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Burgess RR. What is in the black box? The discovery of the sigma factor and the subunit structure of E. coli RNA polymerase. J Biol Chem 2021; 297:101310. [PMID: 34673029 PMCID: PMC8569590 DOI: 10.1016/j.jbc.2021.101310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
This Reflections article is focused on the 5 years while I was a graduate student (1964-1969). During this period, I made some of the most significant discoveries of my career. I have written this article primarily for a protein biochemistry audience, my colleagues who shared this exciting time in science, and the many scientists over the last 50 years who have contributed to our knowledge of transcriptional machinery and their regulation. It is also written for today's graduate students, postdocs, and scientists who may not know much about the discoveries and technical advances that are now taken for granted, to show that even with methods primitive by today's standards, we were still able to make foundational advances. I also hope to provide a glimpse into how fortunate I was to be a graduate student over 50 years ago in the golden age of molecular biology.
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Affiliation(s)
- Richard R Burgess
- James D. Watson Professor Emeritus of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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2
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Burgess RR. Gentle antibody-mimetic affinity chromatography with polyol-responsive nanoCLAMPs. Protein Expr Purif 2017. [PMID: 28633910 DOI: 10.1016/j.pep.2017.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Richard R Burgess
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, United States
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3
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Efficient, ultra-high-affinity chromatography in a one-step purification of complex proteins. Proc Natl Acad Sci U S A 2017; 114:E5138-E5147. [PMID: 28607052 DOI: 10.1073/pnas.1704872114] [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: 01/03/2023] Open
Abstract
Protein purification is an essential primary step in numerous biological studies. It is particularly significant for the rapidly emerging high-throughput fields, such as proteomics, interactomics, and drug discovery. Moreover, purifications for structural and industrial applications should meet the requirement of high yield, high purity, and high activity (HHH). It is, therefore, highly desirable to have an efficient purification system with a potential to meet the HHH benchmark in a single step. Here, we report a chromatographic technology based on the ultra-high-affinity (Kd ∼ 10-14-10-17 M) complex between the Colicin E7 DNase (CE7) and its inhibitor, Immunity protein 7 (Im7). For this application, we mutated CE7 to create a CL7 tag, which retained the full binding affinity to Im7 but was inactivated as a DNase. To achieve high capacity, we developed a protocol for a large-scale production and highly specific immobilization of Im7 to a solid support. We demonstrated its utility with one-step HHH purification of a wide range of traditionally challenging biological molecules, including eukaryotic, membrane, toxic, and multisubunit DNA/RNA-binding proteins. The system is simple, reusable, and also applicable to pulldown and kinetic activity/binding assays.
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4
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Development of polyol-responsive antibody mimetics for single-step protein purification. Protein Expr Purif 2017; 134:114-124. [DOI: 10.1016/j.pep.2017.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/13/2017] [Accepted: 04/15/2017] [Indexed: 12/11/2022]
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5
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Semedo MC, Karmali A, Martins S, Fonseca L. Novel polyol-responsive monoclonal antibodies against extracellular β-D-glucans from Pleurotus ostreatus. Biotechnol Prog 2015; 32:116-25. [PMID: 26580487 DOI: 10.1002/btpr.2196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/05/2015] [Indexed: 11/06/2022]
Abstract
β-D-glucans from mushroom strains play a major role as biological response modifiers in several clinical disorders. Therefore, a specific assay method is of critical importance to find useful and novel sources of β-d-glucans with anti-tumor activity. Hybridoma technology was used to raise monoclonal antibodies (Mabs) against extracellular β-d-glucans (EBG) from Pleurotus ostreatus. Two of these hybridoma clones (3F8_3H7 and 1E6_1E8_B3) secreting Mabs against EBG from P. ostreatus were selected and 3F8_3H7 was used to investigate if they are polyol-responsive Mabs (PR-Mabs) by using ELlSA-elution assay. This hybridoma cell line secreted Mab of IgM class, which was purified in a single step by gel filtration chromatography on Sephacryl S-300HR, which revealed a protein band on native PAGE with Mr of 917 kDa. Specificity studies of Mab 3F8_3H7 revealed that it recognized a common epitope on several β-d-glucans from different basidiomycete strains as determined by indirect ELlSA and Western blotting under native conditions. This Mab exhibited high apparent affinity constant (KApp) for β-d-glucans from several mushroom strains. However, it revealed differential reactivity to some heat-treated β-d-glucans compared with the native forms suggesting that it binds to a conformation-sensitive epitope on β-d-glucan molecule. Epitope analysis of Mab 3F8_3H7 and 1E6_1E8_B3 was investigated by additivity index parameter, which revealed that they bound to the same epitope on some β-d-glucans and to different epitopes in other antigens. Therefore, these Mab can be used to assay for β-d-glucans as well as to act as powerful probes to detect conformational changes in these biopolymers.
