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Zhao Y, Wang X, Chen P, Zeng X, Bao H, Wang Y, Xu X, Jiang Y, Chen H, Li G. Detection of antibodies against avian influenza virus by protein microarray using nucleoprotein expressed in insect cells. J Vet Med Sci 2014; 77:413-9. [PMID: 25650059 PMCID: PMC4427741 DOI: 10.1292/jvms.14-0207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Avian influenza (AI) is an infectious disease caused by avian influenza viruses (AIVs) which belong to the influenza virus A group. AI causes tremendous economic losses in poultry industry and pose great threatens to human health. Active serologic surveillance is necessary to prevent and control the spread of AI. In this study, a protein microarray using nucleoprotein (NP) of H5N1 AIV expressed in insect cells was developed to detect antibodies against AIV NP protein. The protein microarray was used to test Newcastle disease virus (NDV), infectious bursal disease virus (IBDV), AIV positive and negative sera. The results indicated that the protein microarray could hybridize specifically with antibodies against AIV with strong signals and without cross-hybridization. Moreover, 76 field serum samples were detected by microarray, enzyme-linked immunosorbent assay (ELISA) and hemagglutination inhibition test (HI). The positive rate was 92.1% (70/76), 93.4% (71/76) and 89.4% (68/76) by protein microarray, ELISA and HI test, respectively. Compared with ELISA, the microarray showed 100% (20/20) agreement ratio in chicken and 98.2% (55/56) in ornamental bird. In conclusion, this method provides an alternative serological diagnosis for influenza antibody screening and will provide a basis for the development of protein microarrays that can be used to respectively detect antibodies of different AIV subtypes and other pathogens.
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Affiliation(s)
- Yuhui Zhao
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China
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53
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Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis 2014; 35:3430-40. [PMID: 24890697 PMCID: PMC4250476 DOI: 10.1002/elps.201400153] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.
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Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Weiguo Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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Liu H, Queffélec C, Charlier C, Defontaine A, Fateh A, Tellier C, Talham DR, Bujoli B. Design and optimization of a phosphopeptide anchor for specific immobilization of a capture protein on zirconium phosphonate modified supports. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:13949-13955. [PMID: 25365756 DOI: 10.1021/la5036085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The attachment of affinity proteins onto zirconium phosphonate coated glass slides was investigated by fusing a short phosphorylated peptide sequence at one extremity to enable selective bonding to the active surface via the formation of zirconium phosphate coordinate covalent bonds. In a model study, the binding of short peptides containing zero to four phosphorylated serine units and a biotin end-group was assessed by surface plasmon resonance-enhanced ellipsometry (SPREE) as well as in a microarray format using fluorescence detection of AlexaFluor 647-labeled streptavidin. Significant binding to the zirconated surface was only observed in the case of the phosphopeptides, with the best performance, as judged by streptavidin capture, observed for peptides with three or four phosphorylation sites and when spotted at pH 3. When fusing similar phosphopeptide tags to the affinity protein, the presence of four phosphate groups in the tag allows efficient immobilization of the proteins and efficient capture of their target.
