1
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Jennings MR, Min S, Xu GS, Homayuni K, Suresh B, Haikal YA, Blazeck J. Optimized expression and purification of a human adenosine deaminase in E. coli and characterization of its Asp8Asn variant. Protein Expr Purif 2024; 213:106362. [PMID: 37683902 PMCID: PMC10664833 DOI: 10.1016/j.pep.2023.106362] [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: 05/23/2023] [Revised: 08/22/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
Homo sapiens adenosine deaminase isoform 1 (HsADA1) hydrolyzes adenosine and 2-deoxyadenosine as a key step in the purine nucleoside salvage pathway. Some HsADA1 mutations have severe deleterious effects, as is the case in a severe combined immunodeficiency resulting from loss of enzyme activity (ADA-SCID). Other mutations that reduce enzyme activity, for instance the Asp8Asn (D8N) variant, do not cause ADA-SCID but are correlated with other consequences to health. To ease further study of HsADA1 and its variants, we optimized an inexpensive, recombinant expression process in an Escherichia coli host through multiplexed parameter testing enabled by a lysate-based microtiter plate assay. We demonstrate the importance of gene codon usage, induction time and temperature, and alcohol supplementation towards improving enzyme yield to a final titer of 5 mg per liter of culture. We further show that use of a double-histidine-tag (his-tag) system greatly improves purity. We then utilize our expression and purification framework to produce the HsADA1 D8N variant, which had previously not been purified to homogeneity. We confirm that the D8N variant is ∼30% less active than the wildtype HsADA1 and show that it better retains its activity in human serum. Additionally, we show that both HsADA1 and the D8N variant have heightened activity in serum, driven in part by a previously undescribed phenomenon involving albumin. Therefore, this work presents a valuable process to produce HsADA1 that allows for insights into it and its variants' behavior. We also confirm the utility of lysate-based activity assays towards finding optimal E. coli expression conditions for enzymes and show how fusing his-tags in tandem can enhance product purity.
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Affiliation(s)
- Maria Rain Jennings
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Soohyon Min
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Grace S Xu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Kassandra Homayuni
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Bhavana Suresh
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Yusef Amir Haikal
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - John Blazeck
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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2
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Soto ER, Specht CA, Lee CK, Levitz SM, Ostroff GR. One Step Purification-Vaccine Delivery System. Pharmaceutics 2023; 15:pharmaceutics15051390. [PMID: 37242632 DOI: 10.3390/pharmaceutics15051390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Glucan particles (GPs) are hollow, porous 3-5 µm microspheres derived from the cell walls of Baker's yeast (Saccharomyces cerevisiae). Their 1,3-β-glucan outer shell allows for receptor-mediated uptake by macrophages and other phagocytic innate immune cells expressing β-glucan receptors. GPs have been used for the targeted delivery of a wide range of payloads, including vaccines and nanoparticles, encapsulated inside the hollow cavity of GPs. In this paper, we describe the methods to prepare GP-encapsulated nickel nanoparticles (GP-Ni) for the binding of histidine (His)-tagged proteins. His-tagged Cda2 cryptococcal antigens were used as payloads to demonstrate the efficacy of this new GP vaccine encapsulation approach. The GP-Ni-Cda2 vaccine was shown to be comparable to our previous approach utilizing mouse serum albumin (MSA) and yeast RNA trapping of Cda2 in GPs in a mouse infection model. This novel GP-Ni approach allows for the one-step binding of His-tagged vaccine antigens and encapsulation in an effective delivery vehicle to target vaccines to antigen-presenting cells (APCs), antigen discovery, and vaccine development.
