101
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Bolchi A, Canali E, Santoni A, Spagnoli G, Viarisio D, Accardi R, Tommasino M, Müller M, Ottonello S. Thioredoxin-Displayed Multipeptide Immunogens. Methods Mol Biol 2015; 1348:137-51. [PMID: 26424270 DOI: 10.1007/978-1-4939-2999-3_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fusion to carrier proteins is an effective strategy for stabilizing and providing immunogenicity to peptide epitopes. This is commonly achieved by cross-linking of chemically synthesized peptides to carrier proteins. An alternative approach is internal grafting of selected peptide epitopes to a scaffold protein via double stranded-oligonucleotide insertion or gene synthesis, followed by recombinant expression of the resulting chimeric polypeptide. The scaffold protein should confer immunogenicity to the stabilized and structurally constrained peptide, but also afford easy production of the antigen in recombinant form. A macromolecular scaffold that meets the above criteria is the redox protein thioredoxin, especially bacterial thioredoxin. Here we describe our current methodology for internal grafting of selected peptide epitopes to thioredoxin as tandemly arranged multipeptide repeats ("Thioredoxin Displayed Multipeptide Immunogens"), bacterial expression and purification of the recombinant thioredoxin-multipeptide fusion proteins and their use as antigens for the production of anti-peptide antibodies for prophylactic vaccine as well as diagnostic purposes.
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Affiliation(s)
- Angelo Bolchi
- Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, Parma, Italy
| | - Elena Canali
- Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, Parma, Italy
| | - Andrea Santoni
- Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, Parma, Italy
| | - Gloria Spagnoli
- Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - Rosita Accardi
- Infections and Cancer Biology Group, International Agency for Research on Cancer-World Health Organization, Lyon, France
| | - Massimo Tommasino
- Infections and Cancer Biology Group, International Agency for Research on Cancer-World Health Organization, Lyon, France
| | | | - Simone Ottonello
- Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, Parma, Italy. .,Dipartimento di Bioscienze, Università di Parma, Parco Area delle Scienze 23/A, Parma, 43124, Italy.
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102
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Caramelo-Nunes C, Tomaz CT. Specific recognition of supercoiled plasmid DNA by affinity chromatography using a synthetic aromatic ligand. Methods Mol Biol 2015; 1286:47-54. [PMID: 25749945 DOI: 10.1007/978-1-4939-2447-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Liquid chromatography is the method of choice for the purification of plasmid DNA (pDNA), since it is simple, robust, versatile, and highly reproducible. The most important features of a chromatographic procedure are the use of suitable stationary phases and ligands. As conventional purification protocols are being replaced by more sophisticated and selective procedures, the focus changes toward designing and selecting ligands of high affinity and specificity. In fact, the chemical composition of the chromatographic supports determines the interactions established with the target molecules, allowing their preferential retention over the undesirable ones. Here it is described the selective recognition and purification of supercoiled pDNA by affinity chromatography, using an intercalative molecule (3,8-diamino-6-phenylphenanthridine) as ligand.
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Affiliation(s)
- Catarina Caramelo-Nunes
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal
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103
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Abstract
Antibodies are provided in a variety of formats that include antiserum, hybridoma culture supernatant, or ascites. They can all be used successfully in crude form for the detection of target antigens by immunoassay. However, it is advantageous to use purified antibody in defined quantity to facilitate assay reproducibility, economy, and reduced interference of nonspecific components as well as improved storage, stability, and bio-conjugation. Although not always necessary, the relative simplicity of antibody purification using commercially available protein-A, protein-G, or protein-L resins with basic chromatographic principles warrants purification when antibody source material is available in sufficient quantity. Here, we define three simple methods using immobilized (1) protein-A, (2) protein-G, and (3) protein-L agarose beads to yield highly purified antibody.
