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Abstract
The reversible interaction between an affinity ligand and a complementary receptor has been widely explored in purification systems for several biomolecules. The development of tailored affinity ligands highly specific toward particular target biomolecules is one of the options in affinity purification systems. However, both genetic and chemical modifications in proteins and peptides widen the application of affinity ligand-tag receptors pairs toward universal capture and purification strategies. In particular, this chapter will focus on two case studies highly relevant for biotechnology and biomedical areas, namely the affinity tags and receptors employed on the production of recombinant fusion proteins, and the chemical modification of phosphate groups on proteins and peptides and the subsequent specific capture and enrichment, a mandatory step before further proteomic analysis.
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2
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Çetin K, Denizli A. Immunoaffinity microcryogels for purification of transferrin. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1114-1115:5-12. [DOI: 10.1016/j.jchromb.2019.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/03/2019] [Accepted: 03/17/2019] [Indexed: 12/14/2022]
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3
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Chromatographic separation of hemoglobin variants using robust molecularly imprinted polymers. Talanta 2019; 199:27-31. [PMID: 30952256 DOI: 10.1016/j.talanta.2019.01.125] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/20/2019] [Accepted: 01/22/2019] [Indexed: 11/20/2022]
Abstract
Devising a robust, efficient and cost effective hemoglobin (Hb) purification strategy is one of the key challenges in the development of Hb-based blood substitutes. The aim of this study was to use molecularly imprinted polymers (MIPs) as a novel and efficient chromatographic resin to selectively recognize and purify different Hb variants. The results showed that the Hb-MIP material developed here could selectively recognize and purify various Hb directly from either crude E. coli extracts or human body fluids, such as blood plasma and cerebrospinal fluid (CSF), in one-step. The dynamic binding capacity at 10% breakthrough was around 7.4 mg mL-1resin for adult Hb (HbA) and fetal Hb (HbF). This chromatographic material also allowed identification of changes related to amino acid substitutions on the Hb protein surface. For instance, when an additional lysine residue was introduced, the HbA αY42K mutant eluted later in an Hb-MIP column than wildtype HbA. Additional negative charges on the protein surface, such as aspartate, mitigated the interaction between the protein and imprinted polymers, and therefore an αA19D-αA12D HbF mutant eluted earlier, at -2.7 column volumes compared to wildtype HbF.
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4
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Bulutoglu B, Dooley K, Szilvay G, Blenner M, Banta S. Catch and Release: Engineered Allosterically Regulated β-Roll Peptides Enable On/Off Biomolecular Recognition. ACS Synth Biol 2017; 6:1732-1741. [PMID: 28520402 DOI: 10.1021/acssynbio.7b00089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alternative scaffolds for biomolecular recognition are being developed to overcome some of the limitations associated with immunoglobulin domains. The repeat-in-toxin (RTX) domain is a repeat protein sequence that reversibly adopts the β-roll secondary structure motif specifically upon calcium binding. This conformational change was exploited for controlled biomolecular recognition. Using ribosome display, an RTX peptide library was selected to identify binders to a model protein, lysozyme, exclusively in the folded state of the peptide. Several mutants were identified with low micromolar dissociation constants. After concatenation of the mutants, a 500-fold increase in the overall affinity for lysozyme was achieved leading to a peptide with an apparent dissociation constant of 65 nM. This mutant was immobilized for affinity chromatography experiments, and the on/off nature of the molecular recognition was demonstrated as the target is captured from a mixture in the presence of calcium and is released in the absence of calcium as the RTX peptides lose their β-roll structure. This work presents the design of a new stimulus-responsive scaffold that can be used for environmentally responsive specific molecular recognition and self-assembly.
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Affiliation(s)
- Beyza Bulutoglu
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Kevin Dooley
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Géza Szilvay
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Mark Blenner
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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5
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Banda S, Cao N, Tse-Dinh YC. Distinct Mechanism Evolved for Mycobacterial RNA Polymerase and Topoisomerase I Protein-Protein Interaction. J Mol Biol 2017; 429:2931-2942. [PMID: 28843989 DOI: 10.1016/j.jmb.2017.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/14/2017] [Accepted: 08/19/2017] [Indexed: 01/01/2023]
Abstract
We report here a distinct mechanism of interaction between topoisomerase I and RNA polymerase in Mycobacterium tuberculosis and Mycobacterium smegmatis that has evolved independently from the previously characterized interaction between bacterial topoisomerase I and RNA polymerase. Bacterial DNA topoisomerase I is responsible for preventing the hyper-negative supercoiling of genomic DNA. The association of topoisomerase I with RNA polymerase during transcription elongation could efficiently relieve transcription-driven negative supercoiling. Our results demonstrate a direct physical interaction between the C-terminal domains of topoisomerase I (TopoI-CTDs) and the β' subunit of RNA polymerase of M. smegmatis in the absence of DNA. The TopoI-CTDs in mycobacteria are evolutionarily unrelated in amino acid sequence and three-dimensional structure to the TopoI-CTD found in the majority of bacterial species outside Actinobacteria, including Escherichia coli. The functional interaction between topoisomerase I and RNA polymerase has evolved independently in mycobacteria and E. coli, with distinctively different structural elements of TopoI-CTD utilized for this protein-protein interaction. Zinc ribbon motifs in E. coli TopoI-CTD are involved in the interaction with RNA polymerase. For M. smegmatis TopoI-CTD, a 27-amino-acid tail that is rich in basic residues at the C-terminal end is responsible for the interaction with RNA polymerase. Overexpression of recombinant TopoI-CTD in M. smegmatis competed with the endogenous topoisomerase I for protein-protein interactions with RNA polymerase. The TopoI-CTD overexpression resulted in decreased survival following treatment with antibiotics and hydrogen peroxide, supporting the importance of the protein-protein interaction between topoisomerase I and RNA polymerase during stress response of mycobacteria.
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Affiliation(s)
- Srikanth Banda
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Nan Cao
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
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6
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Fitzgerald J, Leonard P, Darcy E, Sharma S, O'Kennedy R. Immunoaffinity Chromatography: Concepts and Applications. Methods Mol Biol 2017; 1485:27-51. [PMID: 27730547 DOI: 10.1007/978-1-4939-6412-3_3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Antibody-based separation methods, such as immunoaffinity chromatography (IAC), are powerful purification and isolation techniques. Antibodies isolated using these techniques have proven highly efficient in applications ranging from clinical diagnostics to environmental monitoring. Immunoaffinity chromatography is an efficient antibody separation method which exploits the binding efficiency of a ligand to an antibody. Essential to the successful design of any IAC platform is the optimization of critical experimental parameters such as (a) the biological affinity pair, (b) the matrix support, (c) the immobilization coupling chemistry, and (d) the effective elution conditions. These elements and the practicalities of their use are discussed in detail in this review. At the core of all IAC platforms is the high affinity interactions between antibodies and their related ligands; hence, this review entails a brief introduction to the generation of antibodies for use in immunoaffinity chromatography and also provides specific examples of their potential applications.