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Affiliation(s)
- Ernesto R Soto
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Charles A Specht
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Chrono K Lee
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Stuart M Levitz
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Gary R Ostroff
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
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3
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Kattan RE, Ayesh D, Wang W. Analysis of affinity purification-related proteomic data for studying protein-protein interaction networks in cells. Brief Bioinform 2023; 24:bbad010. [PMID: 36682002 PMCID: PMC10025443 DOI: 10.1093/bib/bbad010] [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: 11/07/2022] [Revised: 12/22/2022] [Accepted: 01/02/2023] [Indexed: 01/23/2023] Open
Abstract
During intracellular signal transduction, protein-protein interactions (PPIs) facilitate protein complex assembly to regulate protein localization and function, which are critical for numerous cellular events. Over the years, multiple techniques have been developed to characterize PPIs to elucidate roles and regulatory mechanisms of proteins. Among them, the mass spectrometry (MS)-based interactome analysis has been increasing in popularity due to its unbiased and informative manner towards understanding PPI networks. However, with MS instrumentation advancing and yielding more data than ever, the analysis of a large amount of PPI-associated proteomic data to reveal bona fide interacting proteins become challenging. Here, we review the methods and bioinformatic resources that are commonly used in analyzing large interactome-related proteomic data and propose a simple guideline for identifying novel interacting proteins for biological research.
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Affiliation(s)
- Rebecca Elizabeth Kattan
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Deena Ayesh
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
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4
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Bian W, Jiang H, Feng S, Chen J, Wang W, Li X. Protocol for establishing a protein-protein interaction network using tandem affinity purification followed by mass spectrometry in mammalian cells. STAR Protoc 2022; 3:101569. [PMID: 35874475 PMCID: PMC9304681 DOI: 10.1016/j.xpro.2022.101569] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Identification of protein interactors is fundamental to understanding their functions. Here, we describe a modified protocol for tandem affinity purification coupled with mass spectrometry (TAP/MS), which includes two-step purification. We detail the S-, 2×FLAG-, and Streptavidin-Binding Peptide (SBP)- tandem tags (SFB-tag) system for protein purification. This protocol can be used to identify protein interactors and establish a high-confidence protein-protein interaction network based on computational models. This is particularly useful for identifying bona fide interacting proteins for subsequent functional studies. For complete details on the use and execution of this protocol, please refer to Bian et al. (2021).
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Affiliation(s)
- Weixiang Bian
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Hua Jiang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.
| | - Xu Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.
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5
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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6
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Sakamoto K, Furukawa H, Arafiles JVV, Imanishi M, Matsuura K, Futaki S. Artificial Nanocage Formed via Self-Assembly of β-Annulus Peptide for Delivering Biofunctional Proteins into Cell Interiors. Bioconjug Chem 2022; 33:311-320. [PMID: 35049280 DOI: 10.1021/acs.bioconjchem.1c00534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Nanocarriers that deliver functional proteins to cell interiors are an attractive platform for the intracellular delivery of intact proteins without further modification, with in vivo compatibility. Development of efficient methods for cargo protein encapsulation and release in recipient cell cytosol is needed. Herein, we assess the feasibility of the abovementioned requirements using a protein nanocage (artificial nanocage) without compromising the structure and functions of the original protein and allowing for design flexibility of the surfaces and interiors. The protein nanocage formed via the self-assembly of the β-annulus peptide (24-amino acid peptide) in water was used as a model framework. The nitrilotriacetic acid moiety was displayed on the nanocage lumen for effective encapsulation of hexahistidine-tagged proteins in the presence of Ni2+, and the amphiphilic cationic lytic peptide HAad was displayed on a nanocage surface to attain cell permeability. Successful intracellular delivery of cargo proteins and targeting of cytosolic proteins by a nanobody were achieved, indicating the validity of the approach employed in this study.