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Affiliation(s)
- Robert M Hnasko
- Produce Safety and Microbiology Unit (PSM), Western Regional Research Center (WRRC), Pacific West Area (PWA), Agricultural Research Service (ARS), United States Department of Agriculture (USDA), 800 Buchanan St., Albany, CA, 94710, USA,
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104
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Dual-ligand affinity systems with octapeptide ligands for affinity chromatography of hIgG and monoclonal antibody. J Chromatogr A 2014; 1369:64-72. [DOI: 10.1016/j.chroma.2014.09.083] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 09/22/2014] [Accepted: 09/27/2014] [Indexed: 11/23/2022]
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105
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Alves LP, Ramos SS, Sousa F, Boto REF, Almeida P. A Benzothiazolium Salt as Chromatography Ligand for Protein Purification. Chromatographia 2014. [DOI: 10.1007/s10337-014-2774-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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106
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A mass spectrometry view of stable and transient protein interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:263-82. [PMID: 24952186 DOI: 10.1007/978-3-319-06068-2_11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Through an impressive range of dynamic interactions, proteins succeed to carry out the majority of functions in a cell. These temporally and spatially regulated interactions provide the means through which one single protein can perform diverse functions and modulate different cellular pathways. Understanding the identity and nature of these interactions is therefore critical for defining protein functions and their contribution to health and disease processes. Here, we provide an overview of workflows that incorporate immunoaffinity purifications and quantitative mass spectrometry (frequently abbreviated as IP-MS or AP-MS) for characterizing protein-protein interactions. We discuss experimental aspects that should be considered when optimizing the isolation of a protein complex. As the presence of nonspecific associations is a concern in these experiments, we discuss the common sources of nonspecific interactions and present label-free and metabolic labeling mass spectrometry-based methods that can help determine the specificity of interactions. The effective regulation of cellular pathways and the rapid reaction to various environmental stresses rely on the formation of stable, transient, and fast-exchanging protein-protein interactions. While determining the exact nature of an interaction remains challenging, we review cross-linking and metabolic labeling approaches that can help address this important aspect of characterizing protein interactions and macromolecular assemblies.
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107
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Wehbe M, Labib M, Muharemagic D, Zamay AS, Berezovski MV. Switchable aptamers for biosensing and bioseparation of viruses (SwAps-V). Biosens Bioelectron 2014; 67:280-6. [PMID: 25190090 DOI: 10.1016/j.bios.2014.08.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/08/2014] [Accepted: 08/18/2014] [Indexed: 11/29/2022]
Abstract
There is a widespread interest in the development of aptamer-based affinity chromatographic methods for purification of biomolecules. Regardless of the many advantages exhibited by aptamers when compared to other recognition elements, the lack of an efficient regeneration technique that can be generalized to all targets has encumbered further integration of aptamers into affinity-based purification methods. Here we offer switchable aptamers (SwAps) that have been developed to solve this problem and move aptamer-based chromatography forward. SwAps are controlled-affinity aptamers, which have been employed here to purify vesicular stomatitis virus (VSV) as a model case, however this technique can be extended to all biologically significant molecules. VSV is one oncolytic virus out of an arsenal of potential candidates shown to provide selective destruction of cancer cells both in vitro and in vivo. These SwAps were developed in the presence of Ca(2+) and Mg(2+) ions where they cannot bind to their target VSV in absence of these cations. Upon addition of EDTA and EGTA, the divalent cations were sequestered from the stabilized aptameric structure causing a conformational change and subsequently release of the virus. Both flow cytometry and electrochemical impedance spectroscopy were employed to estimate the binding affinities between the selected SwAps and VSV and to determine the coefficient of switching (CoS) upon elution. Among fifteen sequenced SwAps, four have exhibited high affinity to VSV and ability to switch upon elution and thus were further integrated into streptavidin-coated magnetic beads for purification of VSV.