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Affiliation(s)
- Magda C Semedo
- Chemical Engineering and Biotechnology Research Center and Departmental Area of Chemical Engineering of Instituto Superior De Engenharia De Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007, Lisboa, Portugal.,Centre for the Research and Technology Agro-Environment and Biological Sciences, Universidade De Trás-os-Montes E Alto Douro, Quinta De Prados, Apartado 1013, 5001-801 Vila Real, Portugal
| | - Amin Karmali
- Chemical Engineering and Biotechnology Research Center and Departmental Area of Chemical Engineering of Instituto Superior De Engenharia De Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007, Lisboa, Portugal.,Centre for the Research and Technology Agro-Environment and Biological Sciences, Universidade De Trás-os-Montes E Alto Douro, Quinta De Prados, Apartado 1013, 5001-801 Vila Real, Portugal
| | - Sónia Martins
- Chemical Engineering and Biotechnology Research Center and Departmental Area of Chemical Engineering of Instituto Superior De Engenharia De Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007, Lisboa, Portugal.,Centre for the Research and Technology Agro-Environment and Biological Sciences, Universidade De Trás-os-Montes E Alto Douro, Quinta De Prados, Apartado 1013, 5001-801 Vila Real, Portugal
| | - Luís Fonseca
- Dept. of Bioengineering, Centre for Biological and Chemical Engineering of Instituto Superior Técnico, Av. Rovisco Pais, 1, 1049-001, Lisboa, Portugal
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6
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Hnilicová J, Jirát Matějčková J, Šiková M, Pospíšil J, Halada P, Pánek J, Krásný L. Ms1, a novel sRNA interacting with the RNA polymerase core in mycobacteria. Nucleic Acids Res 2014; 42:11763-76. [PMID: 25217589 PMCID: PMC4191392 DOI: 10.1093/nar/gku793] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 11/12/2022] Open
Abstract
Small RNAs (sRNAs) are molecules essential for a number of regulatory processes in the bacterial cell. Here we characterize Ms1, a sRNA that is highly expressed in Mycobacterium smegmatis during stationary phase of growth. By glycerol gradient ultracentrifugation, RNA binding assay, and RNA co-immunoprecipitation, we show that Ms1 interacts with the RNA polymerase (RNAP) core that is free of the primary sigma factor (σA) or any other σ factor. This contrasts with the situation in most other species where it is 6S RNA that interacts with RNAP and this interaction requires the presence of σA. The difference in the interaction of the two types of sRNAs (Ms1 or 6S RNA) with RNAP possibly reflects the difference in the composition of the transcriptional machinery between mycobacteria and other species. Unlike Escherichia coli, stationary phase M. smegmatis cells contain relatively few RNAP molecules in complex with σA. Thus, Ms1 represents a novel type of small RNAs interacting with RNAP.