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Affiliation(s)
- Kentarou Sakamoto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hiroto Furukawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | | | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan.,Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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7
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Enhancing the production of physiologically active vitamin D 3 by engineering the hydroxylase CYP105A1 and the electron transport chain. World J Microbiol Biotechnol 2021; 38:14. [PMID: 34877634 DOI: 10.1007/s11274-021-03193-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
In this study, the conversion of vitamin D3 (VD3) to its two active forms 25(OH)VD3 and 1α, 25(OH)2VD3 was carried out by engineering the hydroxylase CYP105A1 and its redox partners Fdx and Fdr. CYP105A1 and Fdx-Fdr were respectively expressed in E. coli BL21(DE3) and purified. The electron transport chain Fdx-Fdr had higher selectivity for the coenzyme NADH than NADPH. HPLC analysis showed that CYP105A1 could hydroxylate the C25 and C1α sites of VD3 and convert VD3 to its active forms. Finally, a one-bacterium-multi-enzyme system was constructed and used in whole-cell catalytic experiments. The results indicated that 2.491 mg/L of 25(OH)VD3 and 0.698 mg/L of 1α, 25(OH)2VD3 were successfully produced under the condition of 1.0% co-solvent DMSO, 1 mM coenzyme NADH and 35 g/L biocatalyst loading. This study contributes to a basis for the industrial production of active VD3 in future.
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8
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Zhao X, Chen Y, Zhang L, Li Z, Wu X, Chen J, Wang F. Molecular cloning and biochemical characterization of a trehalose synthase from Myxococcus sp. strain V11. Protein Expr Purif 2021; 183:105865. [PMID: 33675938 DOI: 10.1016/j.pep.2021.105865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/28/2021] [Accepted: 03/01/2021] [Indexed: 11/30/2022]
Abstract
The tresI gene of Myxococcus sp. strain V11 was cloned, and found to encode a trehalose synthase comprising 551 amino acids. The deduced molecular weight of the encoded TreS I protein 64.7 kDa and the isoelectric point (pI) was predicted to be 5.6. The catalytic cleft consists of the Asp202-Glu244-Asp310 catalytic triad and additional conserved residues. The recombinant (His)6-tag enzyme was expressed in Escherichia coli BL21(DE3) and purified by Ni2+-affinity chromatography, resulting in a specific activity of up to 172.7 U/mg. TLC and HPLC results confirmed that rTreS I can convert maltose into trehalose, with a yield of 61%. The KM and Vmax values of recombinant TreS I for maltose were 0.62 mM and 25.5 mM min-1 mg-1 protein, respectively. TreS I was optimally active at 35° and stable at temperatures of <25 °C. TreS I was stable within a narrow range of pH values, from 6.0 to 7.0. The enzymatic activity was slightly stimulated by Mg2+ and strongly inhibited by Fe3+, Co2+ and Cu2+. TreS I was also strongly inhibited by SDS and weakly by EDTA and TritonX-100.
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Affiliation(s)
- Xiaoyan Zhao
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, PR China
| | - Yunda Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, PR China
| | - Lixia Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, PR China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, PR China
| | - Xiaoyu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, PR China; Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Nanchang, 330045, PR China
| | - Jinyin Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, PR China; Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Nanchang, 330045, PR China
| | - Fei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, PR China; Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables in Jiangxi Province, Nanchang, 330045, PR China.
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9
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Carbamate C-N Hydrolase Gene ameH Responsible for the Detoxification Step of Methomyl Degradation in Aminobacter aminovorans Strain MDW-2. Appl Environ Microbiol 2020; 87:AEM.02005-20. [PMID: 33097501 DOI: 10.1128/aem.02005-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
Methomyl {bis[1-methylthioacetaldehyde-O-(N-methylcarbamoyl)oximino]sulfide} is a highly toxic oxime carbamate insecticide. Several methomyl-degrading microorganisms have been reported so far, but the role of specific enzymes and genes in this process is still unexplored. In this study, a protein annotated as a carbamate C-N hydrolase was identified in the methomyl-degrading strain Aminobacter aminovorans MDW-2, and the encoding gene was termed ameH A comparative analysis between the mass fingerprints of AmeH and deduced proteins of the strain MDW-2 genome revealed AmeH to be a key enzyme of the detoxification step of methomyl degradation. The results also demonstrated that AmeH was a functional homodimer with a subunit molecular mass of approximately 34 kDa and shared the highest identity (27%) with the putative formamidase from Schizosaccharomyces pombe ATCC 24843. AmeH displayed maximal enzymatic activity at 50°C and pH 8.5. Km and k cat of AmeH for methomyl were 87.5 μM and 345.2 s-1, respectively, and catalytic efficiency (k cat/Km ) was 3.9 μM-1 s-1 Phylogenetic analysis revealed AmeH to be a member of the FmdA_AmdA superfamily. Additionally, five key amino acid residues (162, 164, 191, 193, and 207) of AmeH were identified by amino acid variations.IMPORTANCE Based on the structural characteristic, carbamate insecticides can be classified into oxime carbamates (methomyl, aldicarb, oxamyl, etc.) and N-methyl carbamates (carbaryl, carbofuran, isoprocarb, etc.). So far, research on the degradation of carbamate pesticides has mainly focused on the detoxification step and hydrolysis of their carbamate bond. Several genes, such as cehA, mcbA, cahA, and mcd, and their encoding enzymes have also been reported to be involved in the detoxification step. However, none of these enzymes can hydrolyze methomyl. In this study, a carbamate C-N hydrolase gene, ameH, responsible for the detoxification step of methomyl in strain MDW-2 was cloned and the key amino acid sites of AmeH were investigated. These findings provide insight into the microbial degradation mechanism of methomyl.
