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Hellwig P, Dittrich A, Heyer R, Reichl U, Benndorf D. Detection, isolation and characterization of phage-host complexes using BONCAT and click chemistry. Front Microbiol 2024; 15:1434301. [PMID: 39296306 PMCID: PMC11409252 DOI: 10.3389/fmicb.2024.1434301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/15/2024] [Indexed: 09/21/2024] Open
Abstract
Introduction Phages are viruses that infect prokaryotes and can shape microbial communities by lysis, thus offering applications in various fields. However, challenges exist in sampling, isolation and accurate prediction of the host specificity of phages as well as in the identification of newly replicated virions in response to environmental challenges. Methods A new workflow using biorthogonal non-canonical amino acid tagging (BONCAT) and click chemistry (CC) allowed the combined analysis of phages and their hosts, the identification of newly replicated virions, and the specific tagging of phages with biotin for affinity chromatography. Results Replication of phage λ in Escherichia coli was selected as a model for workflow development. Specific labeling of phage λ proteins with the non-canonical amino acid 4-azido-L-homoalanine (AHA) during phage development in E. coli was confirmed by LC-MS/MS. Subsequent tagging of AHA with fluorescent dyes via CC allowed the visualization of phages adsorbed to the cell surface by fluorescence microscopy. Flow cytometry enabled the automated detection of these fluorescent phage-host complexes. Alternatively, AHA-labeled phages were tagged with biotin for purification by affinity chromatography. Despite biotinylation the tagged phages could be purified and were infectious after purification. Discussion Applying this approach to environmental samples would enable host screening without cultivation. A flexible and powerful workflow for the detection and enrichment of phages and their hosts in pure cultures has been established. The developed method lays the groundwork for future workflows that could enable the isolation of phage-host complexes from diverse complex microbial communities using fluorescence-activated cell sorting or biotin purification. The ability to expand and customize the workflow through the growing range of compounds for CC offers the potential to develop a versatile toolbox in phage research. This work provides a starting point for these further studies by providing a comprehensive standard operating procedure.
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Affiliation(s)
- Patrick Hellwig
- Chair of Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg, Magdeburg, Germany
| | - Anna Dittrich
- Department of Systems Biology, Institute of Biology, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Robert Heyer
- Multidimensional Omics Analyses Group, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Multidimensional Omics Analyses Group, Faculty of Technology, Bielefeld University, Universitätsstraße, Bielefeld, Germany
| | - Udo Reichl
- Chair of Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg, Magdeburg, Germany
| | - Dirk Benndorf
- Chair of Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg, Magdeburg, Germany
- Department of Microbiology, Anhalt University of Applied Sciences, Köthen, Germany
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Paiva ACF, Lemos AR, Busse P, Martins MT, Silva DO, Freitas MC, Santos SP, Freire F, Barrey EJ, Manival X, Koetzner L, Heinrich T, Wegener A, Grädler U, Bandeiras TM, Schwarz D, Sousa PMF. Extract2Chip-Bypassing Protein Purification in Drug Discovery Using Surface Plasmon Resonance. BIOSENSORS 2023; 13:913. [PMID: 37887106 PMCID: PMC10605449 DOI: 10.3390/bios13100913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
Modern drug discovery relies on combinatorial screening campaigns to find drug molecules targeting specific disease-associated proteins. The success of such campaigns often relies on functional and structural information of the selected therapeutic target, only achievable once its purification is mastered. With the aim of bypassing the protein purification process to gain insights on the druggability, ligand binding, and/or characterization of protein-protein interactions, herein, we describe the Extract2Chip method. This approach builds on the immobilization of site-specific biotinylated proteins of interest, directly from cellular extracts, on avidin-coated sensor chips to allow for the characterization of molecular interactions via surface plasmon resonance (SPR). The developed method was initially validated using Cyclophilin D (CypD) and subsequently applied to other drug discovery projects in which the targets of interest were difficult to express, purify, and crystallize. Extract2Chip was successfully applied to the characterization of Yes-associated protein (YAP): Transcriptional enhancer factor TEF (TEAD1) protein-protein interaction inhibitors, in the validation of a ternary complex assembly composed of Dyskerin pseudouridine synthase 1 (DKC1) and RuvBL1/RuvBL2, and in the establishment of a fast-screening platform to select the most suitable NUAK family SNF1-like kinase 2 (NUAK2) surrogate for binding and structural studies. The described method paves the way for a potential revival of the many drug discovery campaigns that have failed to deliver due to the lack of suitable and sufficient protein supply.
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Affiliation(s)
- Ana C. F. Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana R. Lemos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Philipp Busse
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Madalena T. Martins
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
| | - Diana O. Silva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Micael C. Freitas
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Sandra P. Santos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Filipe Freire
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Evelyne J. Barrey
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Xavier Manival
- IMoPA, CNRS, Université de Lorraine, F-54000 Nancy, France;
| | - Lisa Koetzner
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Timo Heinrich
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Ansgar Wegener
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Ulrich Grädler
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Tiago M. Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Daniel Schwarz
- Merck Healthcare KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; (E.J.B.); (L.K.); (T.H.); (A.W.); (U.G.)
| | - Pedro M. F. Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (A.C.F.P.); (A.R.L.); (P.B.); (M.T.M.); (D.O.S.); (M.C.F.); (S.P.S.); (F.F.); (T.M.B.)
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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Halbi G, Fayer I, Aranovich D, Gat S, Pavan MJ, Nachmias D, Sanchez DS, Brik A, Granek R, Bernheim-Groswasser A. Smart design of universally decorated nanoparticles for drug delivery applications driven by active transport. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:74. [PMID: 37653248 DOI: 10.1140/epje/s10189-023-00331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/25/2023] [Indexed: 09/02/2023]
Abstract
Targeting the cell nucleus remains a challenge for drug delivery. Here, we present a universal platform for the smart design of nanoparticle (NP) decoration that is based on: (i) a spacer polymer, commonly biotin-polyethylene-glycol-thiol, whose grafting density and molecular weight can be tuned for optimized performance, and (ii) protein binding peptides, such as cell penetrating peptides (CPPs), cancer-targeting peptides, or nuclear localization signal (NLS) peptides, that are linked to the PEG free-end by universal chemistry. We manifested our platform with two different bromo-acetamide (Br-Ac) modified NLSs. We used cell extract-based and live cell assays to demonstrate the recruitment of dynein motor proteins, which drive the NP active transport toward the nucleus, and the enhancement of cellular and nuclear entry, manifesting the properties of NLS as a CPP. Our control of the NP decoration scheme, and the modularity of our platform, carry great advantages for nano-carrier design for drug delivery applications.
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Affiliation(s)
- Gal Halbi
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Itay Fayer
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Dina Aranovich
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Shachar Gat
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Mariela J Pavan
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Dikla Nachmias
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Daniel Sevilla Sanchez
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, 3200008, Haifa, Israel
| | - Rony Granek
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Anne Bernheim-Groswasser
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.
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4
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Jang M, Kim S, Song J, Kim S. Highly sensitive and rapid detection of porcine circovirus 2 by avidin-biotin complex based lateral flow assay coupled to isothermal amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:4429-4436. [PMID: 34486596 DOI: 10.1039/d1ay01189h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this study, a new platform for the detection of porcine circovirus 2 was developed by avidin-biotin complex based lateral flow assay (LAMP-LFA). Improved detection sensitivity was attained by using loop mediated isothermal amplification (LAMP) with a low limit of detection (LOD), so the platform can be used to detect even early or asymptomatic stages of infection. LFA, which requires no specialized equipment, facilitates the use of point-of-care (POC) tests. Therefore, by applying LFA, the result can be confirmed accurately with the naked eye. Moreover, this platform has a unique structure using a single-tag detection system. The avidin-biotin interaction is the strongest interaction between proteins and has a higher Kd value than antigen-antibody interactions. Thus, the results are stable and can be clearly confirmed. The high sensitivity of LAMP-LFA enables all steps to be completed in 30 min. As a result, it could be applied to different targets, such as other pathogens. Future POC diagnostic studies are expected to be of great practical benefit.
