteins. Array-based profiling of protein-protein and other biomolecular interactions is a versatile approach, which holds immense potential for multiplex interactome mapping and provides an inclusive representation of the signal transduction pathways and networks. Protein microarrays such as analytical protein microarrays (antigen-antibody interactions, autoantibody screening), RP microarrays (interaction of a particular ligand with all the possible targets in cell), functional protein microarrays (protein-protein or protein-ligand interactions) are implemented for various applications, including analysis of protein interactions and their significance in signalling cascades. Additionally, successful amalgamation of the array-based approaches with different label-free detection techniques allows real-time analysis of interaction kinetics of multiple interaction events simultaneously. This review discusses the prospects, merits and limitations of different variants of array-based techniques and their promising applications for studying the modifications and interactions of biomolecules, and highlights the studies associated with signal transduction pathways and their impact on disease pathobiology.
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Affiliation(s)
- Nikita Gahoi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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9
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Chandra H, Reddy PJ, Srivastava S. Protein microarrays and novel detection platforms. Expert Rev Proteomics 2014; 8:61-79. [DOI: 10.1586/epr.10.99] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Casado-Vela J, Fuentes M, Franco-Zorrilla JM. Screening of Protein–Protein and Protein–DNA Interactions Using Microarrays. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:231-81. [DOI: 10.1016/b978-0-12-800453-1.00008-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Sun H, Chen GYJ, Yao SQ. Recent advances in microarray technologies for proteomics. ACTA ACUST UNITED AC 2013; 20:685-99. [PMID: 23706635 DOI: 10.1016/j.chembiol.2013.04.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 04/01/2013] [Accepted: 04/14/2013] [Indexed: 01/04/2023]
Abstract
Proteins are fundamental components of all living systems and critical drivers of biological functions. The large-scale study of proteins, their structures and functions, is defined as proteomics. This systems-wide analysis leads to a more comprehensive view of the intricate signaling transduction pathways that proteins engage in and improves the overall understanding of the complex processes supporting the living systems. Over the last two decades, the development of high-throughput analytical tools, such as microarray technologies, capable of rapidly analyzing thousands of protein-functioning and protein-interacting events, has fueled the growth of this important field. Herein, we review the most recent advancements in microarray technologies, with a special focus on peptide microarray, small molecule microarray, and protein microarray. These technologies have become prominent players in proteomics and have made significant changes to the landscape of life science and biomedical research. We will elaborate on their performance, advantages, challenges, and future directions.
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Affiliation(s)
- Hongyan Sun
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, PRC.
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12
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Wang J, Barker K, Steel J, Park J, Saul J, Festa F, Wallstrom G, Yu X, Bian X, Anderson KS, Figueroa JD, LaBaer J, Qiu J. A versatile protein microarray platform enabling antibody profiling against denatured proteins. Proteomics Clin Appl 2013; 7:378-83. [PMID: 23027520 DOI: 10.1002/prca.201200062] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/21/2012] [Accepted: 08/23/2012] [Indexed: 11/10/2022]
Abstract
PURPOSE We aim to develop a protein microarray platform capable of presenting both natural and denatured forms of proteins for antibody biomarker discovery. We will further optimize plasma screening protocols to improve detection. EXPERIMENTAL DESIGN We developed a new covalent capture protein microarray chemistry using HaloTag fusion proteins and ligand. To enhance protein yield, we used HeLa cell lysate as an in vitro transcription translation (IVTT) system. Escherichia coli lysates were added to the plasma blocking buffer to reduce nonspecific background. These protein microarrays were probed with plasma samples and autoantibody responses were quantified and compared with or without denaturing buffer treatment. RESULTS We demonstrated that protein microarrays using the covalent attachment chemistry endured denaturing conditions. Blocking with E. coli lysates greatly reduced the background signals and expression with IVTT based on HeLa cell lysates significantly improved the antibody signals on protein microarrays probed with plasma samples. Plasma samples probed on denatured protein arrays produced autoantibody profiles distinct from those probed on natively displayed proteins. CONCLUSIONS AND CLINICAL RELEVANCE This versatile protein microarray platform allows the display of both natural and denatured proteins, offers a new dimension to search for disease-specific antibodies, broadens the repertoire of potential biomarkers, and will potentially yield clinical diagnostics with greater performance.