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Affiliation(s)
- Mohamed Wehbe
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada
| | - Mahmoud Labib
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Anna S Zamay
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada; Institute of Chemistry and Chemical Technology SB RAS, 50 Akademgorodok, Krasnoyarsk 660036, Russia
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108
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Screening of gellan gum as an ionic and hydrophobic chromatographic matrix for biomolecules purification. Sep Purif Technol 2014. [DOI: 10.1016/j.seppur.2014.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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109
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Martins R, Queiroz J, Sousa F. Ribonucleic acid purification. J Chromatogr A 2014; 1355:1-14. [DOI: 10.1016/j.chroma.2014.05.075] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 05/23/2014] [Accepted: 05/27/2014] [Indexed: 11/24/2022]
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110
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Heu W, Choi JM, Lee JJ, Jeong S, Kim HS. Protein binder for affinity purification of human immunoglobulin antibodies. Anal Chem 2014; 86:6019-25. [PMID: 24877609 DOI: 10.1021/ac501158t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The importance of a downstream process for the purification of immunoglobulin antibodies is increasing with the growing application of monoclonal antibodies in many different areas. Although protein A is most commonly used for the affinity purification of antibodies, certain properties could be further improved: higher stability in alkaline solution and milder elution condition. Herein, we present the development of Fc-specific repebody by modular engineering approach and its potential as an affinity ligand for purification of human immunoglobulin antibodies. We previously developed the repebody scaffold composed of Leucine-rich repeat (LRR) modules. The scaffold was shown to be highly stable over a wide range of pH and temperature, exhibiting a modular architecture. We first selected a repebody that binds the Fc fragment of human immunoglobulin G (IgG) through a phage display and increased its binding affinity up to 1.9 × 10(-7) M in a module-by-module approach. The utility of the Fc-specific repebody was demonstrated by the performance of an immobilized repebody in affinity purification of antibodies from a mammalian cell-cultured medium. Bound-antibodies on an immobilized repebody were shown to be eluted at pH 4.0 with high purity (>94.6%) and recovery yield (>95.7%). The immobilized repebody allowed a repetitive purification process more than ten times without any loss of binding capability. The repebody remained almost intact even after incubation with 0.5 M NaOH for 15 days. The present approach could be effectively used for developing a repeat module-based binder for other target molecules for affinity purification.
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Affiliation(s)
- Woosung Heu
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 305-701, Korea
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111
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Gonçalves A, Rocha L, Dias J, Passarinha L, Sousa A. Optimization of a chromatographic stationary phase based on gellan gum using central composite design. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 957:46-52. [DOI: 10.1016/j.jchromb.2014.02.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 01/17/2014] [Accepted: 02/10/2014] [Indexed: 01/27/2023]
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112
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Generation and purification of highly specific antibodies for detecting post-translationally modified proteins in vivo. Nat Protoc 2014; 9:375-95. [PMID: 24457330 DOI: 10.1038/nprot.2014.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Post-translational modifications alter protein structure, affecting activity, stability, localization and/or binding partners. Antibodies that specifically recognize post-translationally modified proteins have a number of uses including immunocytochemistry and immunoprecipitation of the modified protein to purify protein-protein and protein-nucleic acid complexes. However, antibodies directed at modified sites on individual proteins are often nonspecific. Here we describe a protocol to purify polyclonal antibodies that specifically detect the modified protein of interest. The approach uses iterative rounds of subtraction and affinity purification, using stringent washes to remove antibodies that recognize the unmodified protein and low sequence complexity epitopes containing the modified amino acid. Dot blot and western blot assays are used to assess antibody preparation specificity. The approach is designed to overcome the common occurrence that a single round of subtraction and affinity purification is not sufficient to obtain a modified protein-specific antibody preparation. One full round of antibody purification and specificity testing takes 6 d of discontinuous time.
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113
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Barroso T, Branco RJF, Aguiar-Ricardo A, Roque ACA. Structural evaluation of an alternative Protein A biomimetic ligand for antibody purification. J Comput Aided Mol Des 2014; 28:25-34. [DOI: 10.1007/s10822-013-9703-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/23/2013] [Indexed: 11/29/2022]
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114
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Abstract
The availability of purified antibodies is prerequisite for many applications and the appropriate choice(s) of antibody-purification steps is crucial. Numerous methods have been developed for the purification of antibodies; however, affinity chromatography-based methods are the most extensively utilized. These methods are based on highly specific and reversible biological interactions between two molecules (e.g., between receptor and ligand or antibody and antigen). Affinity chromatography offers very high selectivity, involving minimal steps, providing simplicity of approach and rapidity. Implementing an effective protocol often requires meticulous planning and testing in order to achieve high purity and yields of desired antibody types/subtypes. This chapter describes the basic techniques for purification of monoclonal, polyclonal, and recombinant antibodies employing affinity chromatography.
