1
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Zhu H, Zheng X, Ou Y, Wang G, Qu L, Li Q, Zhao X, Zhao X. A universal method for surface-based binding assays by preparing immobilized β 2-adrenergic receptor stationary phase using solid binding peptide as a fusion tag. J Chromatogr A 2024; 1730:465037. [PMID: 38889580 DOI: 10.1016/j.chroma.2024.465037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
Protein functionalized surface has the potential to develop new assays for determining the drug-like properties of potential compounds and discovering specific partners of G protein-coupled receptors (GPCRs). However, a universal method for purifying and immobilizing functional GPCRs has remained elusive. To this end, we developed a general and rapid way to purify and immobilize β2-adrenergic receptor (β2AR) by silicon-specific peptide. We screened CotB1p as a tag from six silica-binding peptides (minTBP-1, CotB1p, SB7, Car9, and Si4-1) by examining their affinity to macroporous silica gel. We investigated the adsorption and desorption of CotB1p-tagged β2-adrenoceptor (β2AR-CotB1p) under diverse conditions to propose a protocol for receptor purification and immobilization. Under optimized conditions, β2AR immobilization were achieved by directly immersing cell lysates harboring the receptor with silica gel, and the elution of the receptor without demonstratable contaminants was realized by including l-arginine/L-lysine in the elutes. This allows purification of the receptor from Escherichia coli (E.coli) lysates with a purity of 95 %. The immobilized receptor was utilized as a stationary phase to reveal the tag impact on ligand-binding outputs by comparing the CotB1p-strategy with a typical covalent method. The KAs of salbutamol, chlorprenaline, tulobuterol, and terbutaline on β2AR-CotB1p column were 1.26 × 106, 6.59 × 106, 7.90 × 106, and 8.97 × 105 M-1 respectively, which were two orders of magnitude higher than those on the Halo-β2AR column. The whole immobilization was accomplished within 30 min without the requirement of any special treatment, resulting in enhanced accuracy for determining receptor-ligand binding parameters. Taken together, CotB1p-mediated strategy is simple, rapid, and universal for purification or immobilization of unstable biomolecules like GPCRs for analytical and biological applications.
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Affiliation(s)
- Huiting Zhu
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xinxin Zheng
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yuanyuan Ou
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Ge Wang
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Lejing Qu
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Qian Li
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xue Zhao
- College of Life Sciences, Northwest University, Xi'an, 710069, China.
| | - Xinfeng Zhao
- College of Life Sciences, Northwest University, Xi'an, 710069, China.
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2
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Ikeda T, Nakasugi Y, Nakagawa M, Matsuura SI, Ikeda T, Ishida T, Funabashi H, Hirota R, Kuroda A. Discovery of long-chain polyamines embedded in the biosilica on the Bacillus cereus spore coat. J Biosci Bioeng 2024; 137:254-259. [PMID: 38342665 DOI: 10.1016/j.jbiosc.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/13/2024]
Abstract
Biosilicification is the process by which organisms incorporate soluble, monomeric silicic acid, Si(OH)4, in the form of polymerized insoluble silica, SiO2. Although the mechanisms underlying eukaryotic biosilicification have been intensively investigated, prokaryotic biosilicification has only recently begun to be studied. We previously reported that biosilicification occurs in the gram-positive, spore-forming bacterium Bacillus cereus, and that silica is intracellularly deposited on the spore coat as a protective coating against acids, although the underlying mechanism is not yet fully understood. In eukaryotic biosilicifying organisms, such as diatoms and siliceous sponges, several relevant biomolecules are embedded in biogenic silica (biosilica). These biomolecules include peptides, proteins, and long-chain polyamines. In this study, we isolated organic compounds embedded in B. cereus biosilica to investigate the biomolecules involved in the prokaryotic biosilicification process and identified long-chain polyamines with a chemical structure of H2N-(CH2)4-[NH-(CH2)3]n-NH2 (n: up to 55). Our results demonstrate the common presence of long-chain polyamines in different evolutionary lineages of biosilicifying organisms, i.e., diatoms, siliceous sponges, and B. cereus, suggesting a common mechanism underlying eukaryotic and prokaryotic biosilicification.
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Affiliation(s)
- Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.
| | - Yukihide Nakasugi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Miki Nakagawa
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Shun-Ichi Matsuura
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Takuji Ikeda
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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3
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Collings K, Boisdon C, Sham TT, Skinley K, Oh HK, Prince T, Ahmed A, Pennington SH, Brownridge PJ, Edwards T, Biagini GA, Eyers CE, Lamb A, Myers P, Maher S. Attaching protein-adsorbing silica particles to the surface of cotton substrates for bioaerosol capture including SARS-CoV-2. Nat Commun 2023; 14:5033. [PMID: 37596260 PMCID: PMC10439164 DOI: 10.1038/s41467-023-40696-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/07/2023] [Indexed: 08/20/2023] Open
Abstract
The novel coronavirus pandemic (COVID-19) has necessitated a global increase in the use of face masks to limit the airborne spread of the virus. The global demand for personal protective equipment has at times led to shortages of face masks for the public, therefore makeshift masks have become commonplace. The severe acute respiratory syndrome caused by coronavirus-2 (SARS-CoV-2) has a spherical particle size of ~97 nm. However, the airborne transmission of this virus requires the expulsion of droplets, typically ~0.6-500 µm in diameter (by coughing, sneezing, breathing, and talking). In this paper, we propose a face covering that has been designed to effectively capture SARS-CoV-2 whilst providing uncompromised comfort and breathability for the wearer. Herein, we describe a material approach that uses amorphous silica microspheres attached to cotton fibres to capture bioaerosols, including SARS CoV-2. This has been demonstrated for the capture of aerosolised proteins (cytochrome c, myoglobin, ubiquitin, bovine serum albumin) and aerosolised inactivated SARS CoV-2, showing average filtration efficiencies of ~93% with minimal impact on breathability.
