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Metal-Chelating Peptides Separation Using Immobilized Metal Ion Affinity Chromatography: Experimental Methodology and Simulation. SEPARATIONS 2022. [DOI: 10.3390/separations9110370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Metal-Chelating Peptides (MCPs), obtained from protein hydrolysates, present various applications in the field of nutrition, pharmacy, cosmetic etc. The separation of MCPs from hydrolysates mixture is challenging, yet, techniques based on peptide-metal ion interactions such as Immobilized Metal Ion Affinity Chromatography (IMAC) seem to be efficient. However, separation processes are time consuming and expensive, therefore separation prediction using chromatography modelling and simulation should be necessary. Meanwhile, the obtention of sorption isotherm for chromatography modelling is a crucial step. Thus, Surface Plasmon Resonance (SPR), a biosensor method efficient to screen MCPs in hydrolysates and with similarities to IMAC might be a good option to acquire sorption isotherm. This review highlights IMAC experimental methodology to separate MCPs and how, IMAC chromatography can be modelled using transport dispersive model and input data obtained from SPR for peptides separation simulation.
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Kielkopf CL, Bauer W, Urbatsch IL. Expressing Cloned Genes for Protein Production, Purification, and Analysis. Cold Spring Harb Protoc 2021; 2021:pdb.top102129. [PMID: 33272973 DOI: 10.1101/pdb.top102129] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Obtaining high quantities of a specific protein directly from native sources is often challenging, particularly when dealing with human proteins. To overcome this obstacle, many researchers take advantage of heterologous expression systems by cloning genes into artificial vectors designed to operate within easily cultured cells, such as Escherichia coli, Pichia pastoris (yeast), and several varieties of insect and mammalian cells. Heterologous expression systems also allow for easy modification of the protein to optimize expression, mutational analysis of specific sites within the protein and facilitate their purification with engineered affinity tags. Some degree of purification of the target protein is usually required for functional analysis. Purification to near homogeneity is essential for characterization of protein structure by X-ray crystallography or nuclear magnetic resonance (NMR) and characterization of the biochemical and biophysical properties of a protein, because contaminating proteins almost always adversely affect the results. Methods for producing and purifying proteins in several different expression platforms and using a variety of vectors are introduced here.
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Dehdashti SM, Acharjee S, Nomani A, Deka M. Production of pharmaceutical active recombinant globular adiponectin as a secretory protein in Withania Somnifera hairy root culture. J Biotechnol 2020; 323:302-312. [PMID: 32682804 DOI: 10.1016/j.jbiotec.2020.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 07/08/2020] [Accepted: 07/15/2020] [Indexed: 01/19/2023]
Abstract
Among various in vitro plant culture systems, hairy root systems seem to be one of the most appealing methods of recombinant protein production due to their advantages in combining both whole-plant cultivation and suspension cell culture platform. This is a report on production and secretion of a recombinant pharmaceutically active protein from hairy roots cultures of Withania somnifera to improve the economic potential of this plant for the production pharmaceutical compounds. In this study, we selected and synthesized a codon-optimized globular adiponectin (gAd) gene with a calreticulin signal peptide and cloned the sequence into a plant expression binary vector containing a nptII gene as a selectable marker gene. The transgenic hairy roots were produced by Agrobacterium rhizogenes-mediated transformation protocol developed by our group. Among ten established nptII positive hairy roots lines, six colons significantly accumulated gAd protein in the biomass and extracellular medium. The presence of gAd was confirmed by western blot analysis of root extracts. The maximum level of hairy root biomass, growth rate (GR), intra- and extracellular gAd expressions were obtained after 25-26 days of culture on MS medium. The maximum level of intra- and extracellular gAd proteins were found to be 15.19 μg/gFW and 215.7 μg/L, respectively, which resulted in a significant decrease in the amount of intra- and extracellular withanolide A and withaferin A production. The addition of PVP, KNO3 and NaCl significantly increased the level of extracellular gAd by approximately 13 folds. This improvement could significantly increase the amount of intra- and extracellular withanolide A and withaferin A production, too. The recombinant gAd produced from W. somnifera is functional as proved by induction the phosphorylation of ACC in C2C12 muscle cells, as its functional amount was 5.1-fold more than gAd produced from E. coli and 45 % lower than CHO cells.
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Affiliation(s)
- Sayed Mehdi Dehdashti
- Department of Bioengineering and Technology, Faculty of Technology, Gauhati University, Guwahati, Assam 781014, India.
| | - Sumita Acharjee
- Department of Agricultural Biotechnology, Assam Agriculture University, Jorhat, Assam 785013, India
| | - Alireza Nomani
- Department of Pharmaceutical Biomaterials, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Manab Deka
- Department of Bioengineering and Technology, Faculty of Technology, Gauhati University, Guwahati, Assam 781014, India.
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Roozbahani GM, Chen X, Zhang Y, Wang L, Guan X. Nanopore detection of metal ions: Current status and future directions. SMALL METHODS 2020; 4:2000266. [PMID: 33365387 PMCID: PMC7751931 DOI: 10.1002/smtd.202000266] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Indexed: 05/27/2023]
Abstract
In this review, we highlight recent research efforts that aimed at developing nanopore sensors for detection of metal ions, which play a crucial role in environmental safety and human health. Protein pores use three stochastic sensing-based strategies for metal ion detection. The first strategy is to construct engineered nanopores with metal ion binding sites, so that the interaction between the target analytes and the nanopore can slow the movement of metal ions in the nano-channel. Second, large molecules such as nucleic acids and especially peptides could be utilized as external selective molecular probes to detect metal ions based on the conformational change of the ligand molecules induced by the metal ion-ligand chelation / coordination interaction. Third, enzymatic reactions can also be used as an alternative to the molecule probe strategy in the situation that a sensitive and selective probe molecule for the target analyte is difficult to obtain. On the other hand, by taking advantage of steady-state analysis, synthetic nanopores mainly use two strategies (modification and modification-free) to detect metals. Given the advantages of high sensitivity & selectivity, and label-free detection, nanopore-based metal ion sensors should find useful application in many fields, including environmental monitoring, medical diagnosis, and so on.