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10
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Wu S, Liu Y, Sun H, Zhong M, Dai B, Pan B, Shen Z. An ssDNA aptamer specific for detection and purification of hexahistidine-tagged proteins. Anal Biochem 2020; 607:113893. [PMID: 32739349 DOI: 10.1016/j.ab.2020.113893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/27/2022]
Abstract
Aptamers are small-sized RNA or ssDNA ligands with a unique structure, which have high specificity and affinity to their cognate targets. Thus, in addition to the extensive values in various bio-medical fields, aptamers can also be alternatively used as affinity ligands in the bioprocess, such as for protein purification. In the present study, a hexahistidine specific aptamer named AptHis-C, was developed through the SELEX methodology, which has high affinity to hexahistidine, and its dissociation constant was as low as 20.8 nM. The structural prediction revealed that AptHis-C contains two connected stem-loop conformations. AptHis-C can only specifically recognize recombinant proteins with the hexahistidine-tag in simple or complex situations, and not to those with other tags. When immobilized on magnetic beads, AptHis-C can be used as a tool for hexahistidine-tagged recombinant protein purification. Its effectiveness is as good as traditional Ni-based beads. Besides, due to the intrinsic characteristics of nucleic acids, such as high thermal/chemical stability, immobilized aptamer-magnetic beads can be reused many times without an obvious decrease of purification effectiveness. This aptamer may represent a novel method for the detection and purification of hexahistidine-tagged recombinant proteins.
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Affiliation(s)
- Shijia Wu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanting Liu
- Department of Oncology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan, China
| | - Hongguang Sun
- Aptamer-Theranostics R&D Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Meizuo Zhong
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bichun Dai
- Aptamer-Theranostics R&D Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Biyao Pan
- Aptamer-Theranostics R&D Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhijian Shen
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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Attri P, Choi S, Kim M, Shiratani M, Cho AE, Lee W. Influence of alkyl chain substitution of ammonium ionic liquids on the activity and stability of tobacco etch virus protease. Int J Biol Macromol 2020; 155:439-446. [DOI: 10.1016/j.ijbiomac.2020.03.175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 02/06/2023]
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Pigmentiphaga sp. Strain D-2 Uses a Novel Amidase To Initiate the Catabolism of the Neonicotinoid Insecticide Acetamiprid. Appl Environ Microbiol 2020; 86:AEM.02425-19. [PMID: 31924619 DOI: 10.1128/aem.02425-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/23/2019] [Indexed: 11/20/2022] Open
Abstract
Acetamiprid, a chloronicotinyl neonicotinoid insecticide, is among the most commonly used insecticides worldwide, and its environmental fate has caused considerable concern. The compound 1-(6-chloropyridin-3-yl)-N-methylmethanamine (IM 1-4) has been reported to be the main intermediate during acetamiprid catabolism in microorganisms, honeybees, and spinach. However, the molecular mechanism underlying the hydrolysis of acetamiprid to IM 1-4 has not yet been elucidated. In this study, a novel amidase (AceAB) that initially hydrolyzes the C-N bond of acetamiprid to generate IM 1-4 was purified and characterized from the acetamiprid-degrading strain Pigmentiphaga sp. strain D-2. Based on peptide profiling of the purified AceAB and the draft genome sequence of strain D-2, aceA (372 bp) and aceB (2,295 bp), encoding the α and β subunits of AceAB, respectively, were cloned and found to be necessary for acetamiprid hydrolysis in strain D-2. The