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Affiliation(s)
- Kieran Collings
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, UK
| | - Cedric Boisdon
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, UK
| | - Tung-Ting Sham
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, UK
| | - Kevin Skinley
- Department of Chemistry, University of Liverpool, Liverpool, UK
| | - Hyun-Kyung Oh
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, UK
| | - Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Adham Ahmed
- Department of Chemistry, University of Liverpool, Liverpool, UK
| | - Shaun H Pennington
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Philip J Brownridge
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Thomas Edwards
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Giancarlo A Biagini
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Amanda Lamb
- Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Applied Health Insights Ltd, Cheshire, UK
| | - Peter Myers
- Department of Chemistry, University of Liverpool, Liverpool, UK.
| | - Simon Maher
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, UK.
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4
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Rocha RA, Esquirol L, Rolland V, Hands P, Speight RE, Scott C. Non-covalent binding tags for batch and flow biocatalysis. Enzyme Microb Technol 2023; 169:110268. [PMID: 37300919 DOI: 10.1016/j.enzmictec.2023.110268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
Enzyme immobilization offers considerable advantage for biocatalysis in batch and continuous flow reactions. However, many currently available immobilization methods require that the surface of the carrier is chemically modified to allow site specific interactions with their cognate enzymes, which requires specific processing steps and incurs associated costs. Two carriers (cellulose and silica) were investigated here, initially using fluorescent proteins as models to study binding, followed by assessment of industrially relevant enzyme performance (transaminases and an imine reductase/glucose oxidoreductase fusion). Two previously described binding tags, the 17 amino acid long silica-binding peptide from the Bacillus cereus CotB protein and the cellulose binding domain from the Clostridium thermocellum, were fused to a range of proteins without impairing their heterologous expression. When fused to a fluorescent protein both tags conferred high avidity specific binding with their respective carriers (low nanomolar Kd values). The CotB peptide (CotB1p) induced protein aggregation in the transaminase and imine reductase/glucose oxidoreductase fusions when incubated with the silica carrier. The Clostridium thermocellum cellulose binding domain (CBDclos) allowed immobilization of all the proteins tested, but immobilization led to loss of enzymatic activity in the transaminases (< 2-fold) and imine reductase/glucose oxidoreductase fusion (> 80%). A transaminase-CBDclos fusion was then successfully used to demonstrate the application of the binding tag in repetitive batch and a continuous-flow reactor.
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Affiliation(s)
- Raquel A Rocha
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology (QUT), Brisbane, Qld 4000, Australia; CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Lygie Esquirol
- CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Vivien Rolland
- CSIRO Agriculture and Food, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Philip Hands
- CSIRO Agriculture and Food, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Robert E Speight
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology (QUT), Brisbane, Qld 4000, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, Qld 4000, Australia
| | - Colin Scott
- CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia.
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Abdelhamid MAA, Son RG, Park KS, Pack SP. Oriented multivalent silaffin-affinity immobilization of recombinant lipase on diatom surface: Reliable loading and high performance of biocatalyst. Colloids Surf B Biointerfaces 2022; 219:112830. [PMID: 36162181 DOI: 10.1016/j.colsurfb.2022.112830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 10/31/2022]
Abstract
Microbial lipases are widely used biocatalysts; however, their functional surface immobilization should be designed for successful industrial applications. One of the unmet challenges is to develop a practical surface immobilization to achieve both high stability and activity of lipases upon the large loading. Herein, we present a silaffin-based multivalent design as a simple and oriented approach for Bacillus subtilis lipase A (LipA) immobilization on economic diatom biosilica matrix to yield highly-stable activity with reliable loading. Specifically, silaffin peptides Sil3H, Sil3K, and Sil3R, as monovalent or divalent genetic fusion tags, selectively immobilized LipA on biosilica surfaces. Sil3K peptide fusion to LipA termini most efficiently produced high catalytic activity upon immobilization. The activity was 70-fold greater than that of immobilized wild-type LipA. Compared to single fusion, the double Sil3K fusion displayed 1.7 higher enzymatic loading combined with high catalytic performances of LipA on biosilica surfaces. The multivalent immobilized LipA was distributed uniformly on biosilica surfaces. The biocatalyst was stable over a wide pH range with 98% retention activity after 10 reuses. The stabilized lipase fusion was compatible with laundry detergents, making it an attractive biocatalyst for detergent formulations. These findings demonstrate that multivalent surface immobilization is a plausible method for developing high-performance biocatalysts suitable for industrial biotechnological applications.
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Affiliation(s)
- Mohamed A A Abdelhamid
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea; Department of Botany and Microbiology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Ryeo Gang Son
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea
| | - Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea.