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Affiliation(s)
- Jenny Fitzgerald
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paul Leonard
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,Biomedical Diagnostics Institute, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Elaine Darcy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Shikha Sharma
- Biomedical Diagnostics Institute, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland. .,Biomedical Diagnostics Institute, Dublin City University, Glasnevin, Dublin 9, Ireland.
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7
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Wu Z, Zhang Y, Zhan S, Lian J, Zhao R, Li K, Tong P, Li X, Yang A, Chen H. Development of immunoaffinity chromatographic method for Ara h 2 isolation. Protein Expr Purif 2016; 131:85-90. [PMID: 27989798 DOI: 10.1016/j.pep.2016.12.002] [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: 11/25/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 10/20/2022]
Abstract
Ara h 2 is considered a major allergen in peanut. Due to the difficulty of separation, Ara h 2 had not been fully studied. Immunoaffinity chromatography (IAC) column can separate target protein with high selectivity, which made it possible to purify Ara h 2 from different samples. In this study, IAC method was developed to purify Ara h 2 and its effect was evaluated. By coupling polyclonal antibody (pAb) on CNBr-activated Sepharose 4B, the column for specific extraction was constructed. The coupling efficiency of the IAC column was higher than 90%, which made the capacity of column reached 0.56 mg per 0.15 g medium (dry weight). The recovery of Ara h 2 ranged from 93% to 100% for different concentrations of pure Ara h 2 solutions in 15 min. After using a column 10 times, about 88% of the column capacity remained. When applied to extract Ara h 2 from raw peanut protein extract and boiled peanut protein extract, the IAC column could recovery 94% and 88% target protein from the mixture. SDS-PAGE and Western blotting analysis confirmed the purified protein was Ara h 2, its purity reached about 90%. Significantly, the IAC column could capture dimer of Ara h 2, which made it feasible to prepared derivative of protein after processing.
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Affiliation(s)
- Zhihua Wu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China.
| | - Ying Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; School of Food Science & Technology, Nanchang University, Nanchang 330047, China
| | - Shaode Zhan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; School of Food Science & Technology, Nanchang University, Nanchang 330047, China
| | - Jun Lian
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; School of Food Science & Technology, Nanchang University, Nanchang 330047, China
| | - Ruifang Zhao
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; School of Food Science & Technology, Nanchang University, Nanchang 330047, China
| | - Kun Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; School of Resources Environment & Chemical Engineering, Nanchang University, Nanchang 330047, China
| | - Ping Tong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; School of Food Science & Technology, Nanchang University, Nanchang 330047, China
| | - Xin Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; School of Food Science & Technology, Nanchang University, Nanchang 330047, China
| | - Anshu Yang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China
| | - Hongbing Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China.
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8
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Yadav DK, Yadav N, Yadav S, Haque S, Tuteja N. An insight into fusion technology aiding efficient recombinant protein production for functional proteomics. Arch Biochem Biophys 2016; 612:57-77. [DOI: 10.1016/j.abb.2016.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 11/27/2022]
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9
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Guzman NA, Guzman DE. An emerging micro-scale immuno-analytical diagnostic tool to see the unseen. Holding promise for precision medicine and P4 medicine. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:14-29. [DOI: 10.1016/j.jchromb.2015.11.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/15/2015] [Accepted: 11/17/2015] [Indexed: 01/10/2023]
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10
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Brgles M, Sviben D, Forčić D, Halassy B. Nonspecific native elution of proteins and mumps virus in immunoaffinity chromatography. J Chromatogr A 2016; 1447:107-14. [PMID: 27090389 DOI: 10.1016/j.chroma.2016.04.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/17/2016] [Accepted: 04/07/2016] [Indexed: 11/19/2022]
Abstract
Immunoaffinity chromatography, based on the antigen-antibody recognition, enables specific purification of any antigen (protein, virus) by its antibody. The problem with immunoaffinity chromatography is the harsh elution conditions required for disrupting strong antigen-antibody interactions, such as low pH buffers, which are often deleterious for the immobilized protein and the protein to be isolated since they can also disrupt the intramolecular forces. Therefore, immunoaffinity chromatography can only be partially used for protein and virus purification. Here we report on a nonspecific elution in immunoaffinity chromatography using native conditions by elution with amino acid solution at physiological pH for which we suppose possible competing mechanism of action. Elution potential of various amino acid solutions was tested using immunoaffinity columns specific for ovalbumin and mumps virus, and protein G affinity column. Results have shown that the most successful elution solutions were those containing imidazole and arginine of high molarity. Imidazole represents aromatic residues readily found at the antigen-antibody interaction surface and arginine is most frequently found on protein surface in general. Therefore, results on their eluting power in immunoaffinity chromatography, which increases with increasing molarity, are in line with the competing mechanism of action. Virus immunoaffinity chromatography resulted in removal on nonviable virus particles, which is important for research and biotechnology purposes. In addition, amino acids are proven stabilizers for proteins and viruses making approach presented in this work a very convenient purification method.
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Affiliation(s)
- Marija Brgles
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Rockefellerova 10, HR-10000 Zagreb, Croatia; Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Croatia.
| | - Dora Sviben
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Rockefellerova 10, HR-10000 Zagreb, Croatia; Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Croatia
| | - Dubravko Forčić
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Rockefellerova 10, HR-10000 Zagreb, Croatia; Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Croatia
| | - Beata Halassy
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Rockefellerova 10, HR-10000 Zagreb, Croatia; Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Croatia
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11
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Determination of 11 quinolones in bovine milk using immunoaffinity stir bar sorptive microextraction and liquid chromatography with fluorescence detection. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1003:67-73. [DOI: 10.1016/j.jchromb.2015.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/07/2015] [Accepted: 09/09/2015] [Indexed: 11/23/2022]
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12
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Quan Q, Szeto SSW, Law HCH, Zhang Z, Wang Y, Chu IK. Fully Automated Multidimensional Reversed-Phase Liquid Chromatography with Tandem Anion/Cation Exchange Columns for Simultaneous Global Endogenous Tyrosine Nitration Detection, Integral Membrane Protein Characterization, and Quantitative Proteomics Mapping in Cerebral Infarcts. Anal Chem 2015; 87:10015-24. [DOI: 10.1021/acs.analchem.5b02619] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Quan Quan
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Samuel S. W. Szeto
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Henry C. H. Law
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Zaijun Zhang
- Institute
of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic
Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University, Guangzhou, Guangdong 510632, China
| | - Yuqiang Wang
- Institute
of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic
Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University, Guangzhou, Guangdong 510632, China
| | - Ivan K. Chu
- Department
of Chemistry, The University of Hong Kong, Hong Kong 999077, China
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13
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Memmedova T, Armutcu C, Uzun L, Denizli A. Polyglycidyl methacrylate based immunoaffinity cryogels for insulin adsorption. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 52:178-85. [DOI: 10.1016/j.msec.2015.03.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 02/01/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
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14
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Ramezani H, Jed Harrison D. DNA strand displacement reaction for programmable release of biomolecules. Chem Commun (Camb) 2015; 51:8307-10. [DOI: 10.1039/c5cc01880c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The DNA strand displacement reaction (SDR) was successfully combined with a fluoroimmunoassay on silica microparticles to accomplish sequence-specific release,in situsample cleanup, and buffer exchange.