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Affiliation(s)
- Hao Liu
- Department of Chemistry, University of Florida , Gainesville, Florida 32611-7200, United States
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Lin Z, Ma Y, Zhao C, Chen R, Zhu X, Zhang L, Yan X, Yang W. An extremely simple method for fabricating 3D protein microarrays with an anti-fouling background and high protein capacity. LAB ON A CHIP 2014; 14:2505-14. [PMID: 24852169 DOI: 10.1039/c4lc00223g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Protein microarrays have become vital tools for various applications in biomedicine and bio-analysis during the past decade. The intense requirements for a lower detection limit and industrialization in this area have resulted in a persistent pursuit to fabricate protein microarrays with a low background and high signal intensity via simple methods. Here, we report on an extremely simple strategy to create three-dimensional (3D) protein microarrays with an anti-fouling background and a high protein capacity by photo-induced surface sequential controlled/living graft polymerization developed in our lab. According to this strategy, "dormant" groups of isopropyl thioxanthone semipinacol (ITXSP) were first introduced to a polymeric substrate through ultraviolet (UV)-induced surface abstraction of hydrogen, followed by a coupling reaction. Under visible light irradiation, the ITXSP groups were photolyzed to initiate surface living graft polymerization of poly(ethylene glycol) methyl methacrylate (PEGMMA), thus introducing PEG brushes to the substrate to generate a full anti-fouling background. Due to the living nature of this graft polymerization, there were still ITXSP groups on the chain ends of the PEG brushes. Therefore, by in situ secondary living graft cross-linking copolymerization of glycidyl methacrylate (GMA) and polyethylene glycol diacrylate (PEGDA), we could finally plant height-controllable cylinder microarrays of a 3D PEG network containing reactive epoxy groups onto the PEG brushes. Through a commonly used reaction of amine and epoxy groups, the proteins could readily be covalently immobilized onto the microarrays. This delicate design aims to overcome two universal limitations in protein microarrays: a full anti-fouling background can effectively eliminate noise caused by non-specific absorption and a 3D reactive network provides a larger protein-loading capacity to improve signal intensity. The results of non-specific protein absorption tests demonstrated that the introduction of PEG brushes greatly improved the anti-fouling properties of the pristine low-density polyethylene (LDPE), for which the absorption to bovine serum albumin was reduced by 83.3%. Moreover, the 3D protein microarrays exhibited a higher protein capacity than the controls to which were attached the same protein on PGMA brushes and monolayer epoxy functional groups. The 3D protein microarrays were used to test the immunoglobulin G (IgG) concentration in human serum, suggesting that they could be used for biomedical diagnosis, which indicates that more potential bio-applications could be developed for these protein microarrays in the future.
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Affiliation(s)
- Zhifeng Lin
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
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56
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Kilb N, Burger J, Roth G. Protein microarray generation by in situ protein expression from template DNA. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Normann Kilb
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
| | - Jürgen Burger
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
- Laboratory for MEMS Applications, Department of Microsystems Engineering—IMTEK University of Freiburg Freiburg Germany
| | - Günter Roth
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
- BIOSS—Centre for Biological Signalling Studies University of Freiburg Freiburg Germany
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57
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Forsberg EM, Sicard C, Brennan JD. Solid-phase biological assays for drug discovery. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:337-359. [PMID: 25000820 DOI: 10.1146/annurev-anchem-071213-020241] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the past 30 years, there has been a significant growth in the use of solid-phase assays in the area of drug discovery, with a range of new assays being used for both soluble and membrane-bound targets. In this review, we provide some basic background to typical drug targets and immobilization protocols used in solid-phase biological assays (SPBAs) for drug discovery, with emphasis on particularly labile biomolecular targets such as kinases and membrane-bound receptors, and highlight some of the more recent approaches for producing protein microarrays, bioaffinity columns, and other devices that are central to small molecule screening by SPBA. We then discuss key applications of such assays to identify drug leads, with an emphasis on the screening of mixtures. We conclude by highlighting specific advantages and potential disadvantages of SPBAs, particularly as they relate to particular assay formats.
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Affiliation(s)
- Erica M Forsberg
- Biointerfaces Institute, McMaster University, Hamilton, Ontario L8S 4L8, Canada;
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58
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Díaz-González M, Muñoz-Berbel X, Jiménez-Jorquera C, Baldi A, Fernández-Sánchez C. Diagnostics Using Multiplexed Electrochemical Readout Devices. ELECTROANAL 2014. [DOI: 10.1002/elan.201400015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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59
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Beeton-Kempen N, Duarte J, Shoko A, Serufuri JM, John T, Cebon J, Blackburn J. Development of a novel, quantitative protein microarray platform for the multiplexed serological analysis of autoantibodies to cancer-testis antigens. Int J Cancer 2014; 135:1842-51. [PMID: 24604332 DOI: 10.1002/ijc.28832] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/18/2014] [Indexed: 01/08/2023]
Abstract
The cancer-testis antigens are a group of unrelated proteins aberrantly expressed in various cancers in adult somatic tissues. This aberrant expression can trigger spontaneous immune responses, a phenomenon exploited for the development of disease markers and therapeutic vaccines. However, expression levels often vary amongst patients presenting the same cancer type, and these antigens are therefore unlikely to be individually viable as diagnostic or prognostic markers. Nevertheless, patterns of antigen expression may provide correlates of specific cancer types and disease progression. Herein, we describe the development of a novel, readily customizable cancer-testis antigen microarray platform together with robust bioinformatics tools, with which to quantify anti-cancer testis antigen autoantibody profiles in patient sera. By exploiting the high affinity between autoantibodies and tumor antigens, we achieved linearity of response and an autoantibody quantitation limit in the pg/mL range-equating to a million-fold serum dilution. By using oriented attachment of folded, recombinant antigens and a polyethylene glycol microarray surface coating, we attained minimal non-specific antibody binding. Unlike other proteomics methods, which typically use lower affinity interactions between monoclonal antibodies and tumor antigens for detection, the high sensitivity and specificity realized using our autoantibody-based approach may facilitate the development of better cancer biomarkers, as well as potentially enabling pre-symptomatic diagnosis. We illustrated the usage of our platform by monitoring the response of a melanoma patient cohort to an experimental therapeutic NY-ESO-1-based cancer vaccine; inter alia, we found evidence of determinant spreading in individual patients, as well as differential CT antigen expression and epitope usage.