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Affiliation(s)
- Jie Wang
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-6401, USA
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13
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Selective Introduction of Sulfhydryl Groups into Recombinant Proteins for Study of Protein–Protein Interactions. Chromatographia 2013. [DOI: 10.1007/s10337-013-2463-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Lochmatter C, Schneider CL, Ingram K, Keiser J, Schifferli JA. Schistosoma mansoni tetraspanning orphan receptor (SmTOR): a new vaccine candidate against schistosomiasis. Clin Exp Immunol 2013; 170:342-57. [PMID: 23121675 DOI: 10.1111/j.1365-2249.2012.04667.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
One approach to fight against schistosomiasis is to develop an efficient vaccine. Schistosoma mansoni tetraspanning orphan receptor (SmTOR) might be a vaccine candidate, as it is a tegument membrane protein expressed most highly in cercariae. In this study we characterized the recombinant first extracellular domain of SmTOR (rSmTORed1) as having the expected property to bind C2 of complement similarly to a smaller peptide of the same domain, and to produce specific and high-titre antibodies in BALB/c mice immunized using complete Freund's adjuvant/incomplete Freund's adjuvant (CFA/IFA). Immunization was protective against parasite infection, as demonstrated by a significant decrease in worm burden in immunized BALB/c mice versus the control groups over two independent trials [64 and 45% reduction for mean adult worm burden in immunized versus phosphate-bufferd saline (PBS) injected mice]. Interestingly, infection by itself did not lead to the generation of anti-rSmTORed1 antibodies, corresponding to the low frequency of specific anti-rSmTORed1 antibodies detected in the sera of patients infected with S. mansoni (2/20; 10%). These data suggest that, as opposed to the natural infection during which SmTOR induces antibodies only rarely, immunization with its smaller first extracellular domain might be more efficient.
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Affiliation(s)
- C Lochmatter
- Immunonephrology Laboratory, Department of Biomedicine, University Hospital Basel, Basel, Switzerland.
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15
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Urh M, Rosenberg M. HaloTag, a Platform Technology for Protein Analysis. CURRENT CHEMICAL GENOMICS 2012; 6:72-8. [PMID: 23213345 PMCID: PMC3480824 DOI: 10.2174/1875397301206010072] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/03/2012] [Accepted: 08/05/2012] [Indexed: 01/01/2023]
Abstract
Understanding protein function and interaction is central to the elucidation of biological processes. Systematic analysis of protein interactions have shown that the eukaryotic proteome is highly interconnected and that biological function frequently depends on the orchestrated action of many proteins. Perturbation of these functions or interactions can lead to various disease states and pharmacologic intervention can result in corrective therapies. The fact that proteins rarely act in isolation, but rather comprise complex machines that stably and/or transiently interact with many different partners at different times, demands the need for robust tools that allow comprehensive global analyses of these events. Here we describe a powerful protein fusion technology, the HaloTag platform, and how it enables the study of many facets of protein biology by offering a broad choice of applications. We review the development of the key aspects of the technology and it's performance in both in vitro and in vivo applications. In particular, we focus on HaloTag's multifunctional utility in protein imaging, protein isolation and display, and in the study of protein complexes and interactions. We demonstrate it's potential to help elucidate important facets of proteomic biology across complex biological systems at the biochemical, cell-based and whole animal level.
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16
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Encell LP, Friedman Ohana R, Zimmerman K, Otto P, Vidugiris G, Wood MG, Los GV, McDougall MG, Zimprich C, Karassina N, Learish RD, Hurst R, Hartnett J, Wheeler S, Stecha P, English J, Zhao K, Mendez J, Benink HA, Murphy N, Daniels DL, Slater MR, Urh M, Darzins A, Klaubert DH, Bulleit RF, Wood KV. Development of a dehalogenase-based protein fusion tag capable of rapid, selective and covalent attachment to customizable ligands. CURRENT CHEMICAL GENOMICS 2012; 6:55-71. [PMID: 23248739 PMCID: PMC3520037 DOI: 10.2174/1875397301206010055] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 04/04/2012] [Accepted: 04/16/2012] [Indexed: 11/22/2022]
Abstract
Our fundamental understanding of proteins and their biological significance has been enhanced by genetic fusion tags, as they provide a convenient method for introducing unique properties to proteins so that they can be examinedin isolation. Commonly used tags satisfy many of the requirements for applications relating to the detection and isolation of proteins from complex samples. However, their utility at low concentration becomes compromised if the binding affinity for a detection or capture reagent is not adequate to produce a stable interaction. Here, we describe HaloTag® (HT7), a genetic fusion tag based on a modified haloalkane dehalogenase designed and engineered to overcome the limitation of affinity tags by forming a high affinity, covalent attachment to a binding ligand. HT7 and its ligand have additional desirable features. The tag is relatively small, monomeric, and structurally compatible with fusion partners, while the ligand is specific, chemically simple, and amenable to modular synthetic design. Taken together, the design features and molecular evolution of HT7 have resulted in a superior alternative to common tags for the overexpression, detection, and isolation of target proteins.