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Affiliation(s)
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- The University of Chinese Academy of Science, Beijing, 100049, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
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Kreher U, Spiccia L, Hearn MTW. Interactions between an amphipathic di-histidine peptide and a metal affinity chromatographic resin derived from a bis(tacn)butane chelating ligand. J Sep Sci 2019; 42:3631-3639. [PMID: 31651081 DOI: 10.1002/jssc.201900908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 11/06/2022]
Abstract
The interactive behavior of an amphipathic peptide with the Cu2+ , Ni2+ , and Zn2+ complexes of 1,4-bis(triazacyclonon-1-yl)butane), bis(tacn)but , immobilized onto Sepharose CL-4B, has been investigated. The effects of incubation time, as well as the incubation buffer pH and ionic strength, have been examined. The binding data have been interrogated using Langmuir, Langmuir-Freundlich, bi-Langmuir, and Temkin isothermal models and Scatchard plots. These results confirm that this amphipathic peptide binds with relatively high capacities to the immobilized Cu2+ - and Ni2+ -1,4-bis(triazacyclonon-1-yl)butane)-Sepharose CL-4B sorbents via at least two discrete sites. However, the corresponding immobilized Zn2+ -sorbent had low binding capacity. Moreover, the magnitude of the binding capacities of these sorbents was dependent on the pH and ionic strength of the incubation buffer. These results are relevant to the isolation of E. coli expressed recombinant proteins that incorporate this and related amphipathic peptide tags, containing two or more histidine residues, located at the N- or C-terminus of the recombinant protein, and the co-purification of low abundance host cell proteins of diverse structure, by immobilized metal ion affinity chromatographic methods.
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Affiliation(s)
- Ute Kreher
- Centre for Green Chemistry, School of Chemistry, Monash University, Clayton, Australia
| | - Leone Spiccia
- Centre for Green Chemistry, School of Chemistry, Monash University, Clayton, Australia
| | - Milton T W Hearn
- Centre for Green Chemistry, School of Chemistry, Monash University, Clayton, Australia
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Mills CE, Ding E, Olsen B. Protein Purification by Ethanol-Induced Phase Transitions of the Elastin-like Polypeptide (ELP). Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b00769] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Carolyn E. Mills
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Erika Ding
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Glover SD, Tommos C. A Quick and Colorful Method to Measure Low-Level Contaminations of Paramagnetic Ni 2+ in Protein Samples Purified by Immobilized Metal Ion Affinity Chromatography. Methods Enzymol 2019; 614:87-106. [PMID: 30611434 DOI: 10.1016/bs.mie.2018.08.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Isotopic labeling of recombinantly expressed proteins is generally required for investigation by modern nuclear magnetic resonance (NMR) methods. Purification strategies of the labeled proteins often include the use of a polyhistidine affinity tag (His-tag) and immobilized metal ion affinity chromatography (IMAC). Described herein are rapid and inexpensive qualitative and quantitative assays to determine the concentration of paramagnetic Ni2+ in protein samples purified by IMAC. Both qualitative and quantitative colorimetric methods detect the amount of Ni2+ via the color change produced when a [Ni(PAR)n]2+ (PAR=4-(2-pyridylazo)resorcinol, n=1, 2) complex is formed. The qualitative assay provides a rapid visual test for the presence of Ni2+ in the low micromolar range in a sample of interest. The usefulness of the spectroscopic quantitative assay is illustrated by: (i) detecting a 12μM Ni2+ contamination in an NMR sample containing 950μM of the 7.5kDa α3W protein purified by a standard His-tag Ni2+/IMAC approach and (ii) showing that the 15N-HSQC spectrum of the α3W NMR sample, containing 1 paramagnetic Ni2+ ion per 80 protein molecules, displays clear line broadening of both water and protein spectral lines. We also (iii) measured Ni2+ release during the equilibration, wash, and elution steps of three commonly used Ni2+/IMAC resins when following manufacturer's protocols. The concentration of Ni2+ detected in elutes of the three resins ranged from 2μM to nearly 1mM.
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Affiliation(s)
- Starla D Glover
- Department of Biochemistry & Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Cecilia Tommos
- Department of Biochemistry & Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States.
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Abstract
A key challenge in chemical biology is to identify small molecule regulators for every single protein. However, protein surfaces are notoriously difficult to recognise with synthetic molecules, often having large flat surfaces that are poorly matched to traditional small molecules. In the surface mimetic approach, a supramolecular scaffold is used to project recognition groups in such a manner as to make multivalent non-covalent contacts over a large area of protein surface. Metal based supramolecular scaffolds offer unique advantages over conventional organic molecules for protein binding, including greater stereochemical and geometrical diversity conferred through the metal centre and the potential for direct assessment of binding properties and even visualisation in cells without recourse to further functionalisation. This feature article will highlight the current state of the art in protein surface recognition using metal complexes as surface mimetics.
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Affiliation(s)
- Sarah H Hewitt
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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Deng L, Xue X, Shen C, Song X, Wang C, Wang N. Insulin chains as efficient fusion tags for prokaryotic expression of short peptides. Protein Expr Purif 2017; 138:46-55. [DOI: 10.1016/j.pep.2017.06.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/22/2017] [Accepted: 06/30/2017] [Indexed: 01/02/2023]
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Hu Y, Romão E, Vertommen D, Vincke C, Morales-Yánez F, Gutiérrez C, Liu C, Muyldermans S. Generation of Nanobodies against SlyD and development of tools to eliminate this bacterial contaminant from recombinant proteins. Protein Expr Purif 2017; 137:64-76. [DOI: 10.1016/j.pep.2017.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/24/2017] [Accepted: 06/27/2017] [Indexed: 12/26/2022]
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Boute N, Lowe P, Berger S, Malissard M, Robert A, Tesar M. NanoLuc Luciferase - A Multifunctional Tool for High Throughput Antibody Screening. Front Pharmacol 2016; 7:27. [PMID: 26924984 PMCID: PMC4758271 DOI: 10.3389/fphar.2016.00027] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/29/2016] [Indexed: 01/22/2023] Open
Abstract
Based on the recent development of NanoLuc luciferase (Nluc), a small (19 kDa), highly stable, ATP independent, bioluminescent protein, an extremely robust and ultra high sensitivity screening system has been developed whereby primary hits of therapeutic antibodies and antibody fragments could be characterized and quantified without purification. This system is very versatile allowing cellular and solid phase ELISA but also homogeneous BRET based screening assays, relative affinity determinations with competition ELISA and direct Western blotting. The new Nluc protein fusion represents a “swiss army knife solution” for today and future high throughput antibody drug screenings.