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Affiliation(s)
- Natasha Beeton-Kempen
- Institute of Infectious Disease and Molecular Medicine/Division of Medical Biochemistry, University of Cape Town, Cape Town, South Africa; Biosciences Division, Council for Scientific and Industrial Research, Pretoria, South Africa
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60
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Wang HC, Yu CC, Liang CF, Huang LD, Hwu JR, Lin CC. Site-Selective Protein Immobilization through 2-Cyanobenzothiazole-Cysteine Condensation. Chembiochem 2014; 15:829-35. [DOI: 10.1002/cbic.201300800] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Indexed: 11/10/2022]
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61
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Syafrizayanti, Betzen C, Hoheisel JD, Kastelic D. Methods for analyzing and quantifying protein–protein interaction. Expert Rev Proteomics 2014; 11:107-20. [DOI: 10.1586/14789450.2014.875857] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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62
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Costantini F, Nascetti A, Scipinotti R, Domenici F, Sennato S, Gazza L, Bordi F, Pogna N, Manetti C, Caputo D, de Cesare G. On-chip detection of multiple serum antibodies against epitopes of celiac disease by an array of amorphous silicon sensors. RSC Adv 2014. [DOI: 10.1039/c3ra46058d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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63
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Li H, Wang M, Qiang W, Hu H, Li W, Xu D. Metal-enhanced fluorescent detection for protein microarrays based on a silver plasmonic substrate. Analyst 2014; 139:1653-60. [DOI: 10.1039/c3an01875j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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64
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Abstract
Protein microarrays are a miniaturized format for assaying functional protein interactions and proteomics using a high-throughput, multiplexed approach. The primary limitations of this technology include the time and cost involved in the production of highly purified individual proteins for arraying and also the limited stability of functional proteins once arrayed. In light of these difficulties, cell-free protein expression systems are being increasingly used to generate protein arrays in situ from coding DNA sequences. This chapter describes the method DNA array to protein array (DAPA) allowing the repeated "printing" of protein arrays directly from a DNA array template using cell-free protein expression. Once the DNA templates have been spotted, the generation of the protein array involves only simple handling procedures and is relatively time and cost-efficient, and protein arrays can easily be produced "on demand" as and when required. The resultant protein array may be used for any downstream applications as for conventionally spotted protein arrays.
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Affiliation(s)
- Elizabeth A Cook
- Protein Technology Group, Babraham Bioscience Technologies Ltd, Babraham Research Campus, Cambridge, UK
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65
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Cretich M, Damin F, Chiari M. Protein microarray technology: how far off is routine diagnostics? Analyst 2014; 139:528-42. [DOI: 10.1039/c3an01619f] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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66
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Steen Redeker E, Ta DT, Cortens D, Billen B, Guedens W, Adriaensens P. Protein Engineering For Directed Immobilization. Bioconjug Chem 2013; 24:1761-77. [DOI: 10.1021/bc4002823] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Erik Steen Redeker
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Duy Tien Ta
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - David Cortens
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Brecht Billen
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Wanda Guedens
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
| | - Peter Adriaensens
- Biomolecule Design Group
(BDG), Institute for Materials Research (IMO), Chemistry Division, Hasselt University, Agoralaan
Building D, 3590 Diepenbeek, Belgium
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67
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Morris MK, Chi A, Melas IN, Alexopoulos LG. Phosphoproteomics in drug discovery. Drug Discov Today 2013; 19:425-32. [PMID: 24141136 DOI: 10.1016/j.drudis.2013.10.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 09/05/2013] [Accepted: 10/10/2013] [Indexed: 12/20/2022]
Abstract
Several important aspects of the drug discovery process, including target identification, mechanism of action determination and biomarker identification as well as drug repositioning, require complete understanding of the effects of drugs on protein phosphorylation in relevant biological systems. Novel high-throughput phosphoproteomic technologies can be employed to measure these phosphorylation events. In this review, we describe the advantages and limitations of state-of-the-art phosphoproteomic approaches such as mass spectrometry and antibody-based technologies in terms of sample and data throughput as well as data quality. We then discuss how datasets from each technology can be analyzed and how the results can be and have been applied to advance different aspects of the drug discovery process.