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17
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Wagner EK, Nath N, Flemming R, Feltenberger JB, Denu JM. Identification and characterization of small molecule inhibitors of a plant homeodomain finger. Biochemistry 2012; 51:8293-306. [PMID: 22994852 DOI: 10.1021/bi3009278] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A number of histone-binding domains are implicated in cancer through improper binding of chromatin. In a clinically reported case of acute myeloid leukemia (AML), a genetic fusion protein between nucleoporin 98 and the third plant homeodomain (PHD) finger of JARID1A drives an oncogenic transcriptional program that is dependent on histone binding by the PHD finger. By exploiting the requirement for chromatin binding in oncogenesis, therapeutics targeting histone readers may represent a new paradigm in drug development. In this study, we developed a novel small molecule screening strategy that utilizes HaloTag technology to identify several small molecules that disrupt binding of the JARID1A PHD finger to histone peptides. Small molecule inhibitors were validated biochemically through affinity pull downs, fluorescence polarization, and histone reader specificity studies. One compound was modified through medicinal chemistry to improve its potency while retaining histone reader selectivity. Molecular modeling and site-directed mutagenesis of JARID1A PHD3 provided insights into the biochemical basis of competitive inhibition.
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Affiliation(s)
- Elise K Wagner
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
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18
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N Peterson S, Kwon K. The HaloTag: Improving Soluble Expression and Applications in Protein Functional Analysis. CURRENT CHEMICAL GENOMICS 2012; 6:8-17. [PMID: 23115610 PMCID: PMC3480702 DOI: 10.2174/1875397301206010008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/13/2012] [Accepted: 07/18/2012] [Indexed: 12/22/2022]
Abstract
Technological and methodological advances have been critical for the rapidly evolving field of proteomics. The development of fusion tag systems is essential for purification and analysis of recombinant proteins. The HaloTag is a 34 KDa monomeric protein derived from a bacterial haloalkane dehalogenase. The majority of fusion tags in use today utilize a reversible binding interaction with a specific ligand. The HaloTag system is unique in that it forms a covalent linkage to its chloroalkane ligand. This linkage permits attachment of the HaloTag to a variety of functional reporters, which can be used to label and immobilize recombinant proteins. The success rate for HaloTag expression of soluble proteins is very high and comparable to maltose binding protein (MBP) tag. Furthermore, cleavage of the HaloTag does not result in protein insolubility that often is observed with the MBP tag. In the present report, we describe applications of the HaloTag system in our ongoing investigation of protein-protein interactions of the Y. pestis Type 3 secretion system on a custom protein microarray. We also describe the utilization of affinity purification/mass spectroscopy (AP/MS) to evaluate the utility of the Halo Tag system to characterize DNA binding activity and protein specificity.
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Affiliation(s)
- Scott N Peterson
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, USA
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Koudelakova T, Bidmanova S, Dvorak P, Pavelka A, Chaloupkova R, Prokop Z, Damborsky J. Haloalkane dehalogenases: Biotechnological applications. Biotechnol J 2012; 8:32-45. [DOI: 10.1002/biot.201100486] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 06/30/2012] [Accepted: 07/20/2012] [Indexed: 12/21/2022]
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Díez P, Dasilva N, González-González M, Matarraz S, Casado-Vela J, Orfao A, Fuentes M. Data Analysis Strategies for Protein Microarrays. MICROARRAYS 2012; 1:64-83. [PMID: 27605336 PMCID: PMC5003438 DOI: 10.3390/microarrays1020064] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/13/2012] [Accepted: 07/31/2012] [Indexed: 01/22/2023]
Abstract
Microarrays constitute a new platform which allows the discovery and characterization of proteins. According to different features, such as content, surface or detection system, there are many types of protein microarrays which can be applied for the identification of disease biomarkers and the characterization of protein expression patterns. However, the analysis and interpretation of the amount of information generated by microarrays remain a challenge. Further data analysis strategies are essential to obtain representative and reproducible results. Therefore, the experimental design is key, since the number of samples and dyes, among others aspects, would define the appropriate analysis method to be used. In this sense, several algorithms have been proposed so far to overcome analytical difficulties derived from fluorescence overlapping and/or background noise. Each kind of microarray is developed to fulfill a specific purpose. Therefore, the selection of appropriate analytical and data analysis strategies is crucial to achieve successful biological conclusions. In the present review, we focus on current algorithms and main strategies for data interpretation.