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Affiliation(s)
- Minju Jang
- Department of Bionanotechnology, Gachon University, Seongnam, 461-70, Republic of Korea.
| | - SeJin Kim
- R&D Center, Philmedi Ltd, Seongnam, 461-70, Republic of Korea
| | - Junkyu Song
- R&D Center, Philmedi Ltd, Seongnam, 461-70, Republic of Korea
| | - Sanghyo Kim
- Department of Bionanotechnology, Gachon University, Seongnam, 461-70, Republic of Korea.
- R&D Center, Philmedi Ltd, Seongnam, 461-70, Republic of Korea
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5
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Perret G, Boschetti E. Aptamer-Based Affinity Chromatography for Protein Extraction and Purification. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:93-139. [PMID: 31485702 DOI: 10.1007/10_2019_106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations. Graphical Abstract Aptamer-protein complexes by X-ray crystallography.
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Ding Y, Williams NH, Hunter CA. A Synthetic Vesicle-to-Vesicle Communication System. J Am Chem Soc 2019; 141:17847-17853. [PMID: 31642667 DOI: 10.1021/jacs.9b09102] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A molecular signal displayed on the external surface of one population of vesicles was used to trigger a catalytic process on the inside of a second population of vesicles. The key recognition event is the transfer of a protein (NeutrAvidin) bound to vesicles displaying desthiobiotin to vesicles displaying biotin. The desthiobiotin-protein complex was used to anchor a synthetic transducer in the outer leaflet of the vesicles, and when the protein was displaced, the transducer translocated across the bilayer to expose a catalytic headgroup to the internal vesicle solution. As a result, an ester substrate encapsulated on the inside of this second population of vesicles was hydrolyzed to give a fluorescence output signal. The protein has four binding sites, which leads to multivalent interactions with membrane-anchored ligands and very high binding affinities. Thus, biotin, which has a dissociation constant 3 orders of magnitude higher than desthiobiotin, did not displace the protein from the membrane-anchored transducer, and membrane-anchored biotin displayed on the surface of a second population of vesicles was required to generate an effective input signal.
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Affiliation(s)
- Yudi Ding
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Nicholas H Williams
- Department of Chemistry , University of Sheffield , Sheffield S3 7HF , United Kingdom
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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Refolding with Simultaneous Purification of Recombinant Core Streptavidin Using Single-step High-performance Hydrophobic Interaction Chromatography. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-019-0041-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Soltani O, Bozorgmehr MR, Momen-Heravi M. Does the single-walled carbon nanotube affect the rate constant of binding of biotin to streptavidin? Molecular dynamics simulation perspective. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.1177/1468678319825710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The interaction of biotin and streptavidin in the presence and absence of a carbon nanotube was studied by molecular dynamics simulation. With respect to the Arrhenius dependence of the rate constants with temperature, those of streptavidin–biotin complex formation ([Formula: see text]) and streptavidin–biotin complex dissociation ([Formula: see text]) were calculated from molecular dynamics simulation trajectories. Nanotube has reduced the amount of and k1and k1. However, the biotin position in streptavidin does not change much. The results obtained from MMPBSA calculations show that the contribution of the van der Waals forces to both systems (in the absence and presence of the nanotube) was greater than that of electrostatic forces. The presence of the nanotube also led to the reduction of van der Waals and electrostatic forces in the interaction of biotin with streptavidin. However, this reduction was greater for electrostatic forces. In the absence of a nanotube, there are four hydrogen bonds between streptavidin and biotin, which are related to the residues Ser27, Tyr43, Ser45 and Ser88. In the presence of the nanotube, the hydrogen bonding of biotin with Ser45 is removed.
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Affiliation(s)
- Orkide Soltani
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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Gao T, Li L, Chen T, Shi L, Yang Y, Li G. DNA-Oriented Shaping of Cell Features for the Detection of Rare Disseminated Tumor Cells. Anal Chem 2018; 91:1126-1132. [DOI: 10.1021/acs.analchem.8b04783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tao Gao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Lingling Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Tianshu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Liu Shi
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Yang Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Genxi Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
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Cohen L, Walt DR. Evaluation of Antibody Biotinylation Approaches for Enhanced Sensitivity of Single Molecule Array (Simoa) Immunoassays. Bioconjug Chem 2018; 29:3452-3458. [PMID: 30272951 DOI: 10.1021/acs.bioconjchem.8b00601] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, we evaluated the performance of Single Molecule Array (Simoa) immunoassays based on various detection antibody biotinylation approaches. Simoa immunoassays, like other sandwich ELISAs, are highly dependent on the interaction of a biotinylated detection antibody with an enzyme conjugated to streptavidin. Thus, we sought to assess whether different biotinylation reagents can improve the performance and sensitivity of Simoa assays. We selected three proteins, GM-CSF, IFNγ, and IL-2, that are present at ultralow levels in many biological samples. We compared the performance of these Simoa assays by using five different biotinylation reagents and varying the amount of molar fold excess biotin during the biotinylation process. We found that the choice of biotinylation reagent and the molar fold excess biotin can highly affect the performance of the Simoa assays, with differences of up to an order of magnitude in sensitivity. We also tested the performance of bulk ELISAs using the different biotinylated detection antibodies and observe differences greater than an order of magnitude in sensitivity. We show that evaluating different strategies for detection antibody biotinylation is a simple approach for optimizing immunoassay performance for enhanced sensitivity.
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Affiliation(s)
- Limor Cohen
- Department of Pathology, Brigham and Women's Hospital , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - David R Walt
- Department of Pathology, Brigham and Women's Hospital , Harvard Medical School , Boston , Massachusetts 02115 , United States
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11
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Novel biotin linker with alkyne and amino groups for chemical labelling of a target protein of a bioactive small molecule. Bioorg Med Chem Lett 2018; 28:783-786. [PMID: 29306572 DOI: 10.1016/j.bmcl.2017.12.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/22/2017] [Accepted: 12/23/2017] [Indexed: 11/24/2022]
Abstract
We synthesized a novel linker (1) with biotin, alkyne and amino groups for the identification of target proteins using a small molecule that contains an azide group (azide probe). The alkyne in the linker bound the azide probe via an azide-alkyne Huisgen cycloaddition. A protein cross-linker effectively bound the conjugate of the linker and an azide probe with a target protein. The covalently bound complex was detected by western blotting. Linker 1 was applied to a model system using an abscisic acid receptor, RCAR/PYR/PYL (PYL). Cross-linked complexes of linker 1, the azide probes and the target proteins were successfully visualized by western blotting. This method of target protein identification was more effective than a previously developed method that uses a second linker with biotin, alkyne, and benzophenone (linker 2) that acts to photo-crosslink target proteins. The system developed in this study is a method for identifying the target proteins of small bioactive molecules and is different from photo-affinity labelling.
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Park M, Pyun JC, Jose J. Orientation and density control of proteins on solid matters by outer membrane coating: Analytical and diagnostic applications. J Pharm Biomed Anal 2017; 147:174-184. [PMID: 28797956 DOI: 10.1016/j.jpba.2017.07.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/28/2017] [Accepted: 07/29/2017] [Indexed: 12/11/2022]
Abstract
Autodisplay is an expression system for the display of recombinant proteins on the outer membrane (OM) of gram negative bacteria and has been developed for translocation studies, whole cell biocatalysis, bioremediation, inhibitor screening, and enzyme refolding. Recently, affinity proteins such as IgG-binding Z-domains and biotin-binding streptavidin have been autodisplayed on the OM of Escherichia coli for analytical and biomedical applications. The secretion mechanism of the autodisplay system was used and orientation and density control of these affinity proteins were determined. Affinity protein-autodisplaying E. coli cells have been used to coat solid supports in immunoassays. For this purpose, the OM of autodisplayed E. coli cells was separated and isolated by the aid of detergents. The structure of the resulting OM liposomes as well as their physico-chemical parameters, were analyzed. OM liposomes were used subsequently for coating various solid matters including microplates and biosensor transducer surfaces and the formation of OM layers were monitored. OM layer formation on solid matters was shown to increase the sensitivity of immunoassays and biosensors. In this review, analytical and diagnostic applications are described in particular concerning orientation and density control of autodisplayed affinity proteins.
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Affiliation(s)
- Min Park
- Integrative Materials Research Institute, Hallym University, Chuncheon-si, Republic of Korea; Department of Materials Science and Engineering, Hallym University, Chuncheon-si, Republic of Korea
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering, Yonsei University, Seoul, Republic of Korea
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, PharmaCampus, Westfälische Wilhelms-Universität, Münster, Germany.