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Affiliation(s)
- Nicolas Boute
- Molecular and Cellular Biology Unit, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en-Genevois, France
| | - Peter Lowe
- Molecular and Cellular Biology Unit, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en-Genevois, France
| | - Sven Berger
- Molecular and Cellular Biology Unit, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en-Genevois, France
| | - Martine Malissard
- Biochemistry Department, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en Genevois, France
| | - Alain Robert
- Molecular and Cellular Biology Unit, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en-Genevois, France
| | - Michael Tesar
- Molecular and Cellular Biology Unit, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en-Genevois, France
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Singh N, Arunkumar A, Chollangi S, Tan ZG, Borys M, Li ZJ. Clarification technologies for monoclonal antibody manufacturing processes: Current state and future perspectives. Biotechnol Bioeng 2015; 113:698-716. [DOI: 10.1002/bit.25810] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/20/2015] [Accepted: 08/20/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Nripen Singh
- Biologics Development; Global Manufacturing and Supply, Bristol-Myers Squibb; 35 South Street Hopkinton Massachusetts 01748
| | - Abhiram Arunkumar
- Biologics Development; Global Manufacturing and Supply, Bristol-Myers Squibb; 35 South Street Hopkinton Massachusetts 01748
| | - Srinivas Chollangi
- Biologics Development; Global Manufacturing and Supply, Bristol-Myers Squibb; 35 South Street Hopkinton Massachusetts 01748
| | - Zhijun George Tan
- Biologics Development; Global Manufacturing and Supply, Bristol-Myers Squibb; 35 South Street Hopkinton Massachusetts 01748
| | - Michael Borys
- Biologics Development; Global Manufacturing and Supply, Bristol-Myers Squibb; 35 South Street Hopkinton Massachusetts 01748
| | - Zheng Jian Li
- Biologics Development; Global Manufacturing and Supply, Bristol-Myers Squibb; 35 South Street Hopkinton Massachusetts 01748
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13
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Bjerga GEK, Williamson AK. Cold shock induction of recombinant Arctic environmental genes. BMC Biotechnol 2015; 15:78. [PMID: 26286037 PMCID: PMC4544801 DOI: 10.1186/s12896-015-0185-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/24/2015] [Indexed: 11/16/2022] Open
Abstract
Background Heterologous expression of psychrophilic enzymes in E. coli is particularly challenging due to their intrinsic instability. The low stability is regarded as a consequence of adaptation that allow them to function at low temperatures. Recombinant production presents a significant barrier to their exploitation for commercial applications in industry. Methods As part of an enzyme discovery project we have investigated the utility of a cold-shock inducible promoter for low-temperature expression of five diverse genes derived from the metagenomes of marine Arctic sediments. After evaluation of their production, we further optimized for soluble production by building a vector suite from which the environmental genes could be expressed as fusions with solubility tags. Results We found that the low-temperature optimized system produced high expression levels for all putatively cold-active proteins, as well as reducing host toxicity for several candidates. As a proof of concept, activity assays with one of the candidates, a putative chitinase, showed that functional protein was obtained using the low-temperature optimized vector suite. Conclusions We conclude that a cold-shock inducible system is advantageous for the heterologous expression of psychrophilic proteins, and may also be useful for expression of toxic mesophilic and thermophilic proteins where properties of the proteins are deleterious to the host cell growth. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0185-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gro Elin Kjæreng Bjerga
- Norstruct, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway. .,Centre for Applied Biotechnology, Uni Research AS, Thormøhlensgt. 55, N-5008, Bergen, Norway.
| | - Adele Kim Williamson
- Norstruct, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway.
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Nickel(II)-immobilized sulfhydryl cotton fiber for selective binding and rapid separation of histidine-tagged proteins. J Chromatogr A 2015; 1405:188-92. [DOI: 10.1016/j.chroma.2015.05.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/16/2015] [Accepted: 05/18/2015] [Indexed: 11/22/2022]
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15
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Zhao G, Jin Z, Allewell NM, Tuchman M, Shi D. Structures of the N-acetyltransferase domain of Xylella fastidiosa N-acetyl-L-glutamate synthase/kinase with and without a His tag bound to N-acetyl-L-glutamate. Acta Crystallogr F Struct Biol Commun 2015; 71:86-95. [PMID: 25615976 PMCID: PMC4304755 DOI: 10.1107/s2053230x14026788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/05/2014] [Indexed: 11/10/2022] Open
Abstract
Structures of the catalytic N-acetyltransferase (NAT) domain of the bifunctional N-acetyl-L-glutamate synthase/kinase (NAGS/K) from Xylella fastidiosa bound to N-acetyl-L-glutamate (NAG) with and without an N-terminal His tag have been solved and refined at 1.7 and 1.4 Å resolution, respectively. The NAT domain with an N-terminal His tag crystallized in space group P4(1)2(1)2, with unit-cell parameters a=b=51.72, c=242.31 Å. Two subunits form a molecular dimer in the asymmetric unit, which contains ∼41% solvent. The NAT domain without an N-terminal His tag crystallized in space group P21, with unit-cell parameters a=63.48, b=122.34, c=75.88 Å, β=107.6°. Eight subunits, which form four molecular dimers, were identified in the asymmetric unit, which contains ∼38% solvent. The structures with and without the N-terminal His tag provide an opportunity to evaluate how the His tag affects structure and function. Furthermore, multiple subunits in different packing environments allow an assessment of the plasticity of the NAG binding site, which might be relevant to substrate binding and product release. The dimeric structure of the X. fastidiosa N-acetytransferase (xfNAT) domain is very similar to that of human N-acetyltransferase (hNAT), reinforcing the notion that mammalian NAGS is evolutionally derived from bifunctional bacterial NAGS/K.
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Affiliation(s)
- Gengxiang Zhao
- Center for Genetic Medicine Research and Department of Integrative Systems Biology, Children’s National Medical Center, The George Washington University, Washington, DC 20010, USA
| | - Zhongmin Jin
- Southeast Regional Collaborative Access Team, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Norma M. Allewell
- Department of Cell Biology and Molecular Genetics and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, USA
| | - Mendel Tuchman
- Center for Genetic Medicine Research and Department of Integrative Systems Biology, Children’s National Medical Center, The George Washington University, Washington, DC 20010, USA
| | - Dashuang Shi
- Center for Genetic Medicine Research and Department of Integrative Systems Biology, Children’s National Medical Center, The George Washington University, Washington, DC 20010, USA
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Abstract
Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, as well as for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future.