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Affiliation(s)
- Paula Díez
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Noelia Dasilva
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - María González-González
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Sergio Matarraz
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Juan Casado-Vela
- Translational Oncology Unit, Instituto de Investigaciones Biomédicas 'Alberto Sols', Spanish National Research Council (CSIC-UAM), 28029 Madrid, Spain.
| | - Alberto Orfao
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Manuel Fuentes
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
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Dixit CK, Kumar A, Kaushik A. Nanosphere lithography-based platform for developing rapid and high sensitivity microarray systems. Biochem Biophys Res Commun 2012; 423:473-7. [PMID: 22683633 DOI: 10.1016/j.bbrc.2012.05.144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 05/26/2012] [Indexed: 10/28/2022]
Abstract
A novel gold nanoarray (NA)-based platform was developed for microarray applications. This novel approach is based upon the principle of nanosphere lithography and can be used for one-step antibody immobilization. The developed platform was checked by functionalizing with cysteine followed by capturing biotinylated antibody and detecting it with dye-conjugated steptravidin. An immunoassay was performed with spiked samples containing human fetuin A antigen. The minimum limits of detection (LOD) of human fetuin A for NA-based and conventional microarray platforms were 50 pg/mL and 50 ng/mL, respectively. The developed approach was highly reproducible and unlike conventional microarray approaches the use of a spotting system was omitted because immobilization was controlled and directed on the predefined arrays. This approach could be an ideal alternative for developing microarrays. And, the ease of the strategy also allows the high throughput production of the microarrays.
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Affiliation(s)
- Chandra K Dixit
- School of Biotechnology, National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland.
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Tessler LA, Mitra RD. Sensitive single-molecule protein quantification and protein complex detection in a microarray format. Proteomics 2011; 11:4731-5. [PMID: 22038904 DOI: 10.1002/pmic.201100361] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/03/2011] [Indexed: 01/21/2023]
Abstract
Single-molecule protein analysis provides sensitive protein quantitation with a digital read-out and is promising for studying biological systems and detecting biomarkers clinically. However, current single-molecule platforms rely on the quantification of one protein at a time. Conventional antibody microarrays are scalable to detect many proteins simultaneously, but they rely on less sensitive and less quantitative quantification by the ensemble averaging of fluorescent molecules. Here, we demonstrate a single-molecule protein assay in a microarray format enabled by an ultra-low background surface and single-molecule imaging. The digital read-out provides a highly sensitive, low femtomolar limit of detection and four orders of magnitude of dynamic range through the use of hybrid digital-analog quantification. From crude cell lysate, we measured levels of p53 and MDM2 in parallel, proving the concept of a digital antibody microarray for use in proteomic profiling. We also applied the single-molecule microarray to detect the p53-MDM2 protein complex in cell lysate. Our study is promising for development and application of single-molecule protein methods because it represents a technological bridge between single-plex and highly multiplex studies.
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Affiliation(s)
- Lee A Tessler
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University, St. Louis, MO 63108, USA
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State of the art in tumor antigen and biomarker discovery. Cancers (Basel) 2011; 3:2554-96. [PMID: 24212823 PMCID: PMC3757432 DOI: 10.3390/cancers3022554] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 05/24/2011] [Accepted: 05/27/2011] [Indexed: 12/22/2022] Open
Abstract
Our knowledge of tumor immunology has resulted in multiple approaches for the treatment of cancer. However, a gap between research of new tumors markers and development of immunotherapy has been established and very few markers exist that can be used for treatment. The challenge is now to discover new targets for active and passive immunotherapy. This review aims at describing recent advances in biomarkers and tumor antigen discovery in terms of antigen nature and localization, and is highlighting the most recent approaches used for their discovery including “omics” technology.