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13
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Laszlo KJ, Bush MF. Interpreting the Collision Cross Sections of Native-like Protein Ions: Insights from Cation-to-Anion Proton-Transfer Reactions. Anal Chem 2017. [PMID: 28636334 DOI: 10.1021/acs.analchem.7b01474] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effects of charge state on structures of native-like cations of serum albumin, streptavidin, avidin, and alcohol dehydrogenase were probed using cation-to-anion proton-transfer reactions (CAPTR), ion mobility, mass spectrometry, and complementary energy-dependent experiments. The CAPTR products all have collision cross-section (Ω) values that are within 5.5% of the original precursor cations. The first CAPTR event for each precursor yields products that have smaller Ω values and frequently exhibit the greatest magnitude of change in Ω resulting from a single CAPTR event. To investigate how the structures of the precursors affect the structures of the products, ions were activated as a function of energy prior to CAPTR. In each case, the Ω values of the activated precursors increase with increasing energy, but the Ω values of the CAPTR products are smaller than the activated precursors. To investigate the stabilities of the CAPTR products, the products were activated immediately prior to ion mobility. These results show that additional structures with smaller or larger Ω values can be populated and that the structures and stabilities of these ions depend most strongly on the identity of the protein and the charge state of the product, rather than the charge state of the precursor or the number of CAPTR events. Together, these results indicate that the excess charges initially present on native-like ions have a modest, but sometimes statistically significant, effect on their Ω values. Therefore, potential contributions from charge state should be considered when using experimental Ω values to elucidate structures in solution.
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Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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14
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Zhan R, Liu B. End Functionalized Nonionic Water-Dispersible Conjugated Polymers. Macromol Rapid Commun 2017; 38. [PMID: 28508508 DOI: 10.1002/marc.201700010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/11/2017] [Indexed: 11/07/2022]
Abstract
2,7-Dibromofluorene monomers carrying two or four oligo(ethylene glycol) (OEG) side chains are synthesized. Heck coupling between the monomers and 1,4-divinylbenzene followed by end capping with [4-(4-bromophenoxy)butyl]carbamic acid tert-butyl ester leads to two nonionic water-dispersible poly(fluorene-alt-1,4-divinylenephenylene)s end-functionalized with amine groups after hydrolysis. In water, the polymer with a lower OEG density (P1) has poor water dispersibility with a quantum yield of 0.24, while the polymer with a higher OEG density (P2) possesses excellent water-dispersibility with a high quantum yield of 0.45. Both polymers show fluorescence enhancement and blue-shifted absorption and emission maxima in the presence of surfactant sodium dodecyl sulfate and dodecyltrimethylammonium bromide. The polymers are also resistant to ionic strength with minimal nonspecific interactions to bovine serum albumin. When biotin is incorporated into the end of the polymer backbones through N-hydroxysuccinimide/amine coupling reaction, the biotinylated polymers interact specifically with streptavidin on solid surface.
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Affiliation(s)
- Ruoyu Zhan
- School of Materials Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai, 201804, China
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 11758, Singapore.,Institute of Materials Research and Engineering, A*STAR, 3 Research Link, 117602, Singapore
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15
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Sun L, Wan J, Schaefer CG, Zhang Z, Tan J, Guo J, Wu L, Wang C. Specific On-site Assembly of Multifunctional Magnetic Nanocargos Based on Highly Efficient and Parallelized Bioconjugation: Toward Personalized Cancer Targeting Therapy. ACS Biomater Sci Eng 2017; 3:381-391. [PMID: 33465935 DOI: 10.1021/acsbiomaterials.6b00773] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The rational design of particle-based cancer theranostic agents, combining diagnostic and therapeutic features in a single entity, has emerged as an effective approach toward personalized cancer therapy; however, creating a flexible assembly of specific targeting ligands with regard to a broad range of tumor tissues and cells is still challenging. Here, we present a convenient and highly variable on-site assembly strategy for the preparation of multifunctional doxorubicin (DOX)-loaded nanocargos with magnetic supraparticles (MSPs) as a core and redox-degradable poly(methylacrylic acid-co-N,N-bis(acryloyl) cystamine) (P(MAA-co-Cy) as the shell, which could be simultaneously modified with multiple targeting ligands through parallelized bioconjugation on the basis of a streptavidin-biotin (SA-BT) interaction. Under physiological conditions similar to those of the cytoplasm of tumor cells, DOX could be released in a controlled manner from these nanocargos to specific tumor sites, while dual-ligand modified nanocargos showed remarkable proliferation inhibition for the HeLa cells and the SK-OV-3 cells that overexpressed both folate as well as integrin receptors. The experimental results demonstrated that the on-site assembly strategy described herein opens access to highly efficient targeting drug delivery systems toward personalized cancer targeting therapy by incorporating functional diversity, which can be easily achieved through highly efficient and parallelized one-step bioconjugation.
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Affiliation(s)
- Luyan Sun
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, 220 Handan Road, Shanghai, 200433, People's Republic of China
| | - Jiaxun Wan
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, 220 Handan Road, Shanghai, 200433, People's Republic of China
| | - Christian G Schaefer
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, 220 Handan Road, Shanghai, 200433, People's Republic of China
| | - Zihao Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, 220 Handan Road, Shanghai, 200433, People's Republic of China
| | - Jing Tan
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, 220 Handan Road, Shanghai, 200433, People's Republic of China
| | - Jia Guo
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, 220 Handan Road, Shanghai, 200433, People's Republic of China
| | - Limin Wu
- Department of Materials Science, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Changchun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, 220 Handan Road, Shanghai, 200433, People's Republic of China
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16
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Martin SC, Vohidov F, Wang H, Knudsen SE, Marzec AA, Ball ZT. Designing Selectivity in Dirhodium Metallopeptide Catalysts for Protein Modification. Bioconjug Chem 2017; 28:659-665. [DOI: 10.1021/acs.bioconjchem.6b00716] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samuel C. Martin
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Farrukh Vohidov
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Haopei Wang
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Sarah E. Knudsen
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Alex A. Marzec
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Zachary T. Ball
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
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17
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Müller JM, Bruhn S, Flaschel E, Friehs K, Risse JM. GAP promoter-based fed-batch production of highly bioactive core streptavidin byPichia pastoris. Biotechnol Prog 2016; 32:855-64. [DOI: 10.1002/btpr.2283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/02/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Jakob Michael Müller
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Simon Bruhn
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Erwin Flaschel
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Karl Friehs
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
| | - Joe Max Risse
- Lehrstuhl Für Fermentationstechnik, Technische Fakultät, Universität Bielefeld; PF 10 01 31 Bielefeld D-33501 Germany
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18
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Strzelczyk P, Bujacz G. Crystal structure and ligand affinity of avidin in the complex with 4′-hydroxyazobenzene-2-carboxylic acid. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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19
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Anabuki T, Tsukahara M, Matsuura H, Takahashi K. Tandem photoaffinity labeling of a target protein using a linker with biotin, alkyne and benzophenone groups and a bioactive small molecule with an azide group. Biosci Biotechnol Biochem 2016; 80:432-9. [DOI: 10.1080/09168451.2015.1104240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
A novel linker containing biotin, alkyne and benzophenone groups (1) was synthesized to identify target proteins using a small molecule probe. This small molecule probe contains an azide group (azide probe) that reacts with an alkyne in 1 via an azide–alkyne Huisgen cycloaddition. Cross-linking of benzophenone to the target protein formed a covalently bound complex consisting of the azide probe and the target protein via 1. The biotin was utilized via biotin–avidin binding to identify the cross-linked complex. To evaluate the effectiveness of 1, it was applied in a model system using an allene oxide synthase (AOS) from the model moss Physcomitrella patens (PpAOS1) and an AOS inhibitor that contained azide group (3). The cross-linked complex consisting of PpAOS1, 1 and 3 was resolved via SDS–PAGE and visualized using a chemiluminescent system. The method that was developed in this study enables the effective identification of target proteins.