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Affiliation(s)
- Michelle E Kimple
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Allison L Brill
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Renee L Pasker
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
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17
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Mu T, Liang W, Ju Y, Wang Z, Wang Z, Roycik MD, Sang QXA, Yu D, Xiang H, Fang X. Efficient soluble expression of secreted matrix metalloproteinase 26 in Brevibacillus choshinensis. Protein Expr Purif 2013; 91:125-33. [PMID: 23921071 DOI: 10.1016/j.pep.2013.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 07/17/2013] [Accepted: 07/19/2013] [Indexed: 11/29/2022]
Abstract
Matrix metalloproteinase 26 (MMP-26) is a novel member of the matrix metalloproteinase family with minimal domain constitution and unknown physiological function. The three-dimensional (3D) structure of the enzyme also remains to be deciphered. Previous studies show that MMP-26 may be expressed in Escherichia coli (E. coli) as inclusion bodies and re-natured with catalytic activity. However, the low re-naturation rate of this method limits its usage in structural studies. In this paper, we tried to clone, express and purify the pro form and catalytic form of MMP-26 (ProMMP-26 and CatMMP-26) in several widely used expression vectors and express the recombinant MMP-26 proteins in E. coli cells. These constructs resulted in insoluble expressions or soluble expressions of MMP-26 with little catalytic activity. We then used Brevibacillus choshinensis (B. choshinensis) as the host system for the soluble and active expression of MMP-26. The enzyme was secreted in soluble form in the supernatant of cell culture medium and purified via a two-step purification process that included Ni(2+) affinity chromatography followed by gel filtration. The yields of purified ProMMP-26 and CatMMP-26 were 12 and 18mg/L, respectively, with high purity and homogeneity. Both ProMMP-26 and CatMMP-26 showed gelatin zymography activity and the purified CatMMP-26 had high enzymatic activity against DQ-gelatin substrate. The large-scale soluble and active protein production for future structural studies of MMP-26 is thus feasible using the B. choshinensis host system.
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Affiliation(s)
- Tianyang Mu
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, Jilin 130012, PR China
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18
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Wang MY, Bentley WE, Vakharia V. Purification of a recombinant protein produced in a baculovirus expression system by immobilized metal affinity chromatography. Biotechnol Bioeng 2012; 43:349-56. [PMID: 18615717 DOI: 10.1002/bit.260430502] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Over the past 10 years, the baculovirus-insect cell system has become a powerful and versatile tool for the expression of a variety of heterologous proteins. In order to simplify separation of a cloned protein from the baculovirus-insect expression system, we have cloned a gene encoding for the protein of interest, a structural protein (VP2) of a strain (E/DEL) of infectious bursal disease virus (IBDV), with a metal ion binding site (His)(5) at its C-terminus. This chimeric protein (VP2H) has been expressed and one-step affinity purified with immobilized metal ions (Ni(+2)). With antigen capture-enzyme-linked immunosorbent assay (AC-ELISA), we determined that the conformation of this chimeric protein was no different from the recombinant wild-type VP2 protein. However, the two proteins (VP2 and VP2H) can be distinguished and resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and detected immunologically following Western blotting. (c) 1994 John Wiley & Sons, Inc.
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Affiliation(s)
- M Y Wang
- Center for Agricultural Biotechnology, Maryland Biotechnology Institute, Maryland 20742
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19
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Jung B, Theato P. Chemical Strategies for the Synthesis of Protein–Polymer Conjugates. BIO-SYNTHETIC POLYMER CONJUGATES 2012. [DOI: 10.1007/12_2012_169] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Ravindran PP, Héroux A, Ye JD. Improvement of the crystallizability and expression of an RNA crystallization chaperone. J Biochem 2011; 150:535-43. [PMID: 21785128 DOI: 10.1093/jb/mvr093] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Crystallizing RNA has been an imperative and challenging task in the world of RNA research. Assistive methods such as chaperone-assisted RNA crystallography (CARC), employing monoclonal antibody fragments (Fabs) as crystallization chaperones have enabled us to obtain RNA crystal structures by forming crystal contacts and providing initial phasing information. Despite the early successes, the crystallization of large RNA-Fab complex remains a challenge in practice. The possible reason for this difficulty is that the Fab scaffold has not been optimized for crystallization in complex with RNA. Here, we have used the surface entropy reduction (SER) technique for the optimization of ΔC209 P4-P6/Fab2 model system. Protruding lysine and glutamate residues were mutated to a set of alanines or serines to construct Fab2SMA or Fab2SMS. Expression with the shake flask approach was optimized to allow large scale production for crystallization. Crystal screening shows that significantly higher crystal-forming ratio was observed for the mutant complexes. As the chosen SER residues are far away from the CDR regions of the Fab, the same set of mutations can now be directly applied to other Fabs binding to a variety of ribozymes and riboswitches to improve the crystallizability of Fab-RNA complex.
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Thielges MC, Chung JK, Axup JY, Fayer MD. Influence of histidine tag attachment on picosecond protein dynamics. Biochemistry 2011; 50:5799-805. [PMID: 21619030 PMCID: PMC3133630 DOI: 10.1021/bi2003923] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Polyhistidine affinity tags are routinely employed as a convenient means of purifying recombinantly expressed proteins. A tacit assumption is commonly made that His tags have little influence on protein structure and function. Attachment of a His tag to the N-terminus of the robust globular protein myoglobin leads to only minor changes to the electrostatic environment of the heme pocket, as evinced by the nearly unchanged Fourier transform infrared spectrum of CO bound to the heme of His-tagged myoglobin. Experiments employing two-dimensional infrared vibrational echo spectroscopy of the heme-bound CO, however, find that significant changes occur to the short time scale (picoseconds) dynamics of myoglobin as a result of His tag incorporation. The His tag mainly reduces the dynamics on the 1.4 ps time scale and also alters protein motions of myoglobin on the slower, >100 ps time scale, as demonstrated by the His tag's influence on the fluctuations of the CO vibrational frequency, which reports on protein structural dynamics. The results suggest that affinity tags may have effects on protein function and indicate that investigators of affinity-tagged proteins should take this into consideration when investigating the dynamics and other properties of such proteins.