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Affiliation(s)
- Jarmila Hnilicová
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Jitka Jirát Matějčková
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Michaela Šiková
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Jiří Pospíšil
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Petr Halada
- Department of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Josef Pánek
- Department of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Libor Krásný
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
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7
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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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Berry SM, Chin EN, Jackson SS, Strotman LN, Goel M, Thompson NE, Alexander CM, Miyamoto S, Burgess RR, Beebe DJ. Weak protein-protein interactions revealed by immiscible filtration assisted by surface tension. Anal Biochem 2013; 447:133-40. [PMID: 24215910 DOI: 10.1016/j.ab.2013.10.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 11/25/2022]
Abstract
Biological mechanisms are often mediated by transient interactions between multiple proteins. The isolation of intact protein complexes is essential to understanding biochemical processes and an important prerequisite for identifying new drug targets and biomarkers. However, low-affinity interactions are often difficult to detect. Here, we use a newly described method called immiscible filtration assisted by surface tension (IFAST) to isolate proteins under defined binding conditions. This method, which gives a near-instantaneous isolation, enables significantly higher recovery of transient complexes compared to current wash-based protocols, which require reequilibration at each of several wash steps, resulting in protein loss. The method moves proteins, or protein complexes, captured on a solid phase through one or more immiscible-phase barriers that efficiently exclude the passage of nonspecific material in a single operation. We use a previously described polyol-responsive monoclonal antibody to investigate the potential of this new method to study protein binding. In addition, difficult-to-isolate complexes involving the biologically and clinically important Wnt signaling pathway were isolated. We anticipate that this simple, rapid method to isolate intact, transient complexes will enable the discoveries of new signaling pathways, biomarkers, and drug targets.
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Affiliation(s)
- Scott M Berry
- Department of Biomedical Engineering, University of Wisconsin at Madison, Madison, WI 53705, USA.
| | - Emily N Chin
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Shawn S Jackson
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Lindsay N Strotman
- Department of Biomedical Engineering, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Mohit Goel
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Nancy E Thompson
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Caroline M Alexander
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Shigeki Miyamoto
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Richard R Burgess
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin at Madison, Madison, WI 53705, USA
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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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10
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Esch AM, Thompson NE, Lamberski JA, Mertz JE, Burgess RR. Production and characterization of monoclonal antibodies to estrogen-related receptor alpha (ERRα) and use in immunoaffinity chromatography. Protein Expr Purif 2012; 84:47-58. [PMID: 22565152 PMCID: PMC3587309 DOI: 10.1016/j.pep.2012.04.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 04/24/2012] [Accepted: 04/26/2012] [Indexed: 11/16/2022]
Abstract
Estrogen-related receptor alpha (ERRα) is an orphan nuclear receptor whose elevated expression is thought to contribute to breast, colon, and ovarian cancers. In order to investigate the role of ERRα in human disease, there is a need for immunological reagents suitable for detection and purification of ERRα. We expressed recombinant human ERRα in Escherichia coli, purified the protein, and used it to generate monoclonal antibodies (mAbs) to ERRα. Nine high-affinity mAbs were chosen for their abilities to detect overexpressed ERRα in enzyme-linked immunosorbent assays (ELISAs) and Western blots, after which isotyping and preliminary epitope mapping was performed. The mAbs were all IgG subtypes and reacted with several different regions of full-length ERRα. A majority of the mAbs were found to be useful for immunoprecipitation of ERRα, and several could detect DNA-bound ERRα in electrophoretic mobility supershift assays (EMSAs) and chromatin immunoprecipitation (ChIP). The suitability of mAbs to detect ERRα in immunofluorescence assays was assessed. One mAb in particular, 2ERR10, could specifically detect endogenous ERRα in mammary carcinoma cells. Finally, we performed assays to screen for mAbs that gently release ERRα in the presence of a low-molecular-weight polyhydroxylated compound (polyol) and nonchaotropic salt. Using gentle immunoaffinity chromatography, we were able to isolate ERRα from mammalian cells by eluting with a polyol-salt solution. Our characterization studies show that these monoclonal antibodies perform well in a variety of biochemical assays. We anticipate that these novel reagents will prove useful for the detection and purification of ERRα in research and clinical applications.