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Affiliation(s)
- Hamid Ramezani
- Department of Chemistry
- University of Alberta
- Edmonton
- T6G 2G2 Canada
| | - D. Jed Harrison
- Department of Chemistry
- University of Alberta
- Edmonton
- T6G 2G2 Canada
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15
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Henriksen ML, Madsen KL, Skjoedt K, Hansen S. Calcium-sensitive immunoaffinity chromatography: Gentle and highly specific retrieval of a scarce plasma antigen, collectin-LK (CL-LK). J Immunol Methods 2014; 413:25-31. [PMID: 25064149 DOI: 10.1016/j.jim.2014.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 07/16/2014] [Accepted: 07/16/2014] [Indexed: 10/25/2022]
Abstract
Immunoaffinity chromatography is a powerful fractionation technique that has become indispensable for protein purification and characterization. However, it is difficult to retrieve bound proteins without using harsh or denaturing elution conditions, and the purification of scarce antigens to homogeneity may be impossible due to contamination with abundant antigens. In this study, we purified the scarce, complement-associated plasma protein complex, collectin LK (CL-LK, complex of collectin liver 1 and kidney 1), by immunoaffinity chromatography using a calcium-sensitive anti-collectin-kidney-1 mAb. This antibody was characterized by binding to CL-LK at hypo- and physiological calcium concentrations and dissociated from CK-LK at hyperphysiological concentrations of calcium. We purified CL-LK from plasma to a purity of 41% and a yield of 38%, resulting in a purification factor of more than 88,000 in a single step. To evaluate the efficiency of this new purification scheme, we purified CL-LK using the same calcium-sensitive mAb in combination with acidic elution buffer and by using calcium-dependent anti-CL-K1 mAbs in combination with EDTA elution buffer. We found that calcium-sensitive immunoaffinity chromatography was superior to the traditional immunoaffinity chromatographies and resulted in a nine-fold improvement of the purification factor. The technique is applicable for the purification of proteins in complex mixtures by single-step fractionation without the denaturation of eluted antigens, and it allows for the purification of scarce proteins that would have otherwise been impossible to purify and, hence, to characterize. This technique may also potentially be applied for the purification of proteins that only interact with calcium ions at hyperphysiological concentrations.
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Affiliation(s)
- Maiken L Henriksen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, J. B. Winsloews Vej 21.1, DK-5000 Odense, Denmark
| | - Kirstine L Madsen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, J. B. Winsloews Vej 21.1, DK-5000 Odense, Denmark
| | - Karsten Skjoedt
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, J. B. Winsloews Vej 21.1, DK-5000 Odense, Denmark
| | - Soren Hansen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, J. B. Winsloews Vej 21.1, DK-5000 Odense, Denmark
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16
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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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17
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PA tag: A versatile protein tagging system using a super high affinity antibody against a dodecapeptide derived from human podoplanin. Protein Expr Purif 2014; 95:240-7. [DOI: 10.1016/j.pep.2014.01.009] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/20/2014] [Accepted: 01/20/2014] [Indexed: 11/23/2022]
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18
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Brower KP, Ryakala VK, Bird R, Godawat R, Riske FJ, Konstantinov K, Warikoo V, Gamble J. Single-step affinity purification of enzyme biotherapeutics: A platform methodology for accelerated process development. Biotechnol Prog 2014; 30:708-17. [DOI: 10.1002/btpr.1870] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/06/2014] [Indexed: 12/25/2022]
Affiliation(s)
- Kevin P. Brower
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Venkat K. Ryakala
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Ryan Bird
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Rahul Godawat
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Frank J. Riske
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Konstantin Konstantinov
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Veena Warikoo
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Jean Gamble
- Analytical Development; Genzyme - A Sanofi Company; One The Mountain Road, Framingham MA 01701
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Schermann SM, Simmons DA, Konermann L. Mass spectrometry-based approaches to protein–ligand interactions. Expert Rev Proteomics 2014; 2:475-85. [PMID: 16097882 DOI: 10.1586/14789450.2.4.475] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
One of the greatest current challenges in proteomics is to develop an understanding of cellular communication and regulation processes, most of which involve noncovalent interactions of proteins with various binding partners. Mass spectrometry plays an important role in all aspects of these research efforts. This article provides a survey of mass spectrometry-based approaches for exploring protein-ligand interactions. A wide array of techniques is available, and the choice of method depends on the specific problem at hand. For example, the high-throughput screening of compound libraries for binding to a specific receptor requires different approaches than structural studies on multiprotein complexes. This review is directed to readers wishing to obtain a concise yet comprehensive overview of existing experimental techniques. Specific emphasis is placed on emerging methods that have been developed within the last few years.
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Affiliation(s)
- Sonya M Schermann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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20
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Pina AS, Batalha IL, Roque ACA. Affinity tags in protein purification and peptide enrichment: an overview. Methods Mol Biol 2014; 1129:147-68. [PMID: 24648075 DOI: 10.1007/978-1-62703-977-2_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The reversible interaction between an affinity ligand and a complementary receptor has been widely explored in purification systems for several biomolecules. The development of tailored affinity ligands highly specific towards particular target biomolecules is one of the options in affinity purification systems. However, both genetic and chemical modifications on proteins and peptides widen the application of affinity ligand-tag receptor pairs towards universal capture and purification strategies. In particular, this chapter will focus on two case studies highly relevant for biotechnology and biomedical areas, namely, the affinity tags and receptors employed on the production of recombinant fusion proteins and the chemical modification of phosphate groups on proteins and peptides and the subsequent specific capture and enrichment, a mandatory step before further proteomic analysis.
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Affiliation(s)
- Ana Sofia Pina
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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Perotti N, Etcheverrigaray M, Kratje R, Oggero M. A versatile ionic strength sensitive tag from a human GM-CSF-derived linear epitope. Protein Expr Purif 2013; 91:10-9. [DOI: 10.1016/j.pep.2013.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/06/2013] [Accepted: 06/14/2013] [Indexed: 11/25/2022]
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22
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Vagenende V, Han AX, Pek HB, Loo BLW. Quantifying the molecular origins of opposite solvent effects on protein-protein interactions. PLoS Comput Biol 2013; 9:e1003072. [PMID: 23696727 PMCID: PMC3656110 DOI: 10.1371/journal.pcbi.1003072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/11/2013] [Indexed: 12/21/2022] Open
Abstract
Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.