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6
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Lee JHZ, Podgorski MN, Moir M, Gee AR, Bell SG. Selective Oxidations Using a Cytochrome P450 Enzyme Variant Driven with Surrogate Oxygen Donors and Light. Chemistry 2022; 28:e202201366. [PMID: 35712785 PMCID: PMC9541349 DOI: 10.1002/chem.202201366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Joel H. Z. Lee
- Department of Chemistry University of Adelaide Adelaide SA 5005 Australia
| | | | - Michael Moir
- National Deuteration Facility Australian Nuclear Science and Technology Organisation (ANSTO) Lucas Heights Sydney NSW 2232 Australia
| | - Alecia R. Gee
- Department of Chemistry University of Adelaide Adelaide SA 5005 Australia
| | - Stephen G. Bell
- Department of Chemistry University of Adelaide Adelaide SA 5005 Australia
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7
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Suyetin M, Rauwolf S, Schwaminger SP, Turrina C, Wittmann L, Bag S, Berensmeier S, Wenzel W. Peptide adsorption on silica surfaces: Simulation and experimental insights. Colloids Surf B Biointerfaces 2022; 218:112759. [PMID: 36027680 DOI: 10.1016/j.colsurfb.2022.112759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022]
Abstract
The understanding of interactions between proteins with silica surface is crucial for a wide range of different applications: from medical devices, drug delivery and bioelectronics to biotechnology and downstream processing. We show the application of EISM (Effective Implicit Surface Model) for discovering the set of peptide interactions with silica surface. The EISM is employed for a high-speed computational screening of peptides to model the binding affinity of small peptides to silica surfaces. The simulations are complemented with experimental data of peptides with silica nanoparticles from microscale thermophoresis and from infrared spectroscopy. The experimental work shows excellent agreement with computational results and verifies the EISM model for the prediction of peptide-surface interactions. 57 peptides, with amino acids favorable for adsorption on Silica surface, are screened by EISM model for obtaining results, which are worth to be considered as a guidance for future experimental and theoretical works. This model can be used as a broad platform for multiple challenges at surfaces which can be applied for multiple surfaces and biomolecules beyond silica and peptides.
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Affiliation(s)
- Mikhail Suyetin
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Rauwolf
- Bioseparation Engineering Group, School of Engineering and Design, Technical University of Munich, 85748, Garching, Germany
| | - Sebastian Patrick Schwaminger
- Bioseparation Engineering Group, School of Engineering and Design, Technical University of Munich, 85748, Garching, Germany; Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, 8010, Graz, Austria.
| | - Chiara Turrina
- Bioseparation Engineering Group, School of Engineering and Design, Technical University of Munich, 85748, Garching, Germany
| | - Leonie Wittmann
- Bioseparation Engineering Group, School of Engineering and Design, Technical University of Munich, 85748, Garching, Germany
| | - Saientan Bag
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sonja Berensmeier
- Bioseparation Engineering Group, School of Engineering and Design, Technical University of Munich, 85748, Garching, Germany.
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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8
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Freitas AI, Domingues L, Aguiar TQ. Bare silica as an alternative matrix for affinity purification/immobilization of His-tagged proteins. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.120448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Strategies for Enzymatic Inactivation of the Veterinary Antibiotic Florfenicol. Antibiotics (Basel) 2022; 11:antibiotics11040443. [PMID: 35453195 PMCID: PMC9029715 DOI: 10.3390/antibiotics11040443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
Large quantities of the antibiotic florfenicol are used in animal farming and aquaculture, contaminating the ecosystem with antibiotic residues and promoting antimicrobial resistance, ultimately leading to untreatable multidrug-resistant pathogens. Florfenicol-resistant bacteria often activate export mechanisms that result in resistance to various structurally unrelated antibiotics. We devised novel strategies for the enzymatic inactivation of florfenicol in different media, such as saltwater or milk. Using a combinatorial approach and selection, we optimized a hydrolase (EstDL136) for florfenicol cleavage. Reaction kinetics were followed by time-resolved NMR spectroscopy. Importantly, the hydrolase remained active in different media, such as saltwater or cow milk. Various environmentally-friendly application strategies for florfenicol inactivation were developed using the optimized hydrolase. As a potential filter device for cost-effective treatment of waste milk or aquacultural wastewater, the hydrolase was immobilized on Ni-NTA agarose or silica as carrier materials. In two further application examples, the hydrolase was used as cell extract or encapsulated with a semi-permeable membrane. This facilitated, for example, florfenicol inactivation in whole milk, which can help to treat waste milk from medicated cows, to be fed to calves without the risk of inducing antibiotic resistance. Enzymatic inactivation of antibiotics, in general, enables therapeutic intervention without promoting antibiotic resistance.
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10
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Liu C, Steer DL, Song H, He L. Superior Binding of Proteins on a Silica Surface: Physical Insight into the Synergetic Contribution of Polyhistidine and a Silica-Binding Peptide. J Phys Chem Lett 2022; 13:1609-1616. [PMID: 35142521 DOI: 10.1021/acs.jpclett.1c03306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Controllable protein attachment onto solid interfaces is essential for the functionality of proteins with broad applications. Silica-binding peptides (SBPs) have emerged as an important tool enabling convenient binding of proteins onto a silica surface. Surprisingly, we found that removal of polyhistidines, a common tag for protein purification, dramatically decrease the binding affinity of a SBP-tagged nanobody onto a silica surface. We hypothesized that polyhistidines and SBPs can be combined to enhance affinity. Through a series of purposely designed SBPs, we identified that the relative orientation of amino acids is a key factor affecting the surface binding strength. One re-engineered SBP, SBP4, exhibits a 4000-fold improvement compared to the original sequence. Guided by physical insights, the work provides a simple strategy that can dramatically improve affinity between a SBP and a silica surface, promising a new way for controllable immobilization of proteins, as demonstrated using nanobodies.
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Affiliation(s)
- Chang Liu
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - David L Steer
- Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Haipeng Song
- Shenzhen Innova Nanobodi Company, 1301 Sightseeing Road, Shengzhen, Guangdong 518000, People's Republic of China
| | - Lizhong He
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
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11
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Liu S, Wang Z, Chen K, Yu L, Shi Q, Dong X, Sun Y. Cascade chiral amine synthesis catalyzed by site-specifically co-immobilized alcohol and amine dehydrogenases. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00514j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sustainable and efficient production of chiral amines was realized with an oriented co-immobilized dual-enzyme system via SiBP-tag.