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Affiliation(s)
- Megan C Thielges
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jean K. Chung
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jun Y. Axup
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305
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22
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Belak ZR, Nair M, Ovsenek N. Parameters for effective in vitro production of zinc finger nucleic acid-binding proteins. Biotechnol Appl Biochem 2011; 58:166-74. [DOI: 10.1002/bab.24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 03/14/2011] [Indexed: 12/21/2022]
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24
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25
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Production and characterization of polyclonal and monoclonal Abs against the RNA-binding protein QKI. Appl Biochem Biotechnol 2010; 164:283-93. [PMID: 21165711 DOI: 10.1007/s12010-010-9134-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 11/19/2010] [Indexed: 10/18/2022]
Abstract
RNA-binding protein QKI, a member of the Signal Transduction and Activation of RNA family, is found to be essential in the blood vessel development and postnatal myelination in central nervous system (Woo et al., Oncogene 28:1176-1186, 2009; Lu et al., Nucleic Acids Res 31(15):4616-4624, 2003; Bohnsack et al., Genesis 44(2):93-104, 2006). However, its wide expression pattern suggests other fundamental roles in vivo (Kondo et al., Mamm Genome 10(7):662-669, 1999). To facilitate the understanding of QKI function in various systems, we prepared the polyclonal and monoclonal antibodies against QKI. To obtain the antigen, recombinant His-tagged QKI was expressed in Escherichia coli and highly purified by Ni(2+)-chelated column combined with hydrophobic and ion exchange methods. Following three types of immunizations with different adjuvants, including Freund's, PAGE gel, and nitrocellulose membrane, only the antiserum produced with Freund's adjuvant is effective for Western blot detection. Several McAb clones are able to recognize both endogenous and over-expressed QKI with high affinity in Western blot and immunofluorescence. The specificity of Ab was validated as weakening, and no specific signals were observed in cells with QKI knocking down. Immunohistochemistry analysis further showed positive staining of QKI in kidney where QKI mRNA was abundantly expressed, ensuring the wide applications of the QKI Abs in the ongoing mechanistic studies.
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Mooney JT, Fredericks D, Hearn MTW. Use of phage display methods to identify heptapeptide sequences for use as affinity purification 'tags' with novel chelating ligands in immobilized metal ion affinity chromatography. J Chromatogr A 2010; 1218:92-9. [PMID: 21159343 DOI: 10.1016/j.chroma.2010.10.113] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 10/22/2010] [Accepted: 10/26/2010] [Indexed: 01/30/2023]
Abstract
This study describes the screening of a peptide phage display library for amino acid sequences that bind with different affinities to a novel class of chelating ligands complexed with Ni²+ ions. These chelating ligands are based on the 1,4,7-triazacyclononane (TACN) structure and have been chosen to allow enhanced efficiency in protein capture and decreased propensity for metal ion leakage in the immobilized metal ion affinity chromatographic (IMAC) purification of recombinant proteins. Utilising high stringency screening conditions, various peptide sequences containing multiple histidine, tryptophan, and/or tyrosine residues were identified amongst the different phage peptide sequences isolated. The structures, and particularly the conserved locations of these key amino acid residues within the selected heptapeptides, form a basis to design specific peptide tags for use with these novel TACN ligands as a new mode of IMAC purification of recombinant proteins.
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Affiliation(s)
- Jane T Mooney
- ARC Special Research Centre for Green Chemistry, Building75, Monash University, Clayton, Victoria 3800, Australia
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27
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Arifin N, Basuni M, Lan CA, Yahya ARM, Noordin R. Purification of BmR1 Recombinant Protein. Protein J 2010; 29:509-15. [DOI: 10.1007/s10930-010-9281-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Molecular modeling and dynamics simulation of a histidine-tagged cytochrome b 5. J Mol Model 2010; 17:971-8. [DOI: 10.1007/s00894-010-0795-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 06/25/2010] [Indexed: 12/17/2022]
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29
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Hughes RA, Ellington AD. Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA. Nucleic Acids Res 2010; 38:6813-30. [PMID: 20571084 PMCID: PMC2965240 DOI: 10.1093/nar/gkq521] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
While a number of aminoacyl tRNA synthetase (aaRS):tRNA pairs have been engineered to alter or expand the genetic code, only the Methanococcus jannaschii tyrosyl tRNA synthetase and tRNA have been used extensively in bacteria, limiting the types and numbers of unnatural amino acids that can be utilized at any one time to expand the genetic code. In order to expand the number and type of aaRS/tRNA pairs available for engineering bacterial genetic codes, we have developed an orthogonal tryptophanyl tRNA synthetase and tRNA pair, derived from Saccharomyces cerevisiae. In the process of developing an amber suppressor tRNA, we discovered that the Escherichia coli lysyl tRNA synthetase was responsible for misacylating the initial amber suppressor version of the yeast tryptophanyl tRNA. It was discovered that modification of the G:C content of the anticodon stem and therefore reducing the structural flexibility of this stem eliminated misacylation by the E. coli lysyl tRNA synthetase, and led to the development of a functional, orthogonal suppressor pair that should prove useful for the incorporation of bulky, unnatural amino acids into the genetic code. Our results provide insight into the role of tRNA flexibility in molecular recognition and the engineering and evolution of tRNA specificity.
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Affiliation(s)
- Randall A Hughes
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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Kanemaru K, Oshima T, Baba Y. Selective recovery of histidine-containing dipeptides based on metal affinity interactions using chemically modified dextran in combination with ultrafiltration. REACT FUNCT POLYM 2010. [DOI: 10.1016/j.reactfunctpolym.2009.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Tamavidin, a versatile affinity tag for protein purification and immobilization. J Biotechnol 2009; 145:317-22. [PMID: 20026208 DOI: 10.1016/j.jbiotec.2009.12.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 11/11/2009] [Accepted: 12/05/2009] [Indexed: 11/24/2022]
Abstract
Tamavidin 2 is a fungal avidin-like protein that binds biotin with high affinity and is highly produced in soluble form in Escherichia coli. By contrast, widely used biotin-binding proteins avidin and streptavidin are rarely produced in soluble form in E. coli. In this study, we describe an efficient system for one-step purification and immobilization of recombinant proteins using tamavidin 2 as an affinity tag. A bacterial sialyltransferase and soybean agglutinin were fused to tamavidin 2 and expressed in E. coli and tobacco BY-2 cells, respectively. High-level expressions of the fusion proteins were detected (80 mg l(-1)E. coli culture for bacterial sialyltransferase-tamavidin 2 and 2 mg l(-1) BY-2 cell culture for soybean agglutinin-tamavidin 2). To immobilize and purify the fusion proteins, biotinylated magnetic microbeads were incubated with the soluble extract from each recombinant host producing the fusion protein and then washed thoroughly. As the result, both fusion proteins were immobilized tightly on the microbeads without substantial loss of activity and simultaneously highly purified (90-95% purity) on the microbeads. Biotin with a longer linker contributed to higher affinity between the fusion protein and biotin. These results suggest that tamavidin fusion technology is a powerful tool for production, purification, and immobilization of recombinant proteins.