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MESH Headings
- Animals
- Antibodies, Monoclonal/biosynthesis
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Blotting, Western
- Cell Line, Tumor
- Chromatography, Affinity/methods
- Electrophoretic Mobility Shift Assay
- Enzyme-Linked Immunosorbent Assay
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Female
- Fluorescent Antibody Technique
- HEK293 Cells
- Histidine/chemistry
- Histidine/metabolism
- Humans
- Immunoprecipitation
- Mice
- Mice, Inbred BALB C
- Oligopeptides/chemistry
- Oligopeptides/metabolism
- Polymers/chemistry
- Receptors, Estrogen/chemistry
- Receptors, Estrogen/immunology
- Receptors, Estrogen/isolation & purification
- Receptors, Estrogen/metabolism
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/isolation & purification
- Recombinant Fusion Proteins/metabolism
- Transfection
- ERRalpha Estrogen-Related Receptor
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Affiliation(s)
- Amanda M. Esch
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Nancy E. Thompson
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Jennifer A. Lamberski
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Janet E. Mertz
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Richard R. Burgess
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, United States
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Huang F, Zhang B, Zhou S, Zhao X, Bian C, Wei Y. Chemical proteomics: terra incognita for novel drug target profiling. CHINESE JOURNAL OF CANCER 2012; 31:507-18. [PMID: 22640626 PMCID: PMC3777519 DOI: 10.5732/cjc.011.10377] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The growing demand for new therapeutic strategies in the medical and pharmaceutic fields has resulted in a pressing need for novel druggable targets. Paradoxically, however, the targets of certain drugs that are already widely used in clinical practice have largely not been annotated. Because the pharmacologic effects of a drug can only be appreciated when its interactions with cellular components are clearly delineated, an integrated deconvolution of drug-target interactions for each drug is necessary. The emerging field of chemical proteomics represents a powerful mass spectrometry (MS)-based affinity chromatography approach for identifying proteome-wide small molecule-protein interactions and mapping these interactions to signaling and metabolic pathways. This technique could comprehensively characterize drug targets, profile the toxicity of known drugs, and identify possible off-target activities. With the use of this technique, candidate drug molecules could be optimized, and predictable side effects might consequently be avoided. Herein, we provide a holistic overview of the major chemical proteomic approaches and highlight recent advances in this area as well as its potential applications in drug discovery.
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Affiliation(s)
- Fuqiang Huang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
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Stalder ES, Nagy LH, Batalla P, Arthur TM, Thompson NE, Burgess RR. The epitope for the polyol-responsive monoclonal antibody 8RB13 is in the flap-domain of the beta-subunit of bacterial RNA polymerase and can be used as an epitope tag for immunoaffinity chromatography. Protein Expr Purif 2011; 77:26-33. [PMID: 21215316 DOI: 10.1016/j.pep.2010.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 12/17/2010] [Accepted: 12/18/2010] [Indexed: 11/16/2022]
Abstract
Polyol-responsive monoclonal antibodies (PR-mAbs) are useful for the purification of proteins in an easy, one step immunoaffinity step. These antibodies allow for gentle purification of proteins and protein complexes using a combination of a low molecular weight polyhydroxylated compound (polyol) and a nonchaotrophic salt in the eluting buffer. mAb 8RB13 has been characterized as one of these PR-mAbs and has been used to purify RNA polymerase from five species of bacteria. Here the epitope for 8RB13 has been identified as PEEKLLRAIFGEKAS, a sequence that is highly conserved in the β-subunit of bacterial RNA polymerase. This sequence is located in the "beta-flap" domain of RNA polymerase (and essentially comprises the "flap-tip helix"), an important binding site for sigma70. This location explains why only the core RNAP is purified using this mAb. This amino acid sequence has been developed into an epitope tag that can be used to purify a target protein from either bacterial or eukaryotic cells when genetically fused to a protein of interest.
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Affiliation(s)
- Elizabeth S Stalder
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, United States
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