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Affiliation(s)
- Tomoaki Anabuki
- Research Faculty of Agriculture, Division of Fundamental Agriscience Research, Hokkaido University, Sapporo, Japan
| | - Miu Tsukahara
- Research Faculty of Agriculture, Division of Fundamental Agriscience Research, Hokkaido University, Sapporo, Japan
| | - Hideyuki Matsuura
- Research Faculty of Agriculture, Division of Fundamental Agriscience Research, Hokkaido University, Sapporo, Japan
| | - Kosaku Takahashi
- Research Faculty of Agriculture, Division of Fundamental Agriscience Research, Hokkaido University, Sapporo, Japan
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20
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Constitutive production and efficient secretion of soluble full-length streptavidin by an Escherichia coli ‘leaky mutant’. J Biotechnol 2016; 221:91-100. [DOI: 10.1016/j.jbiotec.2016.01.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 01/18/2016] [Accepted: 01/22/2016] [Indexed: 11/22/2022]
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21
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Kwon K, Kim C, Lee J, Kim H, Ree M. Self-Assembly-Assisted Biomolecule-Enriched Surface and High Selectivity Performance of Simple Solution-Coatable Biomimicking Brush Copolymers. Biomacromolecules 2016; 17:974-84. [DOI: 10.1021/acs.biomac.5b01635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kyungho Kwon
- Department
of Chemistry, Division of Advanced Materials Science, Pohang Accelerator
Laboratory, Polymer Research Institute, and BK School of Molecular
Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Changsub Kim
- Department
of Chemistry, Division of Advanced Materials Science, Pohang Accelerator
Laboratory, Polymer Research Institute, and BK School of Molecular
Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Jongchan Lee
- Department
of Chemistry, Division of Advanced Materials Science, Pohang Accelerator
Laboratory, Polymer Research Institute, and BK School of Molecular
Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Heesoo Kim
- Department
of Microbiology and Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju 780-714, Republic of Korea
| | - Moonhor Ree
- Department
of Chemistry, Division of Advanced Materials Science, Pohang Accelerator
Laboratory, Polymer Research Institute, and BK School of Molecular
Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
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22
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Koch C, Wabbel K, Eber FJ, Krolla-Sidenstein P, Azucena C, Gliemann H, Eiben S, Geiger F, Wege C. Modified TMV Particles as Beneficial Scaffolds to Present Sensor Enzymes. FRONTIERS IN PLANT SCIENCE 2015; 6:1137. [PMID: 26734040 PMCID: PMC4689848 DOI: 10.3389/fpls.2015.01137] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/30/2015] [Indexed: 05/22/2023]
Abstract
Tobacco mosaic virus (TMV) is a robust nanotubular nucleoprotein scaffold increasingly employed for the high density presentation of functional molecules such as peptides, fluorescent dyes, and antibodies. We report on its use as advantageous carrier for sensor enzymes. A TMV mutant with a cysteine residue exposed on every coat protein (CP) subunit (TMVCys) enabled the coupling of bifunctional maleimide-polyethylene glycol (PEG)-biotin linkers (TMVCys/Bio). Its surface was equipped with two streptavidin [SA]-conjugated enzymes: glucose oxidase ([SA]-GOx) and horseradish peroxidase ([SA]-HRP). At least 50% of the CPs were decorated with a linker molecule, and all thereof with active enzymes. Upon use as adapter scaffolds in conventional "high-binding" microtiter plates, TMV sticks allowed the immobilization of up to 45-fold higher catalytic activities than control samples with the same input of enzymes. Moreover, they increased storage stability and reusability in relation to enzymes applied directly to microtiter plate wells. The functionalized TMV adsorbed to solid supports showed a homogeneous distribution of the conjugated enzymes and structural integrity of the nanorods upon transmission electron and atomic force microscopy. The high surface-increase and steric accessibility of the viral scaffolds in combination with the biochemical environment provided by the plant viral coat may explain the beneficial effects. TMV can, thus, serve as a favorable multivalent nanoscale platform for the ordered presentation of bioactive proteins.
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Affiliation(s)
- Claudia Koch
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Katrin Wabbel
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Fabian J. Eber
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Peter Krolla-Sidenstein
- Chemistry of Oxydic and Organic Interfaces, Karlsruhe Institute of Technology, Institute of Functional InterfacesKarlsruhe, Germany
| | - Carlos Azucena
- Chemistry of Oxydic and Organic Interfaces, Karlsruhe Institute of Technology, Institute of Functional InterfacesKarlsruhe, Germany
| | - Hartmut Gliemann
- Chemistry of Oxydic and Organic Interfaces, Karlsruhe Institute of Technology, Institute of Functional InterfacesKarlsruhe, Germany
| | - Sabine Eiben
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Fania Geiger
- Department of New Materials and Biosystems, Max-Planck-Institute for Intelligent SystemsStuttgart, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
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23
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Avraham O, Meir A, Fish A, Bayer EA, Livnah O. Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail. J Struct Biol 2015; 191:139-48. [DOI: 10.1016/j.jsb.2015.06.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 11/30/2022]
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24
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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25
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Mavrogiannopoulou E, Petrou PS, Koukouvinos G, Yannoukakos D, Siafaka-Kapadai A, Fornal K, Awsiuk K, Budkowski A, Kakabakos SE. Improved DNA microarray detection sensitivity through immobilization of preformed in solution streptavidin/biotinylated oligonucleotide conjugates. Colloids Surf B Biointerfaces 2015; 128:464-472. [PMID: 25805150 DOI: 10.1016/j.colsurfb.2015.02.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/18/2022]
Abstract
A novel immobilization approach involving binding of preformed streptavidin/biotinylated oligonucleotide conjugates onto surfaces coated with biotinylated bovine serum albumin is presented. Microarrays prepared according to the proposed method were compared, in terms of detection sensitivity and specificity, with other immobilization schemes employing coupling of biotinylated oligonucleotides onto directly adsorbed surface streptavidin, or sequential coupling of streptavidin and biotinylated oligonucleotides onto a layer of adsorbed biotinylated bovine serum albumin. A comparison was performed employing biotinylated oligonucleotides corresponding to wild- and mutant-type sequences of seven single point mutations of the BRCA1 gene. With respect to the other immobilization protocols, the proposed oligonucleotide immobilization approach offered the highest hybridization signals (at least 5 times higher) and permitted more elaborative washings, thus providing considerably higher discrimination between complimentary and non-complementary DNA sequences for all mutations tested. In addition, the hybridization kinetics were significantly enhanced compared to two other immobilization protocols, permitting PCR sample analysis in less than 40 min. Thus, the proposed oligonucleotide immobilization approach offered improved detection sensitivity and discrimination ability along with considerably reduced analysis time, and it is expected to find wide application in DNA mutation detection.
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Affiliation(s)
- E Mavrogiannopoulou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - P S Petrou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - G Koukouvinos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - D Yannoukakos
- Molecular Diagnostics Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - A Siafaka-Kapadai
- Biochemistry Lab, Department of Chemistry, University of Athens, GR-15771 Panepistimiopolis, Athens, Greece
| | - K Fornal
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - K Awsiuk
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - A Budkowski
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - S E Kakabakos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece.