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32
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Carlsson J, Mosbach K, Bülow L. Affinity precipitation and site-specific immobilization of proteins carrying polyhistidine tails. Biotechnol Bioeng 2009; 51:221-8. [PMID: 18624332 DOI: 10.1002/(sici)1097-0290(19960720)51:2<221::aid-bit12>3.0.co;2-p] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Proteins carrying genetically attached polyhistidine tails have been purified using affinity precipitation with metal chelates. DNA fragments encoding four or five histidine residues have been genetically fused to the oligomeric enzymes lactate dehydrogenase (Bacillus stearothermophilus), beta-glucoronidase (Escherichia coli), and galactose dehydrogenase (Pseudomonas fluorescens) as well as to the monomeric protein A (Staphylococcus aureus). The chimeric genes were subsequently expressed in E. coli. The engineered enzymes were successfully purified from crude protein solutions using ethylene glycolbis (beta-aminoethyl) tetraacetic acid (EGTA) charged with Zn(2+) as precipitant, whereas protein A, carrying only one attached histidine tail, did not precipitate. However, all of the engineered proteins could be purified on immobilized metal affinity chromatography (IMAC) columns loaded with Zn(2+). The potential of using the same histidine tails for site-specific immobilization of proteins was also investigated. The enzymes were all catalytically active when immobilized on IMAC gels. For instance, immobilized lactate dehydrogenase, carrying tails composed of four histidine residues, displaced 83% of the soluble enzyme activity.
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Affiliation(s)
- J Carlsson
- Department of Pure and Applied Biochemistry, Chemical Center, POB 124, S-221 00 Lund, Sweden
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33
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Abstract
We propose an in vitro selection strategy to identify bacteriophage variants that recognize metal ions in solution. In 6 M urea, phage T7 loses 99.9% of its activity in less than 5 min. Inactivation is accelerated by gold, but slowed by zinc and magnesium. Selection of phage over five generations in the presence of gold, zinc, and magnesium increases phage half-lives 4-, 10-, and 70-fold, respectively. As selections are repeated, phage become increasingly dependent on the specific metal employed in the selection, indicating the suitability of the strategy for optimization of metal-ion recognition.
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Affiliation(s)
- K Gupta
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755-8000, USA
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34
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Tian F, Yang L, Lv F, Zhou P. Modeling and prediction of retention behavior of histidine-containing peptides in immobilized metal-affinity chromatography. J Sep Sci 2009; 32:2159-69. [DOI: 10.1002/jssc.200800739] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Ye G, Schuler AD, Ahmadibeni Y, Morgan JR, Faruqui A, Huang K, Sun G, Zebala JA, Parang K. Synthesis and evaluation of phosphopeptides containing iminodiacetate groups as binding ligands of the Src SH2 domain. Bioorg Chem 2009; 37:133-42. [PMID: 19539345 DOI: 10.1016/j.bioorg.2009.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 05/14/2009] [Accepted: 05/15/2009] [Indexed: 11/25/2022]
Abstract
Phosphopeptide pTyr-Glu-Glu-Ile (pYEEI) has been introduced as an optimal Src SH2 domain ligand. Peptides, Ac-K(IDA)pYEEIEK(IDA) (1), Ac-KpYEEIEK (2), Ac-K(IDA)pYEEIEK (3), and Ac-KpYEEIEK(IDA) (4), containing 0-2 iminodiacetate (IDA) groups at the N- and C-terminal lysine residues were synthesized and evaluated as the Src SH2 domain binding ligands. Fluorescence polarization assays showed that peptide 1 had a higher binding affinity (K(d) = 0.6 microM) to the Src SH2 domain when compared with Ac-pYEEI (K(d) = 1.7 microM), an optimal Src SH2 domain ligand, and peptides 2-4 (K(d) = 2.9-52.7 microM). The binding affinity of peptide 1 to the SH2 domain was reduced by more than 2-fold (K(d) = 1.6 microM) upon addition of Ni(2+) (300 microM), possibly due to modest structural effect of Ni(2+) on the protein as shown by circular dichroism experimental results. The binding affinity of 1 was restored in the presence of EDTA (300 microM) (K(d) = 0.79 microM). These studies suggest that peptides containing IDA groups may be used for designing novel SH2 domain binding ligands.
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Affiliation(s)
- Guofeng Ye
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
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36
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Millner P, Hays H, Vakurov A, Pchelintsev N, Billah M, Rodgers M. Nanostructured transducer surfaces for electrochemical biosensor construction—Interfacing the sensing component with the electrode. Semin Cell Dev Biol 2009; 20:34-40. [DOI: 10.1016/j.semcdb.2009.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 01/23/2009] [Indexed: 10/21/2022]
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37
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YANG H, YANG XH, CHEN YQ, PAN M. Preparation and Immunochromatographic Assay of Biological Probes with Fe Nanowires/Chitosan/Antibody. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2009. [DOI: 10.1016/s1872-2040(08)60087-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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Chen P, Hu T, Jiang M, Guo D. Synthesis in Escherichia coli cells and characterization of the active exoribonuclease of severe acute respiratory syndrome coronavirus. Mol Biol 2009; 43:410-417. [PMID: 32214468 PMCID: PMC7089200 DOI: 10.1134/s0026893309030091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 04/30/2008] [Indexed: 11/23/2022]
Abstract
The nsp14 protein, an exoribonuclease of the DEDD superfamily encoded by severe acute respiratory syndrome coronavirus (SARS-CoV), was expressed in fusion with different affinity tags. The recombinant nsp14 proteins with either GST fusion or 6-histidine tag were shown to possess ribonuclease activity but nsp14 with a short MGHHHHHHGS tag sequence at the N-terminus increased the solubility of nsp14 protein and facilitated the protein purification. Mutations of the conserved residues of nsp14 resulted in significant attenuation but not abolishment of the ribonuclease activity. Combination of fluorescence and circular dichroism spectroscopy analyses showed that the conformational stability of nsp14 protein varied with many external factors such as pH, temperature and presence of denaturing chemicals. These results provide new information on the structural features and would be helpful for further characterization of this functionally important protein.