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Affiliation(s)
| | - An Chi
- Merck & Co., Boston, MA, USA
| | - Ioannis N Melas
- ProtATonce Ltd, Athens, Greece; Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece
| | - Leonidas G Alexopoulos
- ProtATonce Ltd, Athens, Greece; Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece.
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68
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Hagan S, Tomlinson A. Tear Fluid Biomarker Profiling: A Review of Multiplex Bead Analysis. Ocul Surf 2013; 11:219-35. [DOI: 10.1016/j.jtos.2013.04.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 04/19/2013] [Accepted: 04/01/2013] [Indexed: 11/30/2022]
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69
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Lee JH, Jung HI. Biochip technology for monitoring posttraumatic stress disorder (PTSD). BIOCHIP JOURNAL 2013. [DOI: 10.1007/s13206-013-7301-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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70
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Min K, Jung D, Jeon Y, Jeoung E, Kwon Y. Site-specific and effective immobilization of proteins by Npu DnaE split-intein mediated protein trans-splicing reaction. BIOCHIP JOURNAL 2013. [DOI: 10.1007/s13206-013-7312-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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71
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Melas IN, Kretsos K, Alexopoulos LG. Leveraging systems biology approaches in clinical pharmacology. Biopharm Drug Dispos 2013; 34:477-88. [PMID: 23983165 PMCID: PMC4034589 DOI: 10.1002/bdd.1859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 08/12/2013] [Indexed: 01/15/2023]
Abstract
Computational modeling has been adopted in all aspects of drug research and development, from the early phases of target identification and drug discovery to the late-stage clinical trials. The different questions addressed during each stage of drug R&D has led to the emergence of different modeling methodologies. In the research phase, systems biology couples experimental data with elaborate computational modeling techniques to capture lifecycle and effector cellular functions (e.g. metabolism, signaling, transcription regulation, protein synthesis and interaction) and integrates them in quantitative models. These models are subsequently used in various ways, i.e. to identify new targets, generate testable hypotheses, gain insights on the drug's mode of action (MOA), translate preclinical findings, and assess the potential of clinical drug efficacy and toxicity. In the development phase, pharmacokinetic/pharmacodynamic (PK/PD) modeling is the established way to determine safe and efficacious doses for testing at increasingly larger, and more pertinent to the target indication, cohorts of subjects. First, the relationship between drug input and its concentration in plasma is established. Second, the relationship between this concentration and desired or undesired PD responses is ascertained. Recognizing that the interface of systems biology with PK/PD will facilitate drug development, systems pharmacology came into existence, combining methods from PK/PD modeling and systems engineering explicitly to account for the implicated mechanisms of the target system in the study of drug–target interactions. Herein, a number of popular system biology methodologies are discussed, which could be leveraged within a systems pharmacology framework to address major issues in drug development.
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Affiliation(s)
- Ioannis N Melas
- National Technical University of Athens, Athens, Greece; Protatonce Ltd, Athens, Greece
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72
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Lam SW, Jimenez CR, Boven E. Breast cancer classification by proteomic technologies: current state of knowledge. Cancer Treat Rev 2013; 40:129-38. [PMID: 23891266 DOI: 10.1016/j.ctrv.2013.06.006] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/20/2013] [Accepted: 06/25/2013] [Indexed: 11/26/2022]
Abstract
Breast cancer is traditionally considered as a heterogeneous disease. Molecular profiling of breast cancer by gene expression studies has provided us an important tool to discriminate a number of subtypes. These breast cancer subtypes have been shown to be associated with clinical outcome and treatment response. In order to elucidate the functional consequences of altered gene expressions related to each breast cancer subtype, proteomic technologies can provide further insight by identifying quantitative differences at the protein level. In recent years, proteomic technologies have matured to an extent that they can provide proteome-wide expressions in different clinical materials. This technology can be applied for the identification of proteins or protein profiles to further refine breast cancer subtypes or for discovery of novel protein biomarkers pointing towards metastatic potential or therapy resistance in a specific subtype. In this review, we summarize the current state of knowledge of proteomic research on molecular breast cancer classification and discuss important aspects of the potential usefulness of proteomics for discovery of breast cancer-associated protein biomarkers in the clinic.