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26
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Cornilleau T, Audrain H, Guillemet A, Hermange P, Fouquet E. General Last-Step Labeling of Biomolecule-Based Substrates by [12C], [13C], and [11C] Carbon Monoxide. Org Lett 2015; 17:354-7. [DOI: 10.1021/ol503471e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Thomas Cornilleau
- Université de Bordeaux, Institut des Sciences Moléculaires, UMR-CNRS 5255, 351, Cours de la
Libération, 33405 Talence Cedex, France
| | - Hélène Audrain
- Department
of Nuclear Medicine and PET Center, Aarhus University Hospital, Nørrebrogade 44, DK-8000 Aarhus, Denmark
| | - Aude Guillemet
- Université de Bordeaux, Institut des Sciences Moléculaires, UMR-CNRS 5255, 351, Cours de la
Libération, 33405 Talence Cedex, France
| | - Philippe Hermange
- Université de Bordeaux, Institut des Sciences Moléculaires, UMR-CNRS 5255, 351, Cours de la
Libération, 33405 Talence Cedex, France
| | - Eric Fouquet
- Université de Bordeaux, Institut des Sciences Moléculaires, UMR-CNRS 5255, 351, Cours de la
Libération, 33405 Talence Cedex, France
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27
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Taskinen B, Zauner D, Lehtonen SI, Koskinen M, Thomson C, Kähkönen N, Kukkurainen S, Määttä JAE, Ihalainen TO, Kulomaa MS, Gruber HJ, Hytönen VP. Switchavidin: Reversible Biotin–Avidin–Biotin Bridges with High Affinity and Specificity. Bioconjug Chem 2014; 25:2233-43. [DOI: 10.1021/bc500462w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Barbara Taskinen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Dominik Zauner
- Institute
of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Soili I. Lehtonen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Tampere University Hospital, PL 2000, FI-33521 Tampere, Finland
| | - Masi Koskinen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Chloe Thomson
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Niklas Kähkönen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Tampere University Hospital, PL 2000, FI-33521 Tampere, Finland
| | - Sampo Kukkurainen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Juha A. E. Määttä
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
| | - Teemu O. Ihalainen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
| | - Markku S. Kulomaa
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Tampere University Hospital, PL 2000, FI-33521 Tampere, Finland
| | - Hermann J. Gruber
- Institute
of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Vesa P. Hytönen
- BioMediTech, University of Tampere, Biokatu 6, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu
4, FI-33520 Tampere, Finland
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28
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Spiller KL, Nassiri S, Witherel CE, Anfang RR, Ng J, Nakazawa KR, Yu T, Vunjak-Novakovic G. Sequential delivery of immunomodulatory cytokines to facilitate the M1-to-M2 transition of macrophages and enhance vascularization of bone scaffolds. Biomaterials 2014; 37:194-207. [PMID: 25453950 DOI: 10.1016/j.biomaterials.2014.10.017] [Citation(s) in RCA: 484] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/02/2014] [Indexed: 01/22/2023]
Abstract
In normal tissue repair, macrophages exhibit a pro-inflammatory phenotype (M1) at early stages and a pro-healing phenotype (M2) at later stages. We have previously shown that M1 macrophages initiate angiogenesis while M2 macrophages promote vessel maturation. Therefore, we reasoned that scaffolds that promote sequential M1 and M2 polarization of infiltrating macrophages should result in enhanced angiogenesis and healing. To this end, we first analyzed the in vitro kinetics of macrophage phenotype switch using flow cytometry, gene expression, and cytokine secretion analysis. Then, we designed scaffolds for bone regeneration based on modifications of decellularized bone for a short release of interferon-gamma (IFNg) to promote the M1 phenotype, followed by a more sustained release of interleukin-4 (IL4) to promote the M2 phenotype. To achieve this sequential release profile, IFNg was physically adsorbed onto the scaffolds, while IL4 was attached via biotin-streptavidin binding. Interestingly, despite the strong interactions between biotin and streptavidin, release studies showed that biotinylated IL4 was released over 6 days. These scaffolds promoted sequential M1 and M2 polarization of primary human macrophages as measured by gene expression of ten M1 and M2 markers and secretion of four cytokines, although the overlapping phases of IFNg and IL4 release tempered polarization to some extent. Murine subcutaneous implantation model showed increased vascularization in scaffolds releasing IFNg compared to controls. This study demonstrates that scaffolds for tissue engineering can be designed to harness the angiogenic behavior of host macrophages towards scaffold vascularization.
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Affiliation(s)
- Kara L Spiller
- Department of Biomedical Engineering, Columbia University, 622 West 168th Street, VC12-234, New York, NY 10032, USA; School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut St., Philadelphia 19104, PA, USA.
| | - Sina Nassiri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut St., Philadelphia 19104, PA, USA.
| | - Claire E Witherel
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut St., Philadelphia 19104, PA, USA.
| | - Rachel R Anfang
- Department of Biomedical Engineering, Columbia University, 622 West 168th Street, VC12-234, New York, NY 10032, USA.
| | - Johnathan Ng
- Department of Biomedical Engineering, Columbia University, 622 West 168th Street, VC12-234, New York, NY 10032, USA.
| | - Kenneth R Nakazawa
- Department of Biomedical Engineering, Columbia University, 622 West 168th Street, VC12-234, New York, NY 10032, USA.
| | - Tony Yu
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut St., Philadelphia 19104, PA, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, 622 West 168th Street, VC12-234, New York, NY 10032, USA.
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Pina AS, Lowe CR, Roque ACA. Challenges and opportunities in the purification of recombinant tagged proteins. Biotechnol Adv 2014; 32:366-81. [PMID: 24334194 PMCID: PMC7125906 DOI: 10.1016/j.biotechadv.2013.12.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/04/2013] [Accepted: 12/08/2013] [Indexed: 01/05/2023]
Abstract
The purification of recombinant proteins by affinity chromatography is one of the most efficient strategies due to the high recovery yields and purity achieved. However, this is dependent on the availability of specific affinity adsorbents for each particular target protein. The diversity of proteins to be purified augments the complexity and number of specific affinity adsorbents needed, and therefore generic platforms for the purification of recombinant proteins are appealing strategies. This justifies why genetically encoded affinity tags became so popular for recombinant protein purification, as these systems only require specific ligands for the capture of the fusion protein through a pre-defined affinity tag tail. There is a wide range of available affinity pairs "tag-ligand" combining biological or structural affinity ligands with the respective binding tags. This review gives a general overview of the well-established "tag-ligand" systems available for fusion protein purification and also explores current unconventional strategies under development.
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Affiliation(s)
- Ana Sofia Pina
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; IBET-Instituto de Biologia Experimental Tecnológica, Oeiras, Portugal
| | - Christopher R Lowe
- Institute of Biotechnology, Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, CB2 1QT Cambridge, UK
| | - Ana Cecília A Roque
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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30
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Spolaore B, Damiano N, Raboni S, Fontana A. Site-specific derivatization of avidin using microbial transglutaminase. Bioconjug Chem 2014; 25:470-80. [PMID: 24517223 DOI: 10.1021/bc400378h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Avidin conjugates have several important applications in biotechnology and medicine. In this work, we investigated the possibility to produce site-specific derivatives of avidin using microbial transglutaminase (TGase). TGase allows the modification of proteins at the level of Gln or Lys residues using as substrate an alkyl-amine or a Gln-mimicking moiety, respectively. The reaction is site-specific, since Gln and Lys derivatization occurs preferentially at residues embedded in flexible regions of protein substrates. An analysis of the X-ray structure of avidin allowed us to predict Gln126 and Lys127 as potential sites of TGase's attack, because these residues are located in the flexible/unfolded C-terminal region of the protein. Surprisingly, incubation of avidin with TGase in the presence of alkylamine containing substrates (dansylcadaverine, 5-hydroxytryptamine) revealed a very low level of derivatization of the Gln126 residue. Analysis of the TGase reaction on synthetic peptide analogues of the C-terminal portion of avidin indicated that the lack of reactivity of Gln126 was likely due to the fact that this residue is proximal to negatively charged carboxylate groups, thus hampering the interaction of the substrate at the negatively charged active site of TGase. On the other hand, incubation of avidin with TGase in the presence of carbobenzoxy-l-glutaminyl-glycine in order to derivatize Lys residue(s) resulted in a clean and high yield production of an avidin derivative, retaining the biotin binding properties and the quaternary structure of the native protein. Proteolytic digestion of the modified protein, followed by mass spectrometry, allowed us to identify Lys127 as the major site of reaction, together with a minor modification of Lys58. By using TGase, avidin was also conjugated via a Lys-Gln isopeptide bond to a protein containing a single reactive Gln residue, namely, Gln126 of granulocyte-macrophage colony-stimulating factor. TGase can thus be exploited for the site-specific derivatization of avidin with small molecules or proteins.
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Affiliation(s)
- Barbara Spolaore
- CRIBI Biotechnology Centre, University of Padua , Viale G. Colombo 3, 35121 Padua, Italy
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31
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Ahmad F, Kaila K, Blaesse P. Quantitative analysis of surface expression of membrane proteins using cold-adapted proteases. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2013; 73:3.11.1-3.11.12. [PMID: 24510593 DOI: 10.1002/0471140864.ps0311s73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This unit presents an improved method for quantitative analysis of surface expression of membrane proteins utilizing a cold-adapted trypsin. Preservation of the proteolytic activity of the enzyme at 0° to 4°C allows cleavage of surface-expressed membrane proteins at temperatures at which trafficking of the mammalian plasmalemmal proteins is blocked. This provides an important advantage over established trypsin-cleavage protocols since it can be applied to membrane proteins with a fast turnover rate of the membrane pool and a fast recycling rate. Compared to surface biotinylation, the method is less time consuming.