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Affiliation(s)
- P Chen
- 1State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, 430072 PR. China.,2Department of Pathophysiology, Basic Medical College of Zhengzhou University, Zhengzhou, 450001 PR. China
| | - T Hu
- 1State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, 430072 PR. China
| | - M Jiang
- 1State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, 430072 PR. China
| | - D Guo
- 1State Key Laboratory of Virology and Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, 430072 PR. China
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Kondo N, Ebihara A, Ru H, Kuramitsu S, Iwamoto A, Rao Z, Matsuda Z. Thermus thermophilus-derived protein tags that aid in preparation of insoluble viral proteins. Anal Biochem 2008; 385:278-85. [PMID: 19084492 DOI: 10.1016/j.ab.2008.10.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 10/09/2008] [Accepted: 10/21/2008] [Indexed: 10/21/2022]
Abstract
The expression and solubilization of insoluble proteins have been facilitated by the introduction of protein tags. In our analyses of viral protein R (Vpr) of human immunodeficiency virus 1 (HIV-1), however, several conventional tag proteins enhanced its expression but failed to solubilize it. Therefore, we decided to explore whether proteins derived from Thermus thermophilus HB8 (T. th.), a highly heat-stable bacterium, could be used as tag proteins to enhance the solubilization of Vpr. Based on the data accumulated during the recent structural genomics project of T. th., we selected 15 T. th. proteins with high expression levels and solubilities. From this group, we identified a T. th. tag protein that expressed Vpr in a soluble form. Furthermore, two T. th. tag proteins, including the identified one, were found to solubilize the extremely insoluble membrane-spanning domain of the envelope protein of HIV-1. When green fluorescent protein (GFP) was used as a passenger protein of T. th. tags, the brightness and stability of GFP were similar to those of untagged GFP, suggesting that the T. th. tags do not negatively affect the function of the passenger protein. Thus, data of structural genomics can be applied to generate a customized versatile protein tag for protein analyses.
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Affiliation(s)
- Naoyuki Kondo
- Research Center for Asian Infectious Diseases, Institute of Medical Science, University of Tokyo, Shirokanedai, Tokyo, Japan
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40
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Du H, Zhang X, Wang J, Yao X, Hu Z. Novel approaches to predict the retention of histidine-containing peptides in immobilized metal-affinity chromatography. Proteomics 2008; 8:2185-95. [PMID: 18446801 DOI: 10.1002/pmic.200700788] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The new method lazy learning method-local lazy regression (LLR) was first used to model the quantitative structure-retention relationship (QSRR) for predicting and explaining the retention behaviors of peptides in the nickel column in immobilized metal-affinity chromatography (IMAC). The best multilinear regression (BMLR) method implemented in the CODESSA was used to select the most appropriate molecular descriptors from a large set and build a linear regression model. Based on the selected five descriptors, another two approaches, projection pursuit regression (PPR) and LLR were used to build more accurate QSRR models. The coefficients of determination (R(2)) of the best model developed based on LLR were 0.9446 and 0.9252 for the training set and the test set, respectively. By comparison, it was proved that the novel local learning method LLR was a very promising tool for QSRR modeling with excellent predictive capability for the prediction of imidazole concentration (IMC) values of histidine-containing peptides in IMAC. It could be used in other chromatography research fields and that should facilitate the design and purification of peptides and proteins.
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Affiliation(s)
- Hongying Du
- Department of Chemistry, Lanzhou University, Lanzhou, China
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41
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Kimple ME, Sondek J. Overview of affinity tags for protein purification. ACTA ACUST UNITED AC 2008; Chapter 9:9.9.1-9.9.19. [PMID: 18429272 DOI: 10.1002/0471140864.ps0909s36] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, and for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future.
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42
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Abstract
Determination of a macromolecular structure using x-ray diffraction is a multistep process that involves a plethora of techniques involving molecular biology, bioinformatics, and physical sciences. Counterintuitively, the success of any or all individual steps does not guarantee the success of the overall process. This review examines the difficulties presented by each step on the path from a gene to the final publication, together with certain lucky (or unlucky) circumstances that can affect the velocity along that path.
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43
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Meng J, Walter JG, Kökpinar Ö, Stahl F, Scheper T. Automated Microscale His-tagged Protein Purification Using Ni-NTA Magnetic Agarose Beads. Chem Eng Technol 2008. [DOI: 10.1002/ceat.200700429] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Patchornik G. Purification of His-tagged proteins with [desthiobiotin-BSA-EDTA] conjugates exhibiting resistance to EDTA. Bioconjug Chem 2008; 19:673-9. [PMID: 18311907 DOI: 10.1021/bc700368y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two His-tagged proteins (His 6-P38 and His 6-Protein A) were purified by specific precipitation utilizing nonsoluble macrocomplexes composed of: BSA conjugates (modified with desthiobiotin-NHS and EDTA-dianhydride), tetrameric avidin, and Cu2+ ions. The generated pellets containing bound His-tagged proteins are washed with EDTA (25-100 mM) and then eluted in relatively high purity (> or =90%) devoid the macrocomplexes. Three different BSA conjugates were synthesized (DB-BSA-EDTA, DB-BSA-EDTA-A, DB-BSA-EDTA-B) and their adsorption capacities (3.8-6.4 micromol/g of BSA conjugate) as well as the recovery yields of His-tagged proteins obtained with them (44-84%) determined. The data demonstrate that capacity is dependent on the stochiometric ratio of modifying reagents (i.e., desthiobiotin-NHS and EDTA-dianhydride) used during the synthesis of the BSA conjugates. Copper ions were found to be significantly superior to Zn2+, Co2+, and Ni2+. BSA conjugates could be regenerated in moderate yields (74-83%) by incubating them at 88 degrees C in the presence of biotin (10 mM) at pH 7. The absence of resins leads to formation of small pellets (1-5 mg) and utilization of minute volumes of elution buffer (50-100 microL). Hence, concentrated preparations can be obtained, and a reconcentration step may be circumvented.
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Affiliation(s)
- Guy Patchornik
- Affisink Biotechnology Ltd, 11 Hamaccabee St. Kiryat-Ono 55572, Israel.
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45
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Kumar A, Galaev IY, Mattiasson B. Affinity precipitation of proteins using metal chelates. Methods Mol Biol 2008; 421:37-52. [PMID: 18826046 DOI: 10.1007/978-1-59745-582-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Metal affinity precipitation has been successfully developed as a simple purification process for the proteins that have affinity for the metal ions. The copolymers of vinylimidazole with N-isopropylacrylamide are easily synthesized by radical polymerization. When loaded with Cu(II) and Ni(II) ions, these copolymers are capable of selectively precipitating proteins with natural metal-binding groups or histidine-tagged recombinant proteins.
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Affiliation(s)
- Ashok Kumar
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, India
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46
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Parsy CB, Chapman CJ, Barnes AC, Robertson JF, Murray A. Two-step method to isolate target recombinant protein from co-purified bacterial contaminant SlyD after immobilised metal affinity chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 853:314-9. [PMID: 17459787 DOI: 10.1016/j.jchromb.2007.03.046] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 03/15/2007] [Accepted: 03/25/2007] [Indexed: 11/17/2022]
Abstract
As part of a study to purify the internal domain of HER2 (ICD) from recombinant expression, through metal immobilised affinity chromatography (IMAC), we encountered a contaminant, SlyD, a 29 kDa native E. coli protein. SlyD is a recurrent contaminant, with a histidine rich domain enabling binding to IMAC columns and thus co-elution with the target protein. Research has been carried out on this protein and its purification, however, no work mentions how to treat it as a true contaminant or describe procedures to isolate it from target proteins. In this report, we described a two-step chromatographic method for the purification of ICD, including IMAC as a capture step and size exclusion chromatography (SEC) as a polishing step. IMAC allowed us to purify ICD from bacterial crude with SlyD co-eluting. SEC then allowed us to resolve ICD from SlyD and achieve a purity greater than 95% for ICD. However, this method has been developed to accommodate any protein whose molecular weight is different enough from SlyD to be separated by SEC.