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Affiliation(s)
- Si Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Zhenfu Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Kun Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Linling Yu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Qinghong Shi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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12
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Kang SY, Pokhrel A, Bratsch S, Benson JJ, Seo SO, Quin MB, Aksan A, Schmidt-Dannert C. Engineering Bacillus subtilis for the formation of a durable living biocomposite material. Nat Commun 2021; 12:7133. [PMID: 34880257 PMCID: PMC8654922 DOI: 10.1038/s41467-021-27467-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/17/2021] [Indexed: 01/23/2023] Open
Abstract
Engineered living materials (ELMs) are a fast-growing area of research that combine approaches in synthetic biology and material science. Here, we engineer B. subtilis to become a living component of a silica material composed of self-assembling protein scaffolds for functionalization and cross-linking of cells. B. subtilis is engineered to display SpyTags on polar flagella for cell attachment to SpyCatcher modified secreted scaffolds. We engineer endospore limited B. subtilis cells to become a structural component of the material with spores for long-term storage of genetic programming. Silica biomineralization peptides are screened and scaffolds designed for silica polymerization to fabricate biocomposite materials with enhanced mechanical properties. We show that the resulting ELM can be regenerated from a piece of cell containing silica material and that new functions can be incorporated by co-cultivation of engineered B. subtilis strains. We believe that this work will serve as a framework for the future design of resilient ELMs.
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Affiliation(s)
- Sun-Young Kang
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Anaya Pokhrel
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Sara Bratsch
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Joey J. Benson
- grid.17635.360000000419368657Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Seung-Oh Seo
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Maureen B. Quin
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Alptekin Aksan
- grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA ,grid.17635.360000000419368657Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN, 55455, USA. .,BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA.
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13
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Rauwolf S, Steegmüller T, Schwaminger SP, Berensmeier S. Purification of a peptide tagged protein via an affinity chromatographic process with underivatized silica. Eng Life Sci 2021; 21:549-557. [PMID: 34690628 PMCID: PMC8518568 DOI: 10.1002/elsc.202100019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/06/2021] [Accepted: 05/25/2021] [Indexed: 11/11/2022] Open
Abstract
Silica is widely used for chromatography resins due to its high mechanical strength, column efficiency, easy manufacturing (i.e. controlled size and porosity), and low-cost. Despite these positive attributes to silica, it is currently used as a backbone for chromatographic resins in biotechnological downstream processing. The aim of this study is to show how the octapeptide (RH)4 can be used as peptide tag for high-purity protein purification on bare silica. The tag possesses a high affinity to deprotonated silanol groups because the tag's arginine groups interact with the surface via an ion pairing mechanism. A chromatographic workflow to purify GFP fused with (RH)4 could be implemented. Purities were determined by SDS-PAGE and RP-HPLC. The equilibrium binding capacity of the fusion protein GFP-(RH)4 on silica is 450 mg/g and the dynamic binding capacity around 3 mg/mL. One-step purification from clarified lysate achieved a purity of 93% and a recovery of 94%. Overloading the column enhances the purity to >95%. Static experiments with different buffers showed variability of the method making the system independent from buffer choice. Our designed peptide tag allows bare silica to be utilized in preparative chromatography for downstream bioprocessing; thus, providing a cost saving factor regarding expensive surface functionalization. Underivatized silica in combination with our (RH)4 peptide tag allows the purification of proteins, in all scales, without relying on complex resins.
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Affiliation(s)
- Stefan Rauwolf
- Department of Mechanical EngineeringTechnical University of MunichMunichGermany
| | - Tobias Steegmüller
- Department of Mechanical EngineeringTechnical University of MunichMunichGermany
| | | | - Sonja Berensmeier
- Department of Mechanical EngineeringTechnical University of MunichMunichGermany
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14
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Ikeda T. Bacterial biosilicification: a new insight into the global silicon cycle. Biosci Biotechnol Biochem 2021; 85:1324-1331. [PMID: 33877302 DOI: 10.1093/bbb/zbab069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/08/2021] [Indexed: 11/13/2022]
Abstract
Biosilicification is the process by which organisms incorporate soluble, monomeric silicic acid, Si(OH)4, in the form of polymerized insoluble silica, SiO2. Biosilicifying eukaryotes, including diatoms, siliceous sponges, and higher plants, have been the targets of intense research to study the molecular mechanisms underlying biosilicification. By contrast, prokaryotic biosilicification has been less well studied, partly because the biosilicifying capability of well-known bacteria was not recognized until recently. This review summarizes recent findings on bacterial extracellular and intracellular biosilicification, the latter of which has been demonstrated only recently in bacteria. The topics discussed herein include bacterial (and archaeal) extracellular biosilicification in geothermal environments, encapsulation of Bacillus spores within a silica layer, and silicon accumulation in marine cyanobacteria. The possible contribution of bacterial biosilicification to the global silicon cycle is also discussed.
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Affiliation(s)
- Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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15
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Kim YS, Lee HJ, Park SH, Kim YC, Ahn J. Expression and purification of soluble and active human enterokinase light chain in Escherichia coli. ACTA ACUST UNITED AC 2021; 30:e00626. [PMID: 34026576 PMCID: PMC8134707 DOI: 10.1016/j.btre.2021.e00626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 11/30/2022]
Abstract
Recombinant production of soluble, active enterokinase (EK) is challenging. Maltose binding protein-fusion improves EK solubility but reduces activity. GroEL/ES and Erv2/PDI induces correct refolding and improves EK activity. Replacing free cysteine with serine dramatically improves EK activity.