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Affiliation(s)
- Faraz Ahmad
- Department of Biosciences and Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Kai Kaila
- Department of Biosciences and Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Peter Blaesse
- Department of Biosciences and Neuroscience Center, University of Helsinki, Helsinki, Finland.,Institute of Physiology I, Westfälische Wilhelms-University Münster, Münster, Germany
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32
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Reder-Christ K, Schmitz P, Bota M, Gerber U, Falkenstein-Paul H, Fuss C, Enachescu M, Bendas G. A dry membrane protection technique to allow surface acoustic wave biosensor measurements of biological model membrane approaches. SENSORS (BASEL, SWITZERLAND) 2013; 13:12392-405. [PMID: 24064603 PMCID: PMC3821348 DOI: 10.3390/s130912392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/03/2013] [Accepted: 09/06/2013] [Indexed: 12/13/2022]
Abstract
Model membrane approaches have attracted much attention in biomedical sciences to investigate and simulate biological processes. The application of model membrane systems for biosensor measurements is partly restricted by the fact that the integrity of membranes critically depends on the maintenance of an aqueous surrounding, while various biosensors require a preconditioning of dry sensors. This is for example true for the well-established surface acoustic wave (SAW) biosensor SAM®5 blue. Here, a simple drying procedure of sensor-supported model membranes is introduced using the protective disaccharide trehalose. Highly reproducible model membranes were prepared by the Langmuir-Blodgett technique, transferred to SAW sensors and supplemented with a trehalose solution. Membrane rehydration after dry incorporation into the SAW device becomes immediately evident by phase changes. Reconstituted model membranes maintain their full functionality, as indicated by biotin/avidin binding experiments. Atomic force microscopy confirmed the morphological invariability of dried and rehydrated membranes. Approximating to more physiological recognition phenomena, the site-directed immobilization of the integrin VLA-4 into the reconstituted model membrane and subsequent VCAM-1 ligand binding with nanomolar affinity were illustrated. This simple drying procedure is a novel way to combine the model membrane generation by Langmuir-Blodgett technique with SAW biosensor measurements, which extends the applicability of SAM®5 blue in biomedical sciences.
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Affiliation(s)
- Katrin Reder-Christ
- Pharmaceutical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, Bonn D-53121, Germany; E-Mails: (P.S.); (U.G.); (H.F.-P.); (C.F.); (G.B.)
| | - Patrick Schmitz
- Pharmaceutical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, Bonn D-53121, Germany; E-Mails: (P.S.); (U.G.); (H.F.-P.); (C.F.); (G.B.)
| | - Marian Bota
- Center for Surface Science and Nanotechnology, University Politehnica of Bucharest, 313 Splaiul Independentei, Bucharest, RO-060042, Romania; E-Mails: (M.B.); (M.E.)
| | - Ursula Gerber
- Pharmaceutical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, Bonn D-53121, Germany; E-Mails: (P.S.); (U.G.); (H.F.-P.); (C.F.); (G.B.)
| | - Hildegard Falkenstein-Paul
- Pharmaceutical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, Bonn D-53121, Germany; E-Mails: (P.S.); (U.G.); (H.F.-P.); (C.F.); (G.B.)
| | - Christian Fuss
- Pharmaceutical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, Bonn D-53121, Germany; E-Mails: (P.S.); (U.G.); (H.F.-P.); (C.F.); (G.B.)
| | - Marius Enachescu
- Center for Surface Science and Nanotechnology, University Politehnica of Bucharest, 313 Splaiul Independentei, Bucharest, RO-060042, Romania; E-Mails: (M.B.); (M.E.)
- Academy of Romanian Scientists, 54 Splaiul Independentei, Bucharest, RO-050094, Romania
| | - Gerd Bendas
- Pharmaceutical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, Bonn D-53121, Germany; E-Mails: (P.S.); (U.G.); (H.F.-P.); (C.F.); (G.B.)
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Jensen PF, Jørgensen TJD, Koefoed K, Nygaard F, Sen JW. Affinity capture of biotinylated proteins at acidic conditions to facilitate hydrogen/deuterium exchange mass spectrometry analysis of multimeric protein complexes. Anal Chem 2013; 85:7052-9. [PMID: 23534402 DOI: 10.1021/ac303442y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Characterization of conformational and dynamic changes associated with protein interactions can be done by hydrogen/deuterium exchange mass spectrometry (HDX-MS) by comparing the deuterium uptake in the bound and unbound state of the proteins. Investigation of local hydrogen/deuterium exchange in heteromultimeric protein complexes poses a challenge for the method due to the increased complexity of the mixture of peptides originating from all interaction partners in the complex. Previously, interference of peptides from one interaction partner has been removed by immobilizing the intact protein on beads prior to the HDX-MS experiment. However, when studying protein complexes of more than two proteins, immobilization can possibly introduce steric limitations to the interactions. Here, we present a method based on the high affinity biotin-streptavidin interaction that allows selective capture of biotinylated proteins even under the extreme conditions for hydrogen/deuterium exchange quenching i.e. pH 2.5 and 0 °C. This biotin-streptavidin capture strategy allows hydrogen/deuterium exchange to occur in proteins in solution and enables characterization of specific proteins in heteromultimeric protein complexes without interference of peptides originating from other interaction partners in the complex. The biotin-streptavidin strategy has been successfully implemented in a model system with two recombinant monoclonal antibodies that target nonoverlapping epitopes on the human epidermal growth factor receptor (EGFR). We present a workflow for biotinylation and characterization of recombinant antibodies and demonstrate affinity capture of biotinylated antibodies under hydrogen/deuterium exchange quench conditions by the biotin-streptavidin strategy.
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Strzelczyk P, Bujacz A, Plażuk D, Zakrzewski J, Bujacz G. Structural investigation of the interactions of biotinylruthenocene with avidin. Chem Biol Interact 2013; 204:6-12. [PMID: 23603015 DOI: 10.1016/j.cbi.2013.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/27/2013] [Accepted: 04/11/2013] [Indexed: 11/15/2022]
Abstract
The crystal structure of avidin, a protein from hen egg white, was determined in the form of a complex with biotinylruthenocene. This biotin-derived organometallic ligand is a potential anticancer agent for targeted therapy based upon avidin-biotin technology. Isothermal titration calorimetry experiments, involving avidin complexes with biotin (vitamin H or B7) derivatives, show differences in their affinity to the protein in comparison to its avidin-biotin complex, the strongest known biochemical interaction in Nature. The crystal structure of the first complex of avidin with biotinylruthenocene, determined at 2.5Å resolution (PDB: 4I60), shows unique interactions of the ruthenocene moiety with avidin. Biotin derivatives exhibit weaker affinity to avidin then biotin, which allows their wider use in biotechnology. The specific properties of biotinylruthenocene and the knowledge of its interactions with avidin may be useful in biochemical, medical, and nanotechnological applications.
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Affiliation(s)
- Paweł Strzelczyk
- Institute of Technical Biochemistry, Lodz University of Technology, 90-924 Lodz, Stefanowskiego 4/10, Poland
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Kumar V, Calamaras TD, Haeussler D, Colucci WS, Cohen RA, McComb ME, Pimentel D, Bachschmid MM. Cardiovascular redox and ox stress proteomics. Antioxid Redox Signal 2012; 17:1528-59. [PMID: 22607061 PMCID: PMC3448941 DOI: 10.1089/ars.2012.4706] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
SIGNIFICANCE Oxidative post-translational modifications (OPTMs) have been demonstrated as contributing to cardiovascular physiology and pathophysiology. These modifications have been identified using antibodies as well as advanced proteomic methods, and the functional importance of each is beginning to be understood using transgenic and gene deletion animal models. Given that OPTMs are involved in cardiovascular pathology, the use of these modifications as biomarkers and predictors of disease has significant therapeutic potential. Adequate understanding of the chemistry of the OPTMs is necessary to determine what may occur in vivo and which modifications would best serve as biomarkers. RECENT ADVANCES By using mass spectrometry, advanced labeling techniques, and antibody identification, OPTMs have become accessible to a larger proportion of the scientific community. Advancements in instrumentation, database search algorithms, and processing speed have allowed MS to fully expand on the proteome of OPTMs. In addition, the role of enzymatically reversible OPTMs has been further clarified in preclinical models. CRITICAL ISSUES The identification of OPTMs suffers from limitations in analytic detection based on the methodology, instrumentation, sample complexity, and bioinformatics. Currently, each type of OPTM requires a specific strategy for identification, and generalized approaches result in an incomplete assessment. FUTURE DIRECTIONS Novel types of highly sensitive MS instrumentation that allow for improved separation and detection of modified proteins and peptides have been crucial in the discovery of OPTMs and biomarkers. To further advance the identification of relevant OPTMs in advanced search algorithms, standardized methods for sample processing and depository of MS data will be required.