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Affiliation(s)
- S W Lam
- Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands.
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73
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Chandrasekhar S, Iyer LK, Panchal JP, Topp EM, Cannon JB, Ranade VV. Microarrays and microneedle arrays for delivery of peptides, proteins, vaccines and other applications. Expert Opin Drug Deliv 2013; 10:1155-70. [PMID: 23662940 DOI: 10.1517/17425247.2013.797405] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Peptide and protein microarray and microneedle array technology provides direct information on protein function and potential drug targets in drug discovery and delivery. Because of this unique ability, these arrays are well suited for protein profiling, drug target identification/validation and studies of protein interaction, biochemical activity, immune responses, clinical prognosis and diagnosis and for gene, protein and drug delivery. AREAS COVERED The aim of this review is to describe and summarize past and recent developments of microarrays in their construction, characterization and production and applications of microneedles in drug delivery. The scope and limitations of various technologies in this respect are discussed. EXPERT OPINION This article offers a review of microarray/microneedle technologies and possible future directions in targeting and in the delivery of pharmacologically active compounds for unmet needs in biopharmaceutical research. A better understanding of the production and use of microarrays and microneedles for delivery of peptides, proteins and vaccines is needed.
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Affiliation(s)
- Saradha Chandrasekhar
- Purdue University, Department of Industrial and Physical Pharmacy, West Lafayette, IN 47907, USA
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74
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Kočevar N, Hudler P, Komel R. The progress of proteomic approaches in searching for cancer biomarkers. N Biotechnol 2013; 30:319-26. [DOI: 10.1016/j.nbt.2012.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 11/05/2012] [Indexed: 12/28/2022]
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75
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Ziegler S, Pries V, Hedberg C, Waldmann H. Identifizierung der Zielproteine bioaktiver Verbindungen: Die Suche nach der Nadel im Heuhaufen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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76
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Ziegler S, Pries V, Hedberg C, Waldmann H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 2013; 52:2744-92. [PMID: 23418026 DOI: 10.1002/anie.201208749] [Citation(s) in RCA: 359] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/10/2023]
Abstract
Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.
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Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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Hentschel C, Wagner H, Smiatek J, Heuer A, Fuchs H, Zhang X, Studer A, Chi L. AFM-based force spectroscopy on polystyrene brushes: effect of brush thickness on protein adsorption. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:1850-1856. [PMID: 23343216 DOI: 10.1021/la302212h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Herein we present a study on nonspecific binding of proteins at highly dense packed hydrophobic polystyrene brushes. In this context, an atomic force microscopy tip was functionalized with concanavalin A to perform single-molecule force spectroscopy measurements on polystyrene brushes with thicknesses of 10 and 60 nm, respectively. Polystyrene brushes with thickness of 10 nm show an almost two times stronger protein adsorption than brushes with a thickness of 60 nm: 72 pN for the thinner and 38 pN for the thicker layer, which is in qualitative agreement with protein adsorption studies conducted macroscopically by fluorescence microscopy.
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Affiliation(s)
- Carsten Hentschel
- Physikalisches Institut, Westfälische Wilhelms-Universität, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany
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78
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Whittaker JW. Cell-free protein synthesis: the state of the art. Biotechnol Lett 2013; 35:143-52. [PMID: 23086573 PMCID: PMC3553302 DOI: 10.1007/s10529-012-1075-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/10/2012] [Indexed: 10/27/2022]
Abstract
Cell-free protein synthesis harnesses the synthetic power of biology, programming the ribosomal translational machinery of the cell to create macromolecular products. Like PCR, which uses cellular replication machinery to create a DNA amplifier, cell-free protein synthesis is emerging as a transformative technology with broad applications in protein engineering, biopharmaceutical development, and post-genomic research. By breaking free from the constraints of cell-based systems, it takes the next step towards synthetic biology. Recent advances in reconstituted cell-free protein synthesis (Protein synthesis Using Recombinant Elements expression systems) are creating new opportunities to tailor the reactions for specialized applications including in vitro protein evolution, printing protein microarrays, isotopic labeling, and incorporating nonnatural amino acids.