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Affiliation(s)
- Vincent Vagenende
- Bioprocessing Technology Institute, ASTAR (Agency for Science, Technology and Research), Singapore.
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23
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Song J, Ren H, Li Y, Xu J, Kong H, Tong W, Zhou Y, Gao S, Liu Y, Hui Q, Peng Q, Lu S, Liu Z. rG17PE38, a novel immunotoxin target to gastric cancer with overexpressed CCK-2R. J Drug Target 2013; 21:375-82. [PMID: 23311704 DOI: 10.3109/1061186x.2012.757770] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Gastrin/cholecystokinin subtype 2 receptor (CCK2R) is overexpressed in several types of tumors. Gastrin-17 (G17) peptide has a high affinity with CCK2R. These characters suggest that G17 may be useful for target cancer therapy. PURPOSE Construct a new immunotoxin (IT) targeting of CCK2R overexpressed gastric cancer. METHODS Two ITs were generated using forward and reverse G17 peptides fused with PE38. To get a high yield, codon optimized gene and optimized fermentation parameters were used in large-scale protein expression. An immunoaffinity technique was introduced into pseudomonas exotoxin (PE)-derived IT purification procedure. G17 competition, GST pull-down and indirect immunoflourescence assays were carried out to confirm the interaction between rG17 and CCK2R. Then, several cytotoxic assays were carried out on 18 cell lines, and an in vivo antitumor activity experiment was tested in nude mice. RESULTS The rG17PE38 showed specific cytotoxicity on three gastric cancer cells, while G17PE38 did not. After optimization, the expression level reached about 40% in medium deprived of NaCl. Next, 15-27.5 mg of pure rG17PE38 per 1 L of cultures was obtained. Results of G17 competition, GST pull-down and indirect immunoflourescence assays demonstrated that rG17 have a specific interact with CCK2R. Purified rG17PE38 showed high cytotoxicity on gastric cancer cell lines with the IC50 value of 0.6-4 ng·mL(-1). Treatment of nude mice inoculated with BGC-823 tumor xenografts with rG17PE38 efficiently inhibited tumor size. CONCLUSIONS AND DISCUSSION The present study demonstrates that reversed G17 could be used as target moiety of PE-derived IT and the rG17PE38 could be developed as a new immunotherapy agent. Codon optimized gene could increase the rG17PE38 expression level in E. coli and furthermore NaCl inhibits the rG17PE38 expression in large scale. Meanwhile, our present study inducts an immunoaffinity method in the IT purification procedure, which could purify the PE-derived ITs in native form.
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Affiliation(s)
- Jie Song
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, PR China
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Abstract
The time-controlled transcardiac perfusion crosslinking (tcTPC) method differs from conventional perfusion fixation in that the crosslinking reagent is administered throughout the circulatory system for only a relatively short period of time, thereby allowing limited crosslinking to occur. Bait protein complexes are isolated by affinity capture (AC) under stringent conditions and are recovered from the AC matrix by acidic elution. Affinity-purified proteins are reduced, alkylated, and digested with a specific endoproteinase, such as trypsin. Subsequently, peptides are isotopically labeled, separated by reversed-phase chromatography and analyzed by quantitative tandem mass spectrometry (MS/MS). The proteins crosslinked to the bait protein during tcTPC are identified by database searches with conventional protein identification software. The tcTPC strategy offers unique advantages over alternative approaches for studying a subset of protein complexes which require a particular environment for their structural integrity, such as membrane protein complexes that are notorious for their tendency to dissociate upon detergent solubilization. The sensitivity and utility of this method are influenced by the spatial distribution of chemical groups within the bait protein complexes that can engage in productive crosslinks.
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25
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Li X, Foley EA, Molloy KR, Li Y, Chait BT, Kapoor TM. Quantitative chemical proteomics approach to identify post-translational modification-mediated protein-protein interactions. J Am Chem Soc 2012; 134:1982-5. [PMID: 22239320 DOI: 10.1021/ja210528v] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational modifications (PTMs) (e.g., acetylation, methylation, and phosphorylation) play crucial roles in regulating the diverse protein-protein interactions involved in essentially every cellular process. While significant progress has been made to detect PTMs, profiling protein-protein interactions mediated by these PTMs remains a challenge. Here, we report a method that combines a photo-cross-linking strategy with stable isotope labeling in cell culture (SILAC)-based quantitative mass spectrometry to identify PTM-dependent protein-protein interactions. To develop and apply this approach, we focused on trimethylated lysine-4 at the histone H3 N-terminus (H3K4Me(3)), a PTM linked to actively transcribed gene promoters. Our approach identified proteins previously known to recognize this modification and MORC3 as a new protein that binds H3M4Me(3). This study indicates that our cross-linking-assisted and SILAC-based protein identification (CLASPI) approach can be used to profile protein-protein interactions mediated by PTMs, such as lysine methylation.
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Affiliation(s)
- Xiang Li
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York 10065, USA
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26
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Young CL, Britton ZT, Robinson AS. Recombinant protein expression and purification: A comprehensive review of affinity tags and microbial applications. Biotechnol J 2012; 7:620-34. [DOI: 10.1002/biot.201100155] [Citation(s) in RCA: 312] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 11/23/2011] [Accepted: 11/29/2011] [Indexed: 12/27/2022]
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27
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Abstract
Antibody-based separation methods, such as immunoaffinity chromatography (IAC), are powerful purification and isolation techniques. Antibodies isolated using these techniques have proven highly efficient in applications ranging from clinical diagnostics to environmental monitoring. IAC is an efficient antibody separation method which exploits the binding efficiency of a ligand to an antibody. Essential to the successful design of any IAC platform is the optimisation of critical experimental parameters such as: (a) the biological affinity pair, (b) the matrix support, (c) the immobilisation coupling chemistry, and (d) the effective elution conditions. These elements and the practicalities of their use are discussed in detail in this review. At the core of all IAC platforms is the high-affinity interactions between antibodies and their related ligands; hence, this review entails a brief introduction to the generation of antibodies for use in IAC and also provides specific examples of their potential applications.