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115
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The hidden potential of small synthetic molecules and peptides as affinity ligands for bioseparations. ACTA ACUST UNITED AC 2013. [DOI: 10.4155/pbp.13.54] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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116
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Barroso T, Lourenço A, Araújo M, Bonifácio VDB, Roque ACA, Aguiar-Ricardo A. A green approach toward antibody purification: a sustainable biomimetic ligand for direct immobilization on (bio)polymeric supports. J Mol Recognit 2013; 26:662-71. [DOI: 10.1002/jmr.2309] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/24/2013] [Accepted: 08/13/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Telma Barroso
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Caparica 2829-516 Portugal
| | - Anita Lourenço
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Caparica 2829-516 Portugal
| | - Marco Araújo
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Caparica 2829-516 Portugal
| | - Vasco D. B. Bonifácio
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Caparica 2829-516 Portugal
| | - Ana C. A. Roque
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Caparica 2829-516 Portugal
| | - Ana Aguiar-Ricardo
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Caparica 2829-516 Portugal
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117
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Dynamic binding capacity and specificity of 3,8-diamino-6-phenylphenanthridine-Sepharose support for purification of supercoiled plasmid deoxyribonucleic acid. J Chromatogr A 2013; 1307:91-8. [DOI: 10.1016/j.chroma.2013.07.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/20/2013] [Accepted: 07/22/2013] [Indexed: 11/21/2022]
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118
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119
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Desire CT, Arrua RD, Talebi M, Lacher NA, Hilder EF. Poly(ethylene glycol)-based monolithic capillary columns for hydrophobic interaction chromatography of immunoglobulin G subclasses and variants. J Sep Sci 2013; 36:2782-92. [DOI: 10.1002/jssc.201300558] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 06/14/2013] [Accepted: 06/14/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Christopher T. Desire
- Australian Centre for Research on Separation Science (ACROSS); School of Chemistry, University of Tasmania; Tasmania Australia
| | - R. Dario Arrua
- Australian Centre for Research on Separation Science (ACROSS); School of Chemistry, University of Tasmania; Tasmania Australia
| | - Mohammad Talebi
- Australian Centre for Research on Separation Science (ACROSS); School of Chemistry, University of Tasmania; Tasmania Australia
| | - Nathan A. Lacher
- Analytical R&D; Pfizer Biotherapeutics Pharmaceutical Sciences; Chesterfield MO USA
| | - Emily F. Hilder
- Australian Centre for Research on Separation Science (ACROSS); School of Chemistry, University of Tasmania; Tasmania Australia
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120
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Barroso T, Hussain A, Roque ACA, Aguiar-Ricardo A. Functional monolithic platforms: Chromatographic tools for antibody purification. Biotechnol J 2013; 8:671-81. [DOI: 10.1002/biot.201200328] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 03/11/2013] [Accepted: 04/10/2013] [Indexed: 12/19/2022]
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121
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Miteva YV, Budayeva HG, Cristea IM. Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem 2013; 85:749-68. [PMID: 23157382 PMCID: PMC3666915 DOI: 10.1021/ac3033257] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Ileana M. Cristea
- Corresponding author: Ileana M. Cristea 210 Lewis Thomas Laboratory Department of Molecular Biology Princeton University Princeton, NJ 08544 Tel: 6092589417 Fax: 6092584575
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122
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Wang Y, Zhang X, Zhang C, Liu Y, Liu X. Isolation of single chain variable fragment (scFv) specific for Cry1C toxin from human single fold scFv libraries. Toxicon 2012; 60:1290-7. [DOI: 10.1016/j.toxicon.2012.08.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/27/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022]
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