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Affiliation(s)
- Céline B Parsy
- OncImmune Limited, Clinical Sciences Building, Nottingham City Hospital, Hucknall Road, and Tumor Immunology Group, University of Nottingham NG5 1PB, UK.
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Liao Y, Cheng Y, Li Q. Preparation of nitrilotriacetic acid/Co2+-linked, silica/boron-coated magnetite nanoparticles for purification of 6×histidine-tagged proteins. J Chromatogr A 2007; 1143:65-71. [PMID: 17204270 DOI: 10.1016/j.chroma.2006.12.063] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 12/08/2006] [Accepted: 12/15/2006] [Indexed: 11/22/2022]
Abstract
In this report, we describe the preparation of novel nitrilotriacetic acid/Co2+-linked, silica/boron-coated magnetite nanoparticles for purification of 6 x His-tagged proteins. The nanoparticles were approximately 200 nm in size and were stable against hydrochloric acid and had negligible non-specific binding for protein. Elimination of non-specific binding by nucleic acids was readily achieved by digestion of samples with DNase and RNase. The modified nanoparticles were used to purify two model proteins: one had a C-terminal 6 x His tag, and the other had an internal 6 x His tag. Both proteins were purified within one hour into single band purity on sodium dodecyl sulfate-polyacrylamide electrophoresis gel.
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Affiliation(s)
- Yiqun Liao
- Molecular Diagnostics Laboratory, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, China
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Mattiasson B, Kumar A, Ivanov AE, Galaev IY. Metal-chelate affinity precipitation of proteins using responsive polymers. Nat Protoc 2007; 2:213-20. [PMID: 17401356 DOI: 10.1038/nprot.2006.440] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Affinity precipitation of proteins uses polymers capable of reversible soluble-insoluble transitions in response to small environmental changes (temperature, pH or solvent composition). Here we describe protocols for (i) the synthesis of responsive polymers with specific affinity to target proteins and (ii) the purification of proteins using these polymers. The purification is based on precipitation of the affinity complex between the protein and the polymer, which is induced by environmental changes. This separation strategy is simpler and more cost effective than conventional affinity column chromatography. Specifically, we describe the synthesis of thermoresponsive 1-vinylimidazole:N-isopropylacrylamide copolymers. The whole procedure takes 2-3 h when applied to purification of recombinant His-tag proteins or proteins with natural metal binding groups by means of metal chelate affinity precipitation. Optimization of the polymer composition and the type of chelating ions allows for target protein yields of 80% and higher.
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Affiliation(s)
- Bo Mattiasson
- Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, SE-22100 Lund, Sweden.
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Tachibana S, Suzuki M, Asano Y. Application of an enzyme chip to the microquantification of l-phenylalanine. Anal Biochem 2006; 359:72-8. [PMID: 17046706 DOI: 10.1016/j.ab.2006.09.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 09/04/2006] [Accepted: 09/06/2006] [Indexed: 02/02/2023]
Abstract
We describe here a new microquantification method of l-phenylalanine concentration in an extract from a dried blood spot by using the diaphorase-resazurin system. To miniaturize the fluorometric enzymatic microplate assay for the diagnosis of phenylketonuria, an enzyme chip immobilized with His-tag fused phenylalanine dehydrogenase (PheDH) was developed. His-tag fused PheDH was immobilized on the surface of nickel-coated slide glass. A microarray sheet (8 x 30 well) was fabricated with poly(dimethylsiloxane) (PDMS) using the photolithographic technique. An enzyme reaction chamber in a double-layered structure was constructed with different types of microarray PDMS sheets on the surface of Ni-coated slide glass immobilized with His-tagged PheDH. To evaluate the affinity toward the Ni-chelating ligand, eight kinds of His-tagged PheDH variants were constructed and expressed. (His)(6)- and (His)(9)-PheDH variants at the N terminus showed high adsorption ratio to Ni-chelating ligand. The V(max) and k(cat) values of the (His)(6)-PheDH variant at the N terminus for l-phenylalanine were higher than those of the (His)(9)-PheDH variant, and the (His)(6)-PheDH variant was found to be most suitable for immobilization onto nickel-coated slide glass. Fluorescence formed by resazurin-coupled enzymatic reaction (in a 0.2-microl reaction mixture) on the enzyme chip exhibited good linearity and a correlation coefficient up to 12.8 mg/dl of the l-phenylalanine-containing sample extracted from a dried blood spot on filter paper.
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Affiliation(s)
- Shinjiro Tachibana
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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Kurz M, Cowieson NP, Robin G, Hume DA, Martin JL, Kobe B, Listwan P. Incorporating a TEV cleavage site reduces the solubility of nine recombinant mouse proteins. Protein Expr Purif 2006; 50:68-73. [PMID: 16798010 DOI: 10.1016/j.pep.2006.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 05/12/2006] [Accepted: 05/14/2006] [Indexed: 11/22/2022]
Abstract
Failure to express soluble proteins in bacteria is mainly attributed to the properties of the target protein itself, as well as the choice of the vector, the purification tag and the linker between the tag and protein, and codon usage. The expression of proteins with fusion tags to facilitate subsequent purification steps is a widely used procedure in the production of recombinant proteins. However, the additional residues can affect the properties of the protein; therefore, it is often desirable to remove the tag after purification. This is usually done by engineering a cleavage site between the tag and the encoded protein that is recognised by a site-specific protease, such as the one from tobacco etch virus (TEV). In this study, we investigated the effect of four different tags on the bacterial expression and solubility of nine mouse proteins. Two of the four engineered constructs contained hexahistidine tags with either a long or short linker. The other two constructs contained a TEV cleavage site engineered into the linker region. Our data show that inclusion of the TEV recognition site directly downstream of the recombination site of the Invitrogen Gateway vector resulted in a loss of solubility of the nine mouse proteins. Our work suggests that one needs to be very careful when making modifications to expression vectors and combining different affinity and fusion tags and cleavage sites.
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Affiliation(s)
- Mareike Kurz
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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