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Affiliation(s)
- Jenny Fitzgerald
- School of Biotechnology, Dublin City University, Dublin, Ireland
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28
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Shi X, Song S, Sun A, Li D, Wu A, Zhang D. Determination of Chloramphenicol Residues in Foods by ELISA and LC-MS/MS Coupled with Molecularly Imprinted Solid Phase Extraction. ANAL LETT 2010. [DOI: 10.1080/00032711003763616] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Fong BA, Gillies AR, Ghazi I, LeRoy G, Lee KC, Westblade LF, Wood DW. Purification of Escherichia coli RNA polymerase using a self-cleaving elastin-like polypeptide tag. Protein Sci 2010; 19:1243-52. [PMID: 20512976 DOI: 10.1002/pro.403] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A self-cleaving elastin-like polypeptide (ELP) tag was used to purify the multisubunit Escherichia coli RNA polymerase (RNAP) via a simple, nonchromatographic method. To accomplish this, the RNAP alpha subunit was tagged with a self-cleaving ELP-intein tag and coexpressed with the beta, beta', and omega subunits. The assembled RNAP was purified with its associated subunits, and was active and acquired at reasonable yield and purity. To remove residual polynucleotides bound to the purified RNAP, two polymer precipitation methods were investigated: polyethyleneimine (PEI) and polyethylene (PEG) precipitation. The PEG procedure was shown to enhance purity and was compatible with downstream ELP-intein purification. Thus, this simple ELP-based method should be applicable for the nonchromatographic purification of other recombinant, in vivo-assembled multisubunit complexes in a single step. Further, the simplicity and low cost of this method will likely facilitate scale up for large-scale production of additional multimeric protein targets. Finally, this technique may have utility in isolating protein interaction partners that associate with a given target.
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Affiliation(s)
- Baley A Fong
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, USA
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30
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Kamezaki Y, Enomoto C, Ishikawa Y, Koyama T, Naya SI, Suzuki T, Sakka K. The Dock tag, an affinity tool for the purification of recombinant proteins, based on the interaction between dockerin and cohesin domains from Clostridium josui cellulosome. Protein Expr Purif 2010; 70:23-31. [PMID: 19836451 DOI: 10.1016/j.pep.2009.09.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 09/29/2009] [Accepted: 09/30/2009] [Indexed: 11/25/2022]
Abstract
Highly specific dockerin-cohesin interaction intrinsically involved in the cellulosome formation in Clostridium josui was applied for the construction of an affinity tag purification system. Amino acid substitutions were introduced into the dockerin domain of C. josui Cel8A at positions 11, 12, 44, and 45 and mutant dockerin domains were examined for their ability as an affinity tag: mutant dockerin-tagged proteins were adsorbed onto a cohesin (Coh2)-coupled Sepharose in the presence of Ca(2+) and desorbed from the protein and Coh2-Sepharose complex by the addition of a chelating agent, EGTA. Single-step purification tests showed that substitution of glycine or serine for isoleucine at position 45 markedly improved the recovery of the recombinant proteins from the proteins and Coh2-Sepharose complex. Surface plasmon resonance analysis of the interaction between the I45G mutant and Coh2 indicated that the mutation decreased binding rate and increased dissociation rate, resulting in decrease in dissociation constant. When model proteins such as JNK3, MAP2K3, IL-8, and pro-IL-18 were expressed as I45G dockerin-tagged proteins in the baculovirus expression system and purified by the single-step purification, purity of all the I45G dockerin-tagged proteins tested was higher than 90%. Furthermore, insertion of a thrombin cleavage site between the dockerin tag and target proteins enabled rapid removal of the tag from the target proteins by thrombin protease. This system, named the Dock tag purification system, can be widely utilized and contributes to various fields in academic and application researches.
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Affiliation(s)
- Yoshiko Kamezaki
- Research Institute of Biological Science, Katakura Industries Co., Ltd., 1548 Shimo-okudomi, Sayama-City, Saitama 350-1332, Japan.
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31
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Abstract
Immunoaffinity chromatography is a powerful tool for purification of proteins and protein complexes. The availability of monoclonal antibodies (mAbs) has revolutionized the field of immunoaffinity chromatography by providing a continuous supply of highly uniform antibody. Before the availability of mAbs, the recovery of the target protein from immobilized polyclonal antibodies usually required very harsh, often denaturing conditions. Although harsh conditions are often still used to disrupt the antigen-antibody interaction when using a mAb, various methods have been developed to exploit the uniformity of the antigen-antibody reaction in order to identify agents or conditions that gently disrupt this interaction and thus result in higher recovery of active protein from immunoaffinity chromatography. We discuss here the use of a specific type of monoclonal antibody that we have designated "polyol-responsive monoclonal antibodies" (PR-mAbs). These are naturally occurring mAbs that have high affinity for the antigen under binding conditions, but have low affinity in the presence of a combination of low molecular weight hydroxylated compounds (polyols) and nonchaotropic salts. Therefore, these PR-mAbs can be used for gentle immunoaffinity chromatography. PR-mAbs can be easily identified and adapted to a powerful protein purification method for a target protein.
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32
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Kiselyova EP, Tsyganova OV, Vashkevich II, Sviridov OV. Immunoaffinity chromatography of human thyroid peroxidase: The stability of the three-dimensional structure and immunoreactivity of antigen and antibodies under various elution conditions. APPL BIOCHEM MICRO+ 2009. [DOI: 10.1134/s0003683809030168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Batalla P, Mateo C, Grazu V, Fernandez-Lafuente R, Guisan JM. Immobilization of antibodies through the surface regions having the highest density in lysine groups on finally inert support surfaces. Process Biochem 2009. [DOI: 10.1016/j.procbio.2008.11.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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34
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Gruschke S, Bußmann BM, Reiche S, Jassoy C. Peptides from the SARS-associated coronavirus as tags for protein expression and purification. Protein Expr Purif 2008; 61:138-41. [PMID: 18565762 PMCID: PMC7129034 DOI: 10.1016/j.pep.2008.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 04/24/2008] [Accepted: 04/26/2008] [Indexed: 11/22/2022]
Abstract
Protein tagging with a peptide is a commonly used technique to facilitate protein detection and to carry out protein purification. Flexibility with respect to the peptide tag is essential since no single tag suites all purposes. This report describes the usage of two short peptides from the SARS-associated coronavirus nucleocapsid (SARS-N) protein as protein tags. Plasmids for the generation of tagged proteins were generated by ligating synthetic oligonucleotides for the peptide-coding regions downstream of the protein coding sequence. The data show recognition of prokaryotically expressed HIV-1 Gag/p24 fusion protein by Western blot and efficient affinity purification using monoclonal antibodies against the tags. The SARS peptide antibody system described presents an alternative tagging opportunity in the growing field of protein science.