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Katz C, Levy-Beladev L, Rotem-Bamberger S, Rito T, Rüdiger SGD, Friedler A. Studying protein–protein interactions using peptide arrays. Chem Soc Rev 2011; 40:2131-45. [DOI: 10.1039/c0cs00029a] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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HaloTag-based purification of functional human kinases from mammalian cells. Protein Expr Purif 2010; 76:154-64. [PMID: 21129486 DOI: 10.1016/j.pep.2010.11.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 11/19/2010] [Accepted: 11/23/2010] [Indexed: 12/20/2022]
Abstract
Although cultured mammalian cells are preferred for producing functional mammalian proteins with appropriate post-translational modifications, purification of recombinant proteins is frequently hampered by low expression. We have addressed this by creating a new method configured specifically for mammalian cell culture that provides rapid detection and efficient purification. This approach is based on HaloTag, a protein fusion tag designed to bind rapidly, selectively and covalently to a series of synthetic ligands that can carry a variety of functional groups, including fluorescent dyes for detection or solid supports for purification. Since the binding of HaloTag to the HaloLink resin is essentially irreversible, it overcomes the equilibrium-based binding limitations associated with affinity tags and enables efficient capture and purification of target protein, even at low expression levels. The target protein is released from the HaloLink resin by specific cleavage using a TEV protease fused to HaloTag (HaloTEV), leaving both HaloTag and HaloTEV permanently attached to the resin and highly pure, tag-free protein in solution. HaloTag fluorescent ligands enable fluorescent labeling of HaloTag fusion proteins, providing a convenient way to monitor expression, and thus facilitate the identification of optimal transient transfection conditions as well as the selection of high expression stable cell lines. The capabilities of this method have been demonstrated by the efficient purification of five functional human kinases from HEK293T cells. In addition, when purifications using FLAG, 3xFLAG, His(6)Tag and HaloTag were performed in parallel, HaloTag was shown to provide significantly higher yields, purity and overall recovery of the expressed proteins.
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Chen Q, Liu Q, Li Z, Zhong W, He W, Xu D. A visual chip-based coimmunoprecipitation technique for analysis of protein-protein interactions. Anal Biochem 2010; 404:244-6. [PMID: 20460096 DOI: 10.1016/j.ab.2010.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 05/05/2010] [Accepted: 05/06/2010] [Indexed: 12/17/2022]
Abstract
Here we report a visual chip-based coimmunoprecipitation (vChip-coIP) platform for analysis of protein-protein interactions (PPIs) by combining advantages of an antibody microarray, traditional coIP, and a silver enhancement detection method. The chip was fabricated by spotting anti-Flag antibody on aldehyde-modified slides, and the resulting platform could assay immunoprecipitate from a small amount of crude cell lysates containing Flag-bait and Myc-prey. The interaction signals are visible using biotinylated anti-Myc antibody and colloidal gold-labeled streptavidin followed by a silver enhancement detection method. It is shown that vChip-coIP is a simple, cost-effective, and highly efficient platform for the comprehensive study of PPIs.
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Affiliation(s)
- Qing Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
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Abstract
New biomarkers are urgently needed to accelerate efforts in developing new drugs and treatments of known diseases. New clinical and translational proteomics studies emerge almost every day. However, discovery of new diagnostic biomarkers lags behind because of variability at every step in proteomics studies (e.g., assembly of a cohort of patients, sample preparation and the nature of body fluids, selection of a profiling method and uniform protocols for data analysis).Quite often, the validation step that follows the discovery phase does not reach desired levels of sensitivity and specificity or reproducibility between laboratories. Mass spectrometry and gel-based methods do not provide enough throughput for screening thousands of clinical samples. Further development of protein arrays may address this issue.Despite many obstacles, proteomics delivers vast amounts of information useful for understanding the molecular mechanisms underlying diseases.
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Affiliation(s)
- Jerzy Silberring
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Kraków, Poland
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Chandra H, Srivastava S. Cell-free synthesis-based protein microarrays and their applications. Proteomics 2009; 10:717-30. [DOI: 10.1002/pmic.200900462] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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High quality protein microarray using in situ protein purification. BMC Biotechnol 2009; 9:72. [PMID: 19698181 PMCID: PMC2746808 DOI: 10.1186/1472-6750-9-72] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 08/23/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC). This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. RESULTS Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG) coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST) composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents protein solubility and denaturation problems caused by buffer exchange steps and freeze-thaw cycles, which are associated with resin-based purification, intermittent protein storage and deposition on microarrays. CONCLUSION An optimized platform for in situ protein purification on microarray slides using His-tagged recombinant proteins is a desirable tool for the screening of novel protein functions and protein-protein interactions. In the context of immunoproteomics, such protein microarrays are complimentary to approaches using non-recombinant methods to discover and characterize bacterial antigens.
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