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Affiliation(s)
- Vikas Kumar
- Vascular Biology Section, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA
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36
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Bingham JP, Andrews EA, Kiyabu SM, Cabalteja CC. Drugs from slugs. Part II--conopeptide bioengineering. Chem Biol Interact 2012; 200:92-113. [PMID: 23063744 DOI: 10.1016/j.cbi.2012.09.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 08/27/2012] [Accepted: 09/17/2012] [Indexed: 11/27/2022]
Abstract
The biological transformation of toxins as research probes, or as pharmaceutical drug leads, is an onerous and drawn out process. Issues regarding changes to pharmacological specificity, desired potency, and bioavailability are compounded naturally by their inherent toxicity. These often scuttle their progress as they move up the narrowing drug development pipeline. Yet one class of peptide toxins, from the genus Conus, has in many ways spearheaded the expansion of new peptide bioengineering techniques to aid peptide toxin pharmaceutical development. What has now emerged is the sequential bioengineering of new research probes and drug leads that owe their lineage to these highly potent and isoform specific peptides. Here we discuss the progressive bioengineering steps that many conopeptides have transitioned through, and specifically illustrate some of the biochemical approaches that have been established to maximize their biological research potential and pharmaceutical worth.
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Affiliation(s)
- Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA.
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37
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Liu T, Nedrow-Byers JR, Hopkins MR, Wu LY, Lee J, Reilly PTA, Berkman CE. Targeting prostate cancer cells with a multivalent PSMA inhibitor-guided streptavidin conjugate. Bioorg Med Chem Lett 2012; 22:3931-4. [PMID: 22607680 PMCID: PMC3526141 DOI: 10.1016/j.bmcl.2012.04.110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 04/17/2012] [Accepted: 04/23/2012] [Indexed: 12/13/2022]
Abstract
Prostate-specific membrane antigen (PSMA), a type II membrane glycoprotein, its high expression is associated with prostate cancer progression, and has been becoming an active target for imaging or therapeutic applications for prostate cancer. On the other hand, streptavidin-biotin system has been successfully employed in pretargeting therapy towards multiple cancers. Herein, we describe the synthesis of bifunctional ligands (biotin-CTT54, biotin-PEG(4)-CTT54, and biotin-PEG(12)-CTT54) possessing two functional motifs separated by a length-varied polyethylene glycol (PEG) spacer: one (CTT54) binds tumor-marker PSMA and the other (biotin) binds streptavidin or avidin. All three compounds exhibited high potencies (IC(50) values: 1.21, 2.53, and 10nM, respectively) and irreversibility; but only biotin-PEG(12)-CTT54 demonstrated specifically labeling PSMA-positive prostate cancer cells in a two-step pretargeting procedure. Additionally, the pre-formulated complex between biotin-PEG(12)-CTT54 and Cy5-streptavidin displayed the improved inhibitory potency (IC(50)=1.86 nM) and irreversibility against PSMA and rapid uptake of streptavidin conjugate into PSMA-positive prostate cancer cells through PSMA-associated internalization. Together, all these results supported a proof-concept that combination of streptavidin and PSMA's biotinylated inhibitor may lead to development of a novel strategy of tumor-targeting imaging or drug delivery towards prostate cancer.
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Affiliation(s)
- Tiancheng Liu
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630
| | | | - Mark R. Hopkins
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630
| | - Lisa Y. Wu
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630
| | - Jeonghoon Lee
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630
| | - Peter T. A. Reilly
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630
| | - Clifford E. Berkman
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630
- Cancer Targeted Technology, Woodinville, Washington 98072
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38
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Khodakov D, Thredgold L, Lenehan CE, Andersson GG, Kobus H, Ellis AV. DNA capture-probe based separation of double-stranded polymerase chain reaction amplification products in poly(dimethylsiloxane) microfluidic channels. BIOMICROFLUIDICS 2012; 6:26503. [PMID: 23761843 PMCID: PMC3386992 DOI: 10.1063/1.4729131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 05/29/2012] [Indexed: 05/12/2023]
Abstract
Herein, we describe the development of a novel primer system that allows for the capture of double-stranded polymerase chain reaction (PCR) amplification products onto a microfluidic channel without any preliminary purification stages. We show that specially designed PCR primers consisting of the main primer sequence and an additional "tag sequence" linked through a poly(ethylene glycol) molecule can be used to generate ds-PCR amplification products tailed with ss-oligonucleotides of two forensically relevant genes (amelogenin and human c-fms (macrophage colony-stimulating factor) proto-oncogene for the CSF-1 receptor (CSF1PO). Furthermore, with a view to enriching and eluting the ds-PCR products of amplification on a capillary electrophoretic-based microfluidic device we describe the capture of the target ds-PCR products onto poly(dimethylsiloxane) microchannels modified with ss-oligonucleotide capture probes.
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Affiliation(s)
- Dmitriy Khodakov
- Flinders Centre for NanoScale Science and Technology, School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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Meir A, Bayer EA, Livnah O. Structural adaptation of a thermostable biotin-binding protein in a psychrophilic environment. J Biol Chem 2012; 287:17951-62. [PMID: 22493427 DOI: 10.1074/jbc.m112.357186] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Shwanavidin is an avidin-like protein from the marine proteobactrium Shewanella denitrificans, which exhibits an innate dimeric structure while maintaining high affinity toward biotin. A unique residue (Phe-43) from the L3,4 loop and a distinctive disulfide bridge were shown to account for the high affinity toward biotin. Phe-43 emulates the function and position of the critical intermonomeric Trp that characterizes the tetrameric avidins but is lacking in shwanavidin. The 18 copies of the apo-monomer revealed distinctive snapshots of L3,4 and Phe-43, providing rare insight into loop flexibility, binding site accessibility, and psychrophilic adaptation. Nevertheless, as in all avidins, shwanavidin also displays high thermostability properties. The unique features of shwanavidin may provide a platform for the design of a long sought after monovalent form of avidin, which would be ideal for novel types of biotechnological application.
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Affiliation(s)
- Amit Meir
- Department of Biological Chemistry, the Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
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40
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Prasad G, Amoroso JW, Borketey LS, Schnarr NA. N-activated β-lactams as versatile reagents for acyl carrier protein labeling. Org Biomol Chem 2012; 10:1992-2002. [PMID: 22293823 DOI: 10.1039/c2ob06846j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acyl carrier proteins are critical components of fatty acid and polyketide biosynthesis. Their primary function is to shuttle intermediates between active sites via a covalently bound phosphopantetheine arm. Small molecules capable of acylating this prosthetic group will provide a simple and reversible means of introducing novel functionality onto carrier protein domains. A series of N-activated β-lactams are prepared to examine site-specific acylation of the phosphopantetheine-thiol. In general, β-lactams are found to be significantly more reactive than our previously studied β-lactones. Selectivity for the holo over apo-form of acyl carrier proteins is demonstrated indicating that only the phosphopantetheine-thiol is modified. Incorporation of an N-propargyloxycarbonyl group provides an alkyne handle for conjugation to fluorophores and affinity labels. The utility of these groups for mechanistic interrogation of a critical step in polyketide biosynthesis is examined through comparison to traditional probes. In all, we expect the probes described in this study to serve as valuable and versatile tools for mechanistic interrogation.
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Affiliation(s)
- Gitanjeli Prasad
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street, Amherst, Massachusetts 01003, USA
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41
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Mahammed A, Gross Z. Chlorosulfonated corrole: a versatile synthon for advanced materials. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424610002768] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The easily accessible 2,17-bis-chlorosulfonated 5,10,15-trispentafluorophenylcorrole is demonstrated as a highly versatile synthon for the preparation of corroles with functional groups that may be used for advanced applications and materials. Examples presented here are useful for donor-acceptor dyads, water-solubility inducing carbohydrates, chirality-inducing sugars and amino acids, and biotin-avidin technology.