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Affiliation(s)
| | | | | | - Christian Jassoy
- Institute of Virology, Faculty of Medicine, Max Bürger Research Centre, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
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35
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Nogi T, Sangawa T, Tabata S, Nagae M, Tamura-Kawakami K, Beppu A, Hattori M, Yasui N, Takagi J. Novel affinity tag system using structurally defined antibody-tag interaction: application to single-step protein purification. Protein Sci 2008; 17:2120-6. [PMID: 18787202 DOI: 10.1110/ps.038299.108] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Biologically important human proteins often require mammalian cell expression for structural studies, presenting technical and economical problems in the production/purification processes. We introduce a novel affinity peptide tagging system that uses a low affinity anti-peptide monoclonal antibody. Concatenation of the short recognition sequence enabled the successful engineering of an 18-residue affinity tag with ideal solution binding kinetics, providing a low-cost purification means when combined with nondenaturing elution by water-miscible organic solvents. Three-dimensional information provides a firm structural basis for the antibody-peptide interaction, opening opportunities for further improvements/modifications.
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Affiliation(s)
- Terukazu Nogi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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36
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Purification of GFP fusion proteins with high purity and yield by monoclonal antibody-coupled affinity column chromatography. Protein Expr Purif 2008; 59:138-43. [DOI: 10.1016/j.pep.2008.01.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 01/20/2008] [Accepted: 01/23/2008] [Indexed: 10/22/2022]
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37
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Sibler AP, Baltzinger M, Choulier L, Desplancq D, Altschuh D. SPR identification of mild elution conditions for affinity purification of E6 oncoprotein, using a multivariate experimental design. J Mol Recognit 2008; 21:46-54. [DOI: 10.1002/jmr.865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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38
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Martins S, Lourenço S, Karmali A, Serralheiro ML. Monoclonal Antibodies Recognize Conformational Epitopes on Wild-type and Recombinant Mutant Amidases from Pseudomonas aeruginosa. Mol Biotechnol 2007; 37:136-45. [PMID: 17914174 DOI: 10.1007/s12033-007-0040-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/26/2022]
Abstract
Hybridoma technology was used to raise monoclonal antibodies (MAbs) against wild-type amidase from Pseudomonas aeruginosa. Hybridoma clones secreting polyol-responsive MAbs (PR-MAbs) were screened that bind antigen tightly. but release under mild- and non-denaturing elution conditions, which can be used as ligands in immunoaffinity chromatography. Two of these hybridoma clones (C9E4 and B1E4) secreting MAbs against wild-type amidase were selected in order to check if they are PR-MAbs by using ELISA-elution assay. These hybridoma cell lines secreted MAbs of IgG class which were purified in a single step by Protein A-Sepharose CL-4B chromatography, which revealed two protein bands on SDS-PAGE. Specificity studies of MAb C9E4 revealed that it recognized a common epitope on wild-type and mutant T103I amidases as determined by direct ELISA, as well as by Western blotting under native conditions. This MAb exhibited a higher-affinity constant (K) for the mutant T103I amidase than for the wild-type enzyme. However, this MAb did not recognize either wild-type or mutant T103I enzymes under denaturing conditions suggesting that it binds to a conformation-sensitive epitope on amidase molecule. On the other hand, it also does not recognize either native or denatured forms of mutant C91A amidase suggesting that this substitution disrupted the conformational epitope present on amidase molecule. Furthermore, MAb C9E4 inhibited about 80% of wild-type amidase activity, whereas it activated about 80% of mutant amidase (T103I) activity. However, this MAb did not affect mutant C91A amidase activity which is in agreement with other results presented in this work. The data presented in this work suggest that this MAb acts as a powerful probe to detect conformational changes in native and denatured amidases as well as to differentiate wild-type and mutant (T103I and C91A) amidases.
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Affiliation(s)
- Sónia Martins
- Centro de Investigação de Engenharia Química e Biotecnologia, Instituto Superior de Engenharia de Lisboa, Rua Conselheiro Emídio Navarro, Lisbon, 1950-062, Portugal
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39
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Shi X, Wu A, Zheng S, Li R, Zhang D. Molecularly imprinted polymer microspheres for solid-phase extraction of chloramphenicol residues in foods. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 850:24-30. [PMID: 17126085 DOI: 10.1016/j.jchromb.2006.10.057] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Revised: 10/30/2006] [Accepted: 10/31/2006] [Indexed: 11/19/2022]
Abstract
Preparation of molecularly imprinted polymer microspheres (MIPMs) for chloramphenicol (CAP) by aqueous suspension polymerization is reported for the first time in this study. The resulting MIPMs had the ability to specifically adsorb CAP, and the molecularly imprinted solid phase extraction (MISPE) based on the MIPMs was shown to be applicable for clean-up and preconcentration of trace CAP in milk and shrimp samples with high recoveries of 92.7% and 84.9%, respectively. Combined with MISPE, the conventional HPLC-UV analysis sensitivity for CAP in foods could be significantly increased.
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Affiliation(s)
- Xizhi Shi
- Shanghai Jiao Tong University - Shanghai Institutes for Biological Sciences - Pennsylvania State University Joint Center for Life Sciences, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
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40
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Probasco MD, Thompson NE, Burgess RR. Immunoaffinity purification and characterization of RNA polymerase from Shewanella oneidensis. Protein Expr Purif 2007; 55:23-30. [PMID: 17507238 DOI: 10.1016/j.pep.2007.03.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 03/28/2007] [Accepted: 03/29/2007] [Indexed: 11/21/2022]
Abstract
Shewanella oneidensis is of particular interest for research because of its unique ability to use a variety of metals as final respiratory electron acceptors and reduce them into insoluble oxides. A collection of monoclonal antibodies (mAbs) that were prepared towards Escherichia coli RNA polymerase (RNAP) was tested for reactivity with proteins extracted from S. oneidensis. Two polyol-responsive monoclonal antibodies (PR-mAbs) were used to purify RNA polymerase from S. oneidensis using immunoaffinity purification techniques. A collection of mAbs towards E. coli sigma subunits was also examined for cross-reactivity with S. oneidensis proteins. Reactions were identified with mAbs to E. coli sigma(70) and sigma(54). These mAbs will be useful tools for immunoaffinity purifying and studying the transcriptional machinery of S. oneidensis.
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Affiliation(s)
- Mitchell D Probasco
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
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41
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Jones WT, Harvey D, Kirk C, Rakonjac J, Sun X, Frearson N, Samarrai TA. A novel peptide tag for detection and purification of recombinant expressed proteins. Protein Expr Purif 2007; 53:404-10. [PMID: 17317216 DOI: 10.1016/j.pep.2007.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 01/10/2007] [Accepted: 01/11/2007] [Indexed: 11/26/2022]
Abstract
Peptide tags have proven useful for the detection and purification of recombinant proteins. However cross reactions of antibodies raised to the tag are frequently observed due to the presence of host proteins containing all or parts of the tag. In this report we have identified a unique viral peptide sequence, R-tag, that by blast searches is absent from the commonly expression hosts Arabidopsis thaliana, Escherichia coli, Pichia pastoris and mouse myeloma cell NSO. We have prepared monoclonal antibodies to this peptide and confirmed the absence of this peptide sequence from the above genomes by Western blotting. We have also modified protein expression vectors to incorporate this sequence as a fusion tag in expressed proteins and shown its use to successfully purify recombinant proteins by immunoaffinity procedures.