Human enterokinase light chain (hEKL) specifically cleaves the sequence (Asp)4-Lys↓X (D4K), making this a frequently used enzyme for site-specific cleavage of recombinant fusion proteins. However, hEKL production from Escherichia coli is limited due to intramolecular disulphide bonds. Here, we present strategies to obtain soluble and active hEKL from E. coli by expressing the hEKL variant C112S fused with maltose-binding protein (MBP) through D4K and molecular chaperons including GroEL/ES. The fusion protein self-cleaved in vivo, thereby removing the MBP in the E. coli cells. Thus, the self-cleaved hEKL variant was released into the culture medium. One-step purification using HisTrap™ chromatography purified the hEKL variant exhibiting an enzymatic activity of 3.1 × 103 U/mL (9.934 × 105 U/mg). The approaches presented here greatly simplify the purification of hEKL from E. coli without requiring refolding processes.
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Affiliation(s)
- Young Su Kim
- Department of Chemical and Biomolecular Engineering, KAIST, Daejeon 34141, Republic of Korea.,Biotechnology Process Engineering Center, KRIBB, Cheongju 28116, Republic of Korea
| | - Hye-Jeong Lee
- Biotechnology Process Engineering Center, KRIBB, Cheongju 28116, Republic of Korea
| | - Sang-Hyun Park
- Biotechnology Process Engineering Center, KRIBB, Cheongju 28116, Republic of Korea.,Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Yeu-Chun Kim
- Department of Chemical and Biomolecular Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, KRIBB, Cheongju 28116, Republic of Korea.,Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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16
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Abdelhamid MAA, Pack SP. Biomimetic and bioinspired silicifications: Recent advances for biomaterial design and applications. Acta Biomater 2021; 120:38-56. [PMID: 32447061 DOI: 10.1016/j.actbio.2020.05.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022]
Abstract
The rational design and controllable synthesis of functional silica-based materials have gained increased interest in a variety of biomedical and biotechnological applications due to their unique properties. The current review shows that marine organisms, such as siliceous sponges and diatoms, could be the inspiration for the fabrication of advanced biohybrid materials. Several biomolecules were involved in the molecular mechanism of biosilicification in vivo. Mimicking their behavior, functional silica-based biomaterials have been generated via biomimetic and bioinspired silicification in vitro. Additionally, several advanced technologies were developed for in vitro and in vivo immobilization of biomolecules with potential applications in biocatalysis, biosensors, bioimaging, and immunoassays. A thin silica layer could coat a single living cell or virus as a protective shell offering new opportunities in biotechnology and nanomedicine fields. Promising nanotechnologies have been developed for drug encapsulation and delivery in a targeted and controlled manner, in particular for poorly soluble hydrophobic drugs. Moreover, biomimetic silica, as a morphogenetically active biocompatible material, has been utilized in the field of bone regeneration and in the development of biomedical implantable devices. STATEMENT OF SIGNIFICANCE: In nature, silica-based biomaterials, such as diatom frustules and sponge spicules, with high mechanical and physical properties were created under biocompatible conditions. The fundamental knowledge underlying the molecular mechanisms of biosilica formation could inspire engineers and chemists to design novel hybrid biomaterials using molecular biomimetic strategies. The production of such biohybrid materials brings the biosilicification field closer to practical applications. This review starts with the biosilicification process of sponges and diatoms with recently updated researches. Then, this article covers recent advances in the design of silica-based biomaterials and their potential applications in the fields of biotechnology and nanomedicine, highlighting several promising technologies for encapsulation of functional proteins and living cells, drug delivery and the preparation of scaffolds for bone regeneration.
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Affiliation(s)
- Mohamed A A Abdelhamid
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea; Department of Botany and Microbiology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong 30019, Republic of Korea.
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17
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Zhang X, Chen J, Li E, Hu C, Luo SZ, He C. Ultrahigh Adhesion Force Between Silica-Binding Peptide SB7 and Glass Substrate Studied by Single-Molecule Force Spectroscopy and Molecular Dynamic Simulation. Front Chem 2020; 8:600918. [PMID: 33330393 PMCID: PMC7729015 DOI: 10.3389/fchem.2020.600918] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022] Open
Abstract
Many proteins and peptides have been identified to effectively and specifically bind on certain surfaces such as silica, polystyrene and titanium dioxide. It is of great interest, in many areas such as enzyme immobilization, surface functionalization and nanotechnology, to understand how these proteins/peptides bind to solid surfaces. Here we use single-molecule force spectroscopy (SMFS) based on atomic force microscopy to directly measure the adhesion force between a silica-binding peptide SB7 and glass surface at single molecule level. SMFS results show that the adhesion force of a single SB7 detaching from the glass surface distributes in two populations at ~220 pN and 610 pN, which is higher than the unfolding forces of most mechanically stable proteins and the unbinding forces of most stable protein-protein interactions. Molecular dynamics simulation reveals that the electrostatic interactions between positively charged arginine residues and the silica surface dominates the binding of SB7 on silica. Our study provides experimental evidence and molecular mechanism at the single-molecule level for the SB7-based immobilization of proteins on silica-based surface, which is able to withstand high mechanical forces, making it an ideal fusion tag for silica surface immobilization or peptide-base adhesive materials.