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Affiliation(s)
- James W Whittaker
- Division of Environmental and Biomolecular Systems, Institute for Environmental Health, Oregon Health and Science University, 20000 N.W. Walker Road, Beaverton, OR 97006-8921, USA.
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79
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Brault ND, White AD, Taylor AD, Yu Q, Jiang S. Directly functionalizable surface platform for protein arrays in undiluted human blood plasma. Anal Chem 2013; 85:1447-53. [PMID: 23298516 DOI: 10.1021/ac303462u] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Protein arrays are a high-throughput approach for proteomic profiling, vital for achieving a greater understanding of biological systems, in addition to disease diagnostics and monitoring therapeutic treatments. In this work, zwitterionic carboxybetaine polymer (pCB) coated substrates were investigated as an array surface platform to enable convenient amino-coupling chemistry on a single directly functionalizable and unblocked film for the sensitive detection of target analytes from undiluted human blood plasma. Using a surface plasmon resonance (SPR) imaging sensor, the antibody immobilization conditions which provided excellent spot morphology and the largest antigen response were determined. It was found that pCB functionalization and the corresponding antigen detection both increased with pH and antibody concentration. Additionally, immobilization only required an aqueous buffer without the need for additives to improve spot quality. The nonspecific protein adsorption to undiluted human plasma on both the antibody immobilized pCB spots and the background were found to be about 9 and 6 ng/cm(2), respectively. A subsequent array consisting of three antibodies spotted onto pCB revealed little cross-reactivity for antigens spiked into the undiluted plasma. The low postfunctionalized nonfouling properties combined with antibody amplification showed similar sensitivities achievable with conventional spectroscopic SPR sensors and the same pCB films, but now with high-throughput capabilities. This represents the first demonstration of low fouling properties following antibody functionalization on protein arrays from undiluted human plasma and indicates the great potential of the pCB platform for high-throughput protein analysis.
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Affiliation(s)
- Norman D Brault
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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80
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Protein Function Microarrays: Design, Use and Bioinformatic Analysis in Cancer Biomarker Discovery and Quantitation. TRANSLATIONAL BIOINFORMATICS 2013. [DOI: 10.1007/978-94-007-5811-7_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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81
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Puch CBMD, Barbier E, Sauvaigo S, Gasparutto D, Breton J. Tools and strategies for DNA damage interactome analysis. Mutat Res 2012; 752:72-83. [PMID: 23220222 DOI: 10.1016/j.mrrev.2012.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 11/01/2012] [Accepted: 11/22/2012] [Indexed: 11/26/2022]
Abstract
DNA is the target of multiple endogenous and exogenous agents generating chemical lesions on the double helix. Cellular DNA damage response pathways rely on a myriad of proteins interacting with DNA alterations. The cartography of this interactome currently includes well known actors of chromatin remodelling, DNA repair or proteins hijacked from their natural functions such as transcription factors. In order to go further into the characterisation of these protein networks, proteomics-based methods began to be used in the early 2000s. The strategies are diverse and include mainly (i) damaged DNA molecules used as targets on protein microarrays, (ii) damaged DNA probes used to trap within complex cellular extracts proteins that are then separated and identified by proteomics, (iii) identification of chromatin- bound proteins after a genotoxic stress, or (iv) identification of proteins associated with other proteins already known to be part of DNA damage interactome. All these approaches have already been performed to find new proteins recognizing oxidised bases, abasic sites, strand breaks or crosslinks generated by anticancer drugs such as nitrogen mustards and platinating agents. Identified interactions are generally confirmed using complementary methods such as electromobility shift assays or surface plasmon resonance. These strategies allowed, for example, demonstration of interactions between cisplatin-DNA crosslinks and PARP-1 or the protein complex PTW/PP. The next challenging step will be to understand the biological repercussions of these newly identified interactions which may help to unravel new mechanisms involved in genetic toxicology, discover new cellular responses to anticancer drugs or identify new biomarkers and therapeutic targets.