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Affiliation(s)
- William T Jones
- The Horticulture and Food Research Institute of New Zealand Ltd, Private Bag 11 030, Palmerston North, New Zealand.
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42
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Schubert P, Hoffman MD, Sniatynski MJ, Kast J. Advances in the analysis of dynamic protein complexes by proteomics and data processing. Anal Bioanal Chem 2006; 386:482-93. [PMID: 16933131 DOI: 10.1007/s00216-006-0609-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 06/05/2006] [Accepted: 06/08/2006] [Indexed: 01/12/2023]
Abstract
Signal transduction governs virtually every cellular function of multicellular organisms, and its deregulation leads to a variety of diseases. This intricate network of molecular interactions is mediated by proteins that are assembled into complexes within individual signaling pathways, and their composition and function is often regulated by different post-translational modifications. Proteomic approaches are commonly used to analyze biological complexes and networks, but often lack the specificity to address the dynamic and hence transient nature of the interactions and the influence of the multiple post-translational modifications that govern these processes. Here we review recent developments in proteomic research to address these limitations, and discuss several technologies that have been developed for this purpose. The synergy between these proteomic and computational tools, when applied together with global methods to the analysis of individual proteins, complexes and pathways, may allow researchers to unravel the underlying mechanisms of signaling networks in greater detail than previously possible.
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Affiliation(s)
- Peter Schubert
- The Biomedical Research Centre, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
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43
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Huang J, Koide A, Nettle KW, Greene GL, Koide S. Conformation-specific affinity purification of proteins using engineered binding proteins: Application to the estrogen receptor. Protein Expr Purif 2006; 47:348-54. [PMID: 16325424 DOI: 10.1016/j.pep.2005.10.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 10/18/2005] [Accepted: 10/19/2005] [Indexed: 11/24/2022]
Abstract
Affinity chromatography coupled with an "affinity tag" has become a powerful and routine technology for the purification of recombinant proteins. However, such tag-based affinity chromatography usually cannot separate different conformational states (e.g., folded and misfolded) of a protein to be purified. Here, we describe a strategy to separate different conformations of a protein by using "tailor-made" affinity chromatography based on engineered binding proteins. Our method involves: (i) engineering of a binding protein specific to a particular conformation of the protein of interest, and (ii) production and immobilization of the binding protein to prepare conformation-specific affinity chromatography media. Using "monobodies," small antibody mimics based on the fibronectin type III domain, as the target-binding proteins, we demonstrated the effectiveness of our method by separating the active form of the estrogen receptor alpha ligand-binding domain (ERalpha-LBD) from a mixture of active and misfolded species and by discriminating two different conformations of ERalpha-LBD bound to different ligands. Our strategy should be generally applicable to the preparation of conformationally homogeneous protein samples.
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Affiliation(s)
- Jin Huang
- Department of Biochemistry and Molecular Biology, The University of Chicago, IL 60637, USA
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Xiao Y, Nieves E, Angeletti RH, Orr GA, Wolkoff AW. Rat organic anion transporting protein 1A1 (Oatp1a1): purification and phosphopeptide assignment. Biochemistry 2006; 45:3357-69. [PMID: 16519530 PMCID: PMC2505048 DOI: 10.1021/bi052437v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Rat organic anion transporting protein 1a1 (oatp1a1), a hepatocyte basolateral plasma membrane protein, mediates transport of various amphipathic compounds. Our previous studies indicated that serine phosphorylation of a single tryptic peptide inhibits its transport activity without changing its cell surface content. The site of phosphorylation is unknown and was the subject of the present study. Following immunoaffinity chromatographic purification from rat liver, oatp1a1 was subjected to trypsin digestion and MALDI-TOF. Except for predicted N-glycosylated peptides, 97% of oatp1a1 tryptic peptides were observed. A single tryptic phosphopeptide was found in the C-terminus (aa 626-647), existing in unphosphorylated or singly or doubly phosphorylated forms and sensitive to alkaline phosphatase treatment. The beta-elimination reaction resulted in a mass loss of 98 or 196 Da from this peptide, and subsequent Michael addition with cysteamine increased masses by the predicated 77 and 154 Da, indicating that oatp1a1 can be singly or doubly phosphorylated at serine or threonine residues in the C-terminal sequence SSATDHT (aa 634-640). Subsequent tandem MS/MS analysis revealed that phosphorylation at S634 accounted for all singly phosphorylated peptide, while phosphorylation at S634 and S635 accounted for all doubly phosphorylated peptide. These findings identify the site of oatp1a1 phosphorylation and demonstrate that it is an ordered process, in which phosphorylation at S634 precedes that at S635. The mechanism by which phosphorylation results in loss of transport activity in hepatocytes remains to be established. Whether phosphorylation near the C-terminus inhibits C-terminal oligomerization of oatp1a1, required for normal transport function, can be speculated upon but is as yet unknown.
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Affiliation(s)
- Yansen Xiao
- Marion Bessin Liver Research Center, Department of Developmental and Molecular Biology, Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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45
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Besanger TR, Hodgson RJ, Green JRA, Brennan JD. Immobilized enzyme reactor chromatography: Optimization of protein retention and enzyme activity in monolithic silica stationary phases. Anal Chim Acta 2006; 564:106-15. [PMID: 17723368 DOI: 10.1016/j.aca.2005.12.066] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Revised: 12/19/2005] [Accepted: 12/29/2005] [Indexed: 11/22/2022]
Abstract
Our group recently reported on the application of protein-doped monolithic silica columns for immobilized enzyme reactor chromatography, which allowed screening of enzyme inhibitors present in mixtures using mass spectrometry for detection. The enzyme was immobilized by entrapment within a bimodal meso/macroporous silica material prepared by a biocompatible sol-gel processing route. While such columns proved to be useful for applications such as screening of protein-ligand interactions, significant amounts of entrapped proteins leached from the columns owing to the high proportion of macropores within the materials. Herein, we describe a detailed study of factors affecting the morphology of protein-doped bioaffinity columns and demonstrate that specific pH values and concentrations of poly(ethylene glycol) can be used to prepare essentially mesoporous columns that retain over 80% of initially loaded enzyme in an active and accessible form and yet still retain sufficient porosity to allow pressure-driven flow in the low muL/min range. Using the enzyme gamma-glutamyl transpeptidase (gamma-GT), we further evaluated the catalytic constants of the enzyme entrapped in capillary columns with different silica morphologies as a function of flowrate and backpressure using the enzyme reactor assay mode. It was found that the apparent activity of the enzyme was highest in mesoporous columns that retained high levels of enzyme. In such columns, enzyme activity increased by approximately 2-fold with increases in both flowrate (from 250 to 1000 nL/min) and backpressure generated (from 500 to 2100 psi) during the chromatographic activity assay owing to increases in k(cat) and decreases in K(M), switching from diffusion controlled to reaction controlled conditions at ca. 2000 psi. These results suggest that columns with minimal macropore volumes (<5%) are advantageous for the entrapment of soluble proteins for bioaffinity and bioreactor chromatography.