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Affiliation(s)
- Atif Mahammed
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Zeev Gross
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
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42
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Traina CA, Bakus RC, Bazan GC. Design and synthesis of monofunctionalized, water-soluble conjugated polymers for biosensing and imaging applications. J Am Chem Soc 2011; 133:12600-7. [PMID: 21751809 DOI: 10.1021/ja202877q] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Water-soluble conjugated polymers with controlled molecular weight characteristics, absence of ionic groups, high emission quantum yields, and end groups capable of selective reactions of wide scope are desirable for improving their performance in various applications and, in particular, fluorescent biosensor schemes. The synthesis of such a structure is described herein. 2-Bromo-7-iodofluorene with octakis(ethylene glycol) monomethyl ether chains at the 9,9'-positions, i.e., compound 4, was prepared as the reactive premonomer. A high-yielding synthesis of the organometallic initiator (dppe)Ni(Ph)Br (dppe = 1,2-bis(diphenylphosphino)ethane) was designed and implemented, and the resulting product was characterized by single-crystal X-ray diffraction techniques. Polymerization of 4 by (dppe)Ni(Ph)Br can be carried out in less than 30 s, affording excellent control over the average molecular weight and polydispersity of the product. Quenching of the polymerization with [2-(trimethylsilyl)ethynyl]magnesium bromide yields silylacetylene-terminated water-soluble poly(fluorene) with a photoluminescence quantum efficiency of 80%. Desilylation, followed by copper-catalyzed azide-alkyne cycloaddition reaction, yields a straightforward route to introduce a wide range of specific end group functionalities. Biotin was used as an example. The resulting biotinylated conjugated polymer binds to streptavidin and acts as a light-harvesting chromophore to optically amplify the emission of Alexa Fluor-488 chromophores bound onto the streptavidin. Furthermore, the biotin end group makes it possible to bind the polymer onto streptavidin-functionalized cross-linked agarose beads and thereby incorporate a large number of optically active segments.
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Affiliation(s)
- Christopher A Traina
- Department of Materials and Chemistry and Biochemistry, Center for Polymers and Organic Solids, University of California, Santa Barbara, California 93106, United States
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44
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Haase M, Schäfer H. Upconverting Nanoparticles. Angew Chem Int Ed Engl 2011; 50:5808-29. [DOI: 10.1002/anie.201005159] [Citation(s) in RCA: 2049] [Impact Index Per Article: 157.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 01/21/2011] [Indexed: 12/12/2022]
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Vendrell M, Molero A, González S, Pérez-Capote K, Lluis C, McCormick PJ, Franco R, Cortés A, Casadó V, Albericio F, Royo M. Biotin Ergopeptide Probes for Dopamine Receptors. J Med Chem 2011; 54:1080-90. [DOI: 10.1021/jm101566d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marc Vendrell
- Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, 08028 Barcelona, Spain
| | - Anabel Molero
- Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, 08028 Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials, and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
| | - Sergio González
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), and Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Kamil Pérez-Capote
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), and Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Carme Lluis
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), and Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Peter J. McCormick
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), and Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Rafael Franco
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), and Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Antoni Cortés
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), and Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Vicent Casadó
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), and Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Fernando Albericio
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials, and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Miriam Royo
- Combinatorial Chemistry Unit, Barcelona Science Park, University of Barcelona, 08028 Barcelona, Spain
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47
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Ly L, Wasinger VC. Protein and peptide fractionation, enrichment and depletion: Tools for the complex proteome. Proteomics 2011; 11:513-34. [DOI: 10.1002/pmic.201000394] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 10/03/2010] [Accepted: 10/18/2010] [Indexed: 12/28/2022]
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Park M, Jose J, Thömmes S, Kim JI, Kang MJ, Pyun JC. Autodisplay of streptavidin. Enzyme Microb Technol 2010; 48:307-11. [PMID: 22112942 DOI: 10.1016/j.enzmictec.2010.12.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Revised: 10/31/2010] [Accepted: 12/11/2010] [Indexed: 10/18/2022]
Abstract
Streptavidin was expressed on the outer membrane of E. coli as a recombinant fusion protein with an autotransporter domain called AIDA-I (adhesin involved in diffuse adherence) using autodisplay technology. The autodisplay of streptavidin was confirmed by SDS-PAGE of the outer membrane proteins, and the number of autodisplayed streptavidin molecules on a single E. coli cell was evaluated with densitometric analysis. The biotin-binding activity of the autodisplayed streptavidin was estimated after treatment with fluorescently labeled biotin by fluorescence microscopy and flow cytometry. The biotin-binding activity of the E. coli with autodisplayed streptavidin was compared with the activity of streptavidin immobilized on magnetic beads. Finally, the outer membrane presenting autodisplayed streptavidin was isolated and layered on a 96-well microplate for an immunoassay.
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Affiliation(s)
- Min Park
- School of Materials and Sciences, College of Engineering, Yonsei University, 134 Shin-chon-dong, Seo-dae-mun-gu, Seoul 120-749, Republic of Korea
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49
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Veggiani G, Zuin J, Beneduce L, Gallotta A, Pengo P, Fassina G. Combinatorial Semisynthesis of Biomarker-IgM Complexes. ACTA ACUST UNITED AC 2010; 15:1274-80. [DOI: 10.1177/1087057110378623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Circulating immune complexes formed by tumor antigens and immunoglobulin M (IgM) represent a novel class of biomarkers with diagnostic value for early cancer detection. The quantitative analysis of these immune complexes is achieved by enzyme-linked immunosorbent assay (ELISA) methods using a purified calibrator from samples of patients with cancer. These complexes obtained from samples of human origin are not suitable for cost-effective production processes with high safety standards. Given the ill-defined biomarker/IgM ratio in these complexes, semisynthesis with retention of functional properties is difficult to achieve and may vary widely according to the batch-to-batch heterogeneity of starting biological preparations. Here the authors describe the development of a combinatorial method for defining the optimal reaction conditions for the reproducible semisynthesis of biomarker-IgM complexes by exploiting the biotin-avidin technology. The method relies on screening by ELISA the 3D composition space defined by the combinatorial variation of biotinylated-biomarker, biotinylated-IgM, and avidin concentrations aiming to select those conditions leading to biomarker-IgM complexes with the highest immunoreactivity. The method allows the reproducible synthesis of species with immunoreactivity comparable to that of natural immune complexes and endowed with sufficient stability to be used as calibrators in ELISA.
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Affiliation(s)
| | - Jessica Zuin
- Xeptagen SpA, Via delle Industrie 9, I-30175 Marghera, Italy
| | - Luca Beneduce
- Xeptagen SpA, Via delle Industrie 9, I-30175 Marghera, Italy
| | - Andrea Gallotta
- Xeptagen SpA, Via delle Industrie 9, I-30175 Marghera, Italy
| | - Paolo Pengo
- Xeptagen SpA, Via delle Industrie 9, I-30175 Marghera, Italy
| | - Giorgio Fassina
- Xeptagen SpA, Via delle Industrie 9, I-30175 Marghera, Italy
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50
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Meir A, Livnah O. Challenging semi-bootstrapping molecular-replacement strategy reveals intriguing crystal packing of rhizavidin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:373-8. [PMID: 20383003 DOI: 10.1107/s1744309110004112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 02/02/2010] [Indexed: 11/11/2022]
Abstract
The structure of rhizavidin, the first dimeric member of the avidin family which maintains high affinity towards biotin, was determined to high resolution by SeMet SAD. Consequently, the structure of the rhizavidin-biotin complex was determined by molecular-replacement methods using the apo structure as the search model; this ran into complications and required combined programs as well as bootstrapping approaches. Although present as a dimer in solution, rhizavidin packs as unique oligomers in both crystal forms. The novel insights derived from the unique molecular-replacement procedure and the crystal-driven oligomeric forms in this work may have utililty in biotechological and nanotechnological applications.
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Affiliation(s)
- Amit Meir
- Department of Biological Chemistry, The Alexander Silverman Institute of Life Sciences, The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
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