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Affiliation(s)
| | - Ewa Barbier
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France
| | - Sylvie Sauvaigo
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France
| | - Didier Gasparutto
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France
| | - Jean Breton
- Laboratoire Lésions des Acides Nucléiques, SCIB, UMR-E3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble, F-38054, France; UFR de Pharmacie, Université Joseph Fourier-Grenoble 1, Domaine de la Merci, La Tronche, F-38706, France.
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82
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Lee JH, Hwang Y, Cheon KA, Jung HI. Emotion-on-a-chip (EOC): evolution of biochip technology to measure human emotion using body fluids. Med Hypotheses 2012; 79:827-32. [PMID: 23036904 DOI: 10.1016/j.mehy.2012.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 08/28/2012] [Accepted: 09/10/2012] [Indexed: 01/10/2023]
Abstract
Recent developments in nano/micro technology have made it possible to construct small-scale sensing chips for the analysis of biological markers such as nucleic acids, proteins, small molecules, and cells. Although biochip technology for the diagnosis of severe physiological diseases (e.g., cancer, diabetes, and cardiovascular disease) has been extensively studied, biochips for the monitoring of human emotions such as stress, fear, depression, and sorrow have not yet been introduced, and the development of such a biochip is in its infancy. Emotion science (or affective engineering) is a rapidly expanding engineering/scientific discipline that has a major impact on human society. The growing interest in the integration of emotion science and engineering is a result of the recent trend of merging various academic fields. In this paper we discuss the potential importance of biochip technology in which human emotion can be precisely measured in real time using body fluids such as blood, saliva, urine, or sweat. We call these biochips emotion-on-a-chip (EOC). The EOC system consists of four parts: (1) collection of body fluids, (2) separation of emotional markers, (3) detection of optical or electrical signals, and (4) display of results. These techniques provide new opportunities to precisely investigate human emotion. Future developments in EOC techniques will combine social and natural sciences to expand their scope of study.
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Affiliation(s)
- Jung-Hyun Lee
- School of Mechanical Engineering, Yonsei University, Seoul, South Korea
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83
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Weissenborn MJ, Wehner JW, Gray CJ, Šardzík R, Eyers CE, Lindhorst TK, Flitsch SL. Formation of carbohydrate-functionalised polystyrene and glass slides and their analysis by MALDI-TOF MS. Beilstein J Org Chem 2012; 8:753-62. [PMID: 23015824 PMCID: PMC3388864 DOI: 10.3762/bjoc.8.86] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 05/02/2012] [Indexed: 01/25/2023] Open
Abstract
Glycans functionalised with hydrophobic trityl groups were synthesised and adsorbed onto polystyrene and glass slides in an array format. The adsorbed glycans could be analysed directly on these minimally conducting surfaces by MALDI-TOF mass spectrometry analysis after aluminium tape was attached to the underside of the slides. Furthermore, the trityl group appeared to act as an internal matrix and no additional matrix was necessary for the MS analysis. Thus, trityl groups can be used as simple hydrophobic, noncovalently linked anchors for ligands on surfaces and at the same time facilitate the in situ mass spectrometric analysis of such ligands.
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Affiliation(s)
- Martin J Weissenborn
- School of Chemistry & Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Johannes W Wehner
- Otto Diels Institute of Organic Chemistry, Christiana Albertina University of Kiel, Otto-Hahn-Platz 3/4, 24098 Kiel, Germany
| | - Christopher J Gray
- School of Chemistry & Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Robert Šardzík
- School of Chemistry & Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Claire E Eyers
- School of Chemistry & Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Thisbe K Lindhorst
- Otto Diels Institute of Organic Chemistry, Christiana Albertina University of Kiel, Otto-Hahn-Platz 3/4, 24098 Kiel, Germany
| | - Sabine L Flitsch
- School of Chemistry & Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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84
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Weissenborn MJ, Castangia R, Wehner JW, Šardzík R, Lindhorst TK, Flitsch SL. Oxo-ester mediated native chemical ligation on microarrays: an efficient and chemoselective coupling methodology. Chem Commun (Camb) 2012; 48:4444-6. [PMID: 22456682 DOI: 10.1039/c2cc30844d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report a highly efficient and selective method for the coupling of peptides and glycoconjugates bearing N-terminal cysteines to activated surfaces. This chemoselective method generates stable amide linkages without using any thiol additives.