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Affiliation(s)
- Travis R Besanger
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ont. L8S 4M1, Canada
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46
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Fiedler E, Fiedler M, Proetzel G, Scheuermann T, Fiedler U, Rudolph R. Affilin™ Molecules. FOOD AND BIOPRODUCTS PROCESSING 2006. [DOI: 10.1205/fbp.05222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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47
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Thompson NE, Jensen DB, Lamberski JA, Burgess RR. Purification of protein complexes by immunoaffinity chromatography: application to transcription machinery. GENETIC ENGINEERING 2006; 27:81-100. [PMID: 16382873 DOI: 10.1007/0-387-25856-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Nancy E Thompson
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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48
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Arnau J, Lauritzen C, Petersen GE, Pedersen J. Current strategies for the use of affinity tags and tag removal for the purification of recombinant proteins. Protein Expr Purif 2005; 48:1-13. [PMID: 16427311 DOI: 10.1016/j.pep.2005.12.002] [Citation(s) in RCA: 449] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 11/22/2005] [Accepted: 12/02/2005] [Indexed: 10/25/2022]
Abstract
Affinity tags are highly efficient tools for protein purification. They allow the purification of virtually any protein without any prior knowledge of its biochemical properties. The use of affinity tags has therefore become widespread in several areas of research e.g., high throughput expression studies aimed at finding a biological function to large numbers of yet uncharacterized proteins. In some cases, the presence of the affinity tag in the recombinant protein is unwanted or may represent a disadvantage for the projected application of the protein, like for clinical use. Therefore, an increasing number of approaches are available at present that are designed for the removal of the affinity tag from the recombinant protein. Most of these methods employ recombinant endoproteases that recognize a specific sequence. These process enzymes can subsequently be removed from the process by affinity purification, since they also include a tag. Here, a survey of the most common affinity tags and the current methods for tag removal is presented, with special emphasis on the removal of N-terminal histidine tags using TAGZyme, a system based on exopeptidase cleavage. In the quest to reduce the significant costs associated with protein purification at large scale, relevant aspects involved in the development of downstream processes for pharmaceutical protein production that incorporate a tag removal step are also discussed. A comparison of the yield of standard vs. affinity purification together with an example of tag removal using TAGZyme is also included.
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Affiliation(s)
- José Arnau
- Unizyme Laboratories A/S, Dr. Neergaards vej 17, DK-2970 Hørsholm, Denmark.
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Heazlewood JL, Tonti-Filippini J, Verboom RE, Millar AH. Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis. PLANT PHYSIOLOGY 2005; 139:598-609. [PMID: 16219920 PMCID: PMC1255979 DOI: 10.1104/pp.105.065532] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Revised: 08/03/2005] [Accepted: 08/08/2005] [Indexed: 05/04/2023]
Abstract
Substantial experimental datasets defining the subcellular location of Arabidopsis (Arabidopsis thaliana) proteins have been reported in the literature in the form of organelle proteomes built from mass spectrometry data (approximately 2,500 proteins). Subcellular location for specific proteins has also been published based on imaging of chimeric fluorescent fusion proteins in intact cells (approximately 900 proteins). Further, the more diverse history of biochemical determination of subcellular location is stored in the entries of the Swiss-Prot database for the products of many Arabidopsis genes (approximately 1,800 proteins). Combined with the range of bioinformatic targeting prediction tools and comparative genomic analysis, these experimental datasets provide a powerful basis for defining the final location of proteins within the wide variety of subcellular structures present inside Arabidopsis cells. We have analyzed these published experimental and prediction data to answer a range of substantial questions facing researchers about the veracity of these approaches to determining protein location and their interrelatedness. We have merged these data to form the subcellular location database for Arabidopsis proteins (SUBA), providing an integrated understanding of protein location, encompassing the plastid, mitochondrion, peroxisome, nucleus, plasma membrane, endoplasmic reticulum, vacuole, Golgi, cytoskeleton structures, and cytosol (www.suba.bcs.uwa.edu.au). This includes data on more than 4,400 nonredundant Arabidopsis protein sequences. We also provide researchers with an online resource that may be used to query protein sets or protein families and determine whether predicted or experimental location data exist; to analyze the nature of contamination between published proteome sets; and/or for building theoretical subcellular proteomes in Arabidopsis using the latest experimental data.
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Affiliation(s)
- Joshua L Heazlewood
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley
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Lamberski JA, Thompson NE, Burgess RR. Expression and purification of a single-chain variable fragment antibody derived from a polyol-responsive monoclonal antibody. Protein Expr Purif 2005; 47:82-92. [PMID: 16216525 DOI: 10.1016/j.pep.2005.08.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Revised: 08/26/2005] [Accepted: 08/26/2005] [Indexed: 10/25/2022]
Abstract
A previously described polyol-responsive monoclonal antibody (PR-mAb) was converted to a single-chain variable fragment (scFv). This antibody, PR-mAb NT73, reacts with the beta' subunit of Escherichia coli RNA polymerase and has been used for the immunoaffinity purification of polymerase. mRNAs encoding the variable regions of the heavy chain (VH) and light chain (VL) were used as the template for cDNA synthesis. The sequences were joined by the addition of a "linker" sequence and then cloned into several expression vectors. A variety of expression plasmids and E. coli hosts were used to determine the optimal expression system. Expression was highest with the pET22b(+) vector and the Rosetta(DE3)pLysS host strain, which produced approximately 60 mg purified His-tagged scFv per liter of culture (3.3 g wet weight cells). Although the production of soluble scFv was preferred, overproduced scFv formed inclusion bodies under every expression condition. Therefore, inclusion bodies had to be isolated, washed, solubilized, and refolded. The FoldIt protein refolding kit and enzyme-linked immunosorbent assay were sequentially used to determine the optimal refolding conditions that would produce active His-tagged scFv. Immobilized metal affinity chromatography was used for the final purification of the refolded active scFv. The polyol-responsiveness of the scFv was determined by an ELISA-elution assay. Although the scFv loses considerable affinity for its antigen, it maintains similar polyol-responsiveness as the parent monoclonal antibody, PR-mAb NT73.
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Affiliation(s)
- Jennifer A Lamberski
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, 1400 University Avenue, Madison, WI 53706, USA.
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