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Affiliation(s)
- Xiaoxu Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijng, China
| | - Jialin Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Enci Li
- State Key Laboratory of Precision Measuring Technology and Instrument, Tianjin University, Tianjin, China
| | - Chunguang Hu
- State Key Laboratory of Precision Measuring Technology and Instrument, Tianjin University, Tianjin, China
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Chengzhi He
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijng, China
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18
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Nakano A, Hirata I, Pham BV, Shakya A, Tanimoto K, Kato K. Evaluation of a peptide motif designed for protein tethering to polymer surfaces. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2020; 32:76-92. [PMID: 32867596 DOI: 10.1080/09205063.2020.1816870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In search for peptide motifs that allow us to efficiently tether fusion proteins onto polymer surfaces, we designed a KLKLKLKLKL (KL5) decapeptide in which basic and hydrophobic amino acids were alternately linked. By means of genetic engineering technology together with a bacterial expression system, the KL5 fusions of epidermal growth factor (EGF), basic fibroblast growth factor, and stromal cell-derived factor-1α were prepared together with their control counterparts without KL5. The adsorption experiments were performed for these fusion proteins on the surface of polystyrene, hydrophilized polystyrene, and polycaprolactone by surface plasmon resonance analysis. To understand the results of the binding assays, the structure of the fusion proteins was predicted by ab initio computer simulation and analyzed empirically by circular dichroism spectroscopy. The result of structural analyses suggested that the KL5 peptide is exposed to the outside and has a negligible effect on the structure of the protein partners. However, it was found that the efficiency of KL5 as a peptide motif greatly depends on protein partners. Our results showed that KL5 exerts most effectively its function as a peptide motif when fused to acidic proteins such as EGF. Indeed, the number of living human mesenchymal stem cells determined after 7-day culture was larger on the polystyrene and polycaprolactone surfaces with EGF tethered through the KL5 peptide than control surfaces. According to the results obtained in this study, we conclude that KL5 is useful as a peptide motif for tethering a specific class of protein partners.
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Affiliation(s)
- Ayana Nakano
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Orthodontics and Craniofacial Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Isao Hirata
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Binh Vinh Pham
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Faculty of Odonto-Stomatology, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh, Vietnam
| | - Ajay Shakya
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Community Dentistry, Chitwan Medical College & Hospital, Tribhuvan University, Bharatpur, Nepal
| | - Kotaro Tanimoto
- Department of Orthodontics and Craniofacial Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Koichi Kato
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Nanomedicine Research Division, Research Institute for Nanodevice and Bio Systems, Hiroshima University, Higashi-Hiroshima, Japan
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19
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Abdelhamid MA, Meligy AM, Yeo KB, Lee CS, Pack SP. Silaffin-3-derived pentalysine cluster as a new fusion tag for one-step immobilization and purification of recombinant Bacillus subtilis catalase on bare silica particles. Int J Biol Macromol 2020; 159:1103-1112. [DOI: 10.1016/j.ijbiomac.2020.04.172] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/02/2020] [Accepted: 04/21/2020] [Indexed: 01/15/2023]
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20
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Xu M, Bailey MJ, Look J, Baneyx F. Affinity purification of Car9-tagged proteins on silica-derivatized spin columns and 96-well plates. Protein Expr Purif 2020; 170:105608. [PMID: 32062023 DOI: 10.1016/j.pep.2020.105608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 01/25/2023]
Abstract
The Car9 affinity tag is a dodecameric silica-binding peptide that can be fused to the N- and C-termini of proteins of interest to enable their rapid and inexpensive purification on underivatized silica in a process that typically relies on l-lysine as an eluent. Here, we show that silica paper spin columns and borosilicate multi-well plates used for plasmid DNA purification are suitable for recovering Car9-tagged proteins with high purity in a workflow compatible with high-throughput experiments. Spin columns typically yield 100 μg of biologically active material that can be recovered in minutes with low concentrations of lysine. Because of their short bed length, spin columns also offer unique advantages, as evidenced by the selective recovery of functional Car9-tagged tobacco etch virus (TEV) protease from a fused and auto-cleaved maltose binding protein (MBP) folding partner that nonspecifically binds to silica in the presence of NaCl. These additional purification modalities should increase the versatility and appeal of the Car9 tag for affinity protein purification.
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Affiliation(s)
- Meng Xu
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA; Department of Material Sciences and Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Matthew J Bailey
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | | | - François Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
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21
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Kim JK, Abdelhamid MA, Pack SP. Direct immobilization and recovery of recombinant proteins from cell lysates by using EctP1-peptide as a short fusion tag for silica and titania supports. Int J Biol Macromol 2019; 135:969-977. [DOI: 10.1016/j.ijbiomac.2019.05.105] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/16/2019] [Accepted: 05/18/2019] [Indexed: 10/26/2022]
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22
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Abdelhamid MAA, Yeo KB, Ki MR, Pack SP. Self-encapsulation and controlled release of recombinant proteins using novel silica-forming peptides as fusion linkers. Int J Biol Macromol 2018; 125:1175-1183. [PMID: 30576734 DOI: 10.1016/j.ijbiomac.2018.12.160] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 01/25/2023]
Abstract
Recently, the potential use of biomimetic silica as smart matrices for the auto-encapsulation and controlled release of functional proteins has gained increased interest because of the mild synthesis conditions. Inspired by biological silicification, in this study, we studied novel silica-forming peptides (SFPs), Volp1 and Salp1, to mediate the generation of silica hybrids in vitro. The fusion of SFPs to model fluorescent proteins directed their auto-encapsulation in wet sol-gel silica materials. Furthermore, the SFPs served as affinity linkers for the immobilization of recombinant proteins in silica. Interestingly, the SFP fusion proteins modulated silicic acid polycondensation and allowed for the self-immobilization of SFP fusion proteins in two distinct silica formulations depending on the ionic strength-precipitated silica particles or wet silica gel. The controlled release of Salp1/Volp1 fusion proteins from silica matrices was significantly greater than that of the silaffin R5 fusion proteins. Subsequently, we showed that multiple SFP-tagged proteins homogenously entrapped within a silica matrix could be separately released following pre-incubation with different concentrations of l-arginine solution. These new findings provide a simple and reproducible route for silica hybrid formation for in situ stable auto-encapsulation and the sustained release of recombinant proteins with potential applications in biotechnology.