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Affiliation(s)
- Martin J Weissenborn
- School of Chemistry & Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M17DN, UK
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85
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Stahl PJ, Cruz JC, Li Y, Michael Yu S, Hristova K. On-the-resin N-terminal modification of long synthetic peptides. Anal Biochem 2012; 424:137-9. [PMID: 22387389 DOI: 10.1016/j.ab.2012.02.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 02/21/2012] [Accepted: 02/22/2012] [Indexed: 12/16/2022]
Abstract
Here we present a highly efficient protocol for on-the-resin coupling of fluorescent dyes or other functional groups to the N-termini of synthetic peptides prior to cleavage and deprotection. The protocol avoids expensive preactivated dyes and instead employs carboxylated dyes activated by large amounts of coupling reagents. The protocol was used to label peptides with low reactivity such as long hydrophobic peptides and peptides with strong tendencies to form sterically shielding structures or aggregates in solution. In all cases, the yields far exceeded those from commercially available preactivated compounds.
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Affiliation(s)
- Patrick J Stahl
- Department of Materials Science and Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
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86
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87
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Hamdi A, Colas P. Yeast two-hybrid methods and their applications in drug discovery. Trends Pharmacol Sci 2012; 33:109-18. [DOI: 10.1016/j.tips.2011.10.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/21/2011] [Accepted: 10/24/2011] [Indexed: 01/08/2023]
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88
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Fan Z, Keum YS, Li QX, Shelver WL, Guo LH. Sensitive immunoassay detection of multiple environmental chemicals on protein microarrays using DNA/dye conjugate as a fluorescent label. ACTA ACUST UNITED AC 2012; 14:1345-52. [DOI: 10.1039/c2em10956e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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89
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Dwane S, Kiely PA. Tools used to study how protein complexes are assembled in signaling cascades. Bioeng Bugs 2011; 2:247-59. [PMID: 22002082 PMCID: PMC3225741 DOI: 10.4161/bbug.2.5.17844] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Revised: 08/19/2011] [Accepted: 08/24/2011] [Indexed: 01/08/2023] Open
Abstract
Most proteins do not function on their own but as part of large signaling complexes that are arranged in every living cell in response to specific environmental cues. Proteins interact with each other either constitutively or transiently and do so with different affinity. When identifying the role played by a protein inside a cell, it is essential to define its particular cohort of binding partners so that the researcher can predict what signaling pathways the protein is engaged in. Once identified and confirmed, the information might allow the interaction to be manipulated by pharmacological inhibitors to help fight disease. In this review, we discuss protein-protein interactions and how they are essential to propagate signals in signaling pathways. We examine some of the high-throughput screening methods and focus on the methods used to confirm specific protein-protein interactions including; affinity tagging, co-immunoprecipitation, peptide array technology and fluorescence microscopy.
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Affiliation(s)
- Susan Dwane
- Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
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90
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Jessulat M, Pitre S, Gui Y, Hooshyar M, Omidi K, Samanfar B, Tan LH, Alamgir M, Green J, Dehne F, Golshani A. Recent advances in protein-protein interaction prediction: experimental and computational methods. Expert Opin Drug Discov 2011; 6:921-35. [PMID: 22646215 DOI: 10.1517/17460441.2011.603722] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Proteins within the cell act as part of complex networks, which allow pathways and processes to function. Therefore, understanding how proteins interact is a significant area of current research. AREAS COVERED This review aims to present an overview of key experimental techniques (yeast two-hybrid, tandem affinity purification and protein microarrays) used to discover protein-protein interactions (PPIs), as well as to briefly discuss certain computational methods for predicting protein interactions based on gene localization, phylogenetic information, 3D structural modeling or primary protein sequence data. Due to the large-scale applicability of primary sequence-based methods, the authors have chosen to focus on this strategy for our review. There is an emphasis on a recent algorithm called Protein Interaction Prediction Engine (PIPE) that can predict global PPIs. The readers will discover recent advances both in the practical determination of protein interaction and the strategies that are available to attempt to anticipate interactions without the time and costs of experimental work. EXPERT OPINION Global PPI maps can help understand the biology of complex diseases and facilitate the identification of novel drug target sites. This study describes different techniques used for PPI prediction that we believe will significantly impact the development of the field in a new future. We expect to see a growing number of similar techniques capable of large-scale PPI predictions.
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Affiliation(s)
- Matthew Jessulat
- Carleton University , Department of Biology , 209 Nesbitt Building, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6 , Canada
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