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Affiliation(s)
- Mohamed A A Abdelhamid
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong, 30019, Republic of Korea; Department of Botany and Microbiology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Ki Baek Yeo
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong, 30019, Republic of Korea
| | - Mi-Ran Ki
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong, 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-Ro 2511, Sejong, 30019, Republic of Korea.
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23
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Limo MJ, Sola-Rabada A, Boix E, Thota V, Westcott ZC, Puddu V, Perry CC. Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications. Chem Rev 2018; 118:11118-11193. [PMID: 30362737 DOI: 10.1021/acs.chemrev.7b00660] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO2, SiO2, and GeO2 has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.
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Affiliation(s)
- Marion J Limo
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Interface and Surface Analysis Centre, School of Pharmacy , University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Anna Sola-Rabada
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Estefania Boix
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Department of Bioproducts and Biosystems , Aalto University , P.O. Box 16100, FI-00076 Aalto , Finland
| | - Veeranjaneyulu Thota
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Zayd C Westcott
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Valeria Puddu
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Carole C Perry
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
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24
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Olmez T, Yuca E, Eyupoglu E, Catalak HB, Sahin O, Seker UOS. Autonomous Synthesis of Fluorescent Silica Biodots Using Engineered Fusion Proteins. ACS OMEGA 2018; 3:585-594. [PMID: 30023783 PMCID: PMC6044564 DOI: 10.1021/acsomega.7b01769] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/03/2018] [Indexed: 06/08/2023]
Abstract
Formation of biological materials is a well-controlled process that is orchestrated by biomolecules such as proteins. Proteins can control the nucleation and mineralization of biomaterials, thereby forming the hard tissues of biological organisms, such as bones, teeth, and shells. In this study, the design and implementation of multifunctional designer proteins are demonstrated for fluorescent silica micro/nanoparticle synthesis. The R5 motif of silaffin polypeptide, which is known for its silicification capability, was fused genetically into three spectrally distinct fluorescent proteins with the intention of forming modified fluorescent proteins. The bifunctional R5 peptide domain served as a tag to provide silica synthesis at ambient conditions. Three functional fusion constructs have been prepared, including GFPmut3-R5, Venus YFP-R5, and mCherry-R5. Recombinant fluorescent proteins were purified using silica-binding peptide tag through silica gel resin. Purified proteins were tested for their binding affinity to silica using quartz crystal microbalance with dissipation monitoring to make sure they can interact strong enough with the silica surfaces. Later, engineered fluorescent proteins were used to synthesize silica nano/microparticles using silica precursor materials. Synthesized silica particles were investigated for their fluorescence properties, including time-resolved fluorescence. Additionally, elemental analysis of the particles was carried out using electron energy loss spectroscopy and energy-filtered transmission electron microscopy. Last, they were tested for their biocompatibility. In this study, we aimed to provide a biomimetic route to synthesize fluorescent silica nanoparticles. Recombinant fluorescent proteins-directed silica nanoparticles synthesis offers a one-step, reliable method to produce fluorescent particles both for biomaterial applications and other nanotechnology applications.
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Affiliation(s)
- Tolga
T. Olmez
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Esra Yuca
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
- Department
of Molecular Biology and Genetics, Faculty of Arts and Science, Yildiz Technical University, Istanbul 34210, Turkey
| | - Erol Eyupoglu
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Hazal B. Catalak
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Ozgur Sahin
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Urartu Ozgur Safak Seker
- UNAM-National
Nanotechnology Research Center,
Institute of Materials Science and Nanotechnology, and Department of
Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
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25
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Affinity purification of Car9-tagged proteins on silica matrices: Optimization of a rapid and inexpensive protein purification technology. Protein Expr Purif 2017; 135:70-77. [DOI: 10.1016/j.pep.2017.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022]
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26
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Klein G, Mathé C, Biola-Clier M, Devineau S, Drouineau E, Hatem E, Marichal L, Alonso B, Gaillard JC, Lagniel G, Armengaud J, Carrière M, Chédin S, Boulard Y, Pin S, Renault JP, Aude JC, Labarre J. RNA-binding proteins are a major target of silica nanoparticles in cell extracts. Nanotoxicology 2016; 10:1555-1564. [PMID: 27705051 DOI: 10.1080/17435390.2016.1244299] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Upon contact with biological fluids, nanoparticles (NPs) are readily coated by cellular compounds, particularly proteins, which are determining factors for the localization and toxicity of NPs in the organism. Here, we improved a methodological approach to identify proteins that adsorb on silica NPs with high affinity. Using large-scale proteomics and mixtures of soluble proteins prepared either from yeast cells or from alveolar human cells, we observed that proteins with large unstructured region(s) are more prone to bind on silica NPs. These disordered regions provide flexibility to proteins, a property that promotes their adsorption. The statistical analyses also pointed to a marked overrepresentation of RNA-binding proteins (RBPs) and of translation initiation factors among the adsorbed proteins. We propose that silica surfaces, which are mainly composed of Si-O- and Si-OH groups, mimic ribose-phosphate molecules (rich in -O- and -OH) and trap the proteins able to interact with ribose-phosphate containing molecules. Finally, using an in vitro assay, we showed that the sequestration of translation initiation factors by silica NPs results in an inhibition of the in vitro translational activity. This result demonstrates that characterizing the protein corona of various NPs would be a relevant approach to predict their potential toxicological effects.
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Affiliation(s)
- Géraldine Klein
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France.,b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Christelle Mathé
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France.,b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Mathilde Biola-Clier
- c Univ. Grenoble Alpes, CEA, INAC-SyMMES, Laboratoire Lésions des Acides Nucléiques , Grenoble , France , and
| | - Stéphanie Devineau
- b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Emilie Drouineau
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Elie Hatem
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Laurent Marichal
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France.,b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Béatrice Alonso
- d CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Laboratory 'Innovative technologies for Detection and Diagnostics', BP 17171 , Bagnols-sur-Cèze , France
| | - Jean-Charles Gaillard
- d CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Laboratory 'Innovative technologies for Detection and Diagnostics', BP 17171 , Bagnols-sur-Cèze , France
| | - Gilles Lagniel
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Jean Armengaud
- d CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Laboratory 'Innovative technologies for Detection and Diagnostics', BP 17171 , Bagnols-sur-Cèze , France
| | - Marie Carrière
- c Univ. Grenoble Alpes, CEA, INAC-SyMMES, Laboratoire Lésions des Acides Nucléiques , Grenoble , France , and
| | - Stéphane Chédin
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Yves Boulard
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Serge Pin
- b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Jean-Philippe Renault
- b LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay , Gif-sur-Yvette , France
| | - Jean-Christophe Aude
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
| | - Jean Labarre
- a I2BC, IBITEC-S, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay , Gif-sur-Yvette , France
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Luo D, Wen C, Zhao R, Liu X, Liu X, Cui J, Liang JG, Liang P. High Level Expression and Purification of Recombinant Proteins from Escherichia coli with AK-TAG. PLoS One 2016; 11:e0156106. [PMID: 27214237 PMCID: PMC4877045 DOI: 10.1371/journal.pone.0156106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/08/2016] [Indexed: 01/01/2023] Open
Abstract
Adenylate kinase (AK) from Escherichia coli was used as both solubility and affinity tag for recombinant protein production. When fused to the N-terminus of a target protein, an AK fusion protein could be expressed in soluble form and purified to near homogeneity in a single step from Blue-Sepherose via affinity elution with micromolar concentration of P1, P5- di (adenosine—5’) pentaphosphate (Ap5A), a transition-state substrate analog of AK. Unlike any other affinity tags, the level of a recombinant protein expression in soluble form and its yield of recovery during each purification step could be readily assessed by AK enzyme activity in near real time. Coupled to a His-Tag installed at the N-terminus and a thrombin cleavage site at the C terminus of AK, the streamlined method, here we dubbed AK-TAG, could also allow convenient expression and retrieval of a cleaved recombinant protein in high yield and purity via dual affinity purification steps. Thus AK-TAG is a new addition to the arsenal of existing affinity tags for recombinant protein expression and purification, and is particularly useful where soluble expression and high degree of purification are at stake.
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Affiliation(s)
- Dan Luo
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | - Caixia Wen
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | - Rongchuan Zhao
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | - Xinyu Liu
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | - Xinxin Liu
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | - Jingjing Cui
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
| | | | - Peng Liang
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Sichuan University, Chengdu, China
- Clover Biopharmaceuticals, Chengdu, China
- GenHunter Corporation, Grassmere Park, Nashville, United States of America
- * E-mail: ;
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28
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Kuroda A, Alexandrov M, Nishimura T, Ishida T. Rapid on-site detection of airborne asbestos fibers and potentially hazardous nanomaterials using fluorescence microscopy-based biosensing. Biotechnol J 2016; 11:757-67. [DOI: 10.1002/biot.201500438] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 05/06/2016] [Accepted: 05/10/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Akio Kuroda
- Department of Molecular Biotechnology; Hiroshima University; Higashi-Hiroshima, Hiroshima Japan
| | - Maxym Alexandrov
- Department of Molecular Biotechnology; Hiroshima University; Higashi-Hiroshima, Hiroshima Japan
| | - Tomoki Nishimura
- Department of Molecular Biotechnology; Hiroshima University; Higashi-Hiroshima, Hiroshima Japan
| | - Takenori Ishida
- Department of Molecular Biotechnology; Hiroshima University; Higashi-Hiroshima, Hiroshima Japan
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29
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Abdelhamid MAA, Ikeda T, Motomura K, Tanaka T, Ishida T, Hirota R, Kuroda A. Application of volcanic ash particles for protein affinity purification with a minimized silica-binding tag. J Biosci Bioeng 2016; 122:633-638. [PMID: 27212265 DOI: 10.1016/j.jbiosc.2016.04.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 10/21/2022]
Abstract
We recently reported that the spore coat protein, CotB1 (171 amino acids), from Bacillus cereus mediates silica biomineralization and that the polycationic C-terminal sequence of CotB1 (14 amino acids), designated CotB1p, serves as a silica-binding tag when fused to other proteins. Here, we reduced the length of this silica-binding tag to only seven amino acids (SB7 tag: RQSSRGR) while retaining its affinity for silica. Alanine scanning mutagenesis indicated that the three arginine residues in the SB7 tag play important roles in binding to a silica surface. Monomeric l-arginine, at concentrations of 0.3-0.5 M, was found to serve as a competitive eluent to release bound SB7-tagged proteins from silica surfaces. To develop a low-cost, silica-based affinity purification procedure, we used natural volcanic ash particles with a silica content of ∼70%, rather than pure synthetic silica particles, as an adsorbent for SB7-tagged proteins. Using green fluorescent protein, mCherry, and mKate2 as model proteins, our purification method achieved 75-90% recovery with ∼90% purity. These values are comparable to or even higher than that of the commonly used His-tag affinity purification. In addition to low cost, another advantage of our method is the use of l-arginine as the eluent because its protein-stabilizing effect would help minimize alteration of the intrinsic properties of the purified proteins. Our approach paves the way for the use of naturally occurring materials as adsorbents for simple, low-cost affinity purification.
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Affiliation(s)
- Mohamed A A Abdelhamid
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan; Department of Botany and Microbiology, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Takeshi Ikeda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.
| | - Kei Motomura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Tatsuya Tanaka
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takenori Ishida
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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