characteristics of AceAB were also systematically investigated. Though AceA and AceB showed 35% to 56% identity to the α and β subunits of the N,N-dimethylformamidase from Paracoccus aminophilus, AceAB was specific for the hydrolysis of acetamiprid and showed no activities to N,N-dimethylformamide or its structural analogs.IMPORTANCE Acetamiprid, among the top neonicotinoid insecticides used worldwide, is one of the most important commercial insecticides. Due to its extensive use, the environmental fate of acetamiprid, especially its microbial degradation, has caused considerable concern. Although the catabolic pathways of acetamiprid in microorganisms have been extensively studied, the molecular mechanisms underlying acetamiprid biodegradation (except for a nitrile hydratase) remain largely unknown, and the enzyme responsible for the biotransformation of acetamiprid into its main intermediate, IM 1-4, have not yet been elucidated. The amidase AceAB and its encoding genes, aceA and aceB, characterized in this study, were found to be necessary and specific for the initial hydrolysis of the C-N bond of acetamiprid to generate IM 1-4 in Pigmentiphaga sp. strain D-2. The finding of the novel amidase AceAB will greatly enhance our understanding of the microbial catabolism of the widely used insecticide acetamiprid at the molecular level.
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Lee TH, Kim KS, Kim JH, Jeong JH, Woo HR, Park SR, Sohn MH, Lee HJ, Rhee JH, Cha SS, Hwang JH, Chung KM. Novel short peptide tag from a bacterial toxin for versatile applications. J Immunol Methods 2020; 479:112750. [PMID: 31981564 DOI: 10.1016/j.jim.2020.112750] [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: 06/24/2019] [Revised: 12/25/2019] [Accepted: 01/21/2020] [Indexed: 11/26/2022]
Abstract
The specific recognition between a monoclonal antibody (mAb) and its epitope can be used in a tag system that has proved valuable in a wide range of biological applications. Herein, we describe a novel tag called RA-tag that is composed of a seven amino acid sequence (DIDLSRI) and recognized by a highly specific mAb, 47RA, against the bacterial toxin Vibrio vulnificus RtxA1/MARTXVv. By using recombinant proteins with the RA-tag at the N-terminal, C-terminal, or an internal site, we demonstrated that the tag system could be an excellent biological system for both protein purification and protein detection in enzyme-linked immunosorbent, Western blot, flow cytometry, and immunofluorescence staining analyses in Escherichia coli, mammalian cell lines, yeast, and plant. In addition, our RA-tag/47RA mAb combination showed high sensitivity and reliable affinity (KD = 5.90 × 10-8 M) when compared with conventional tags. Overall, our results suggest that the RA-tag system could facilitate the development of a broadly applicable tag system for biological research.
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Affiliation(s)
- Tae Hee Lee
- Department of Microbiology and Immunology, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea
| | - Kwang Soo Kim
- Department of Microbiology, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Combinatorial Tumor Immunotherapy Medical Research Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea
| | - Jin Hee Kim
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 63243, Republic of Korea; Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Jae-Ho Jeong
- Department of Microbiology, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Combinatorial Tumor Immunotherapy Medical Research Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - So Ra Park
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk 28160, Republic of Korea
| | - Myung-Ho Sohn
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk 28160, Republic of Korea
| | - Hyeon Ju Lee
- Department of Microbiology and Immunology, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea
| | - Joon Haeng Rhee
- Department of Microbiology, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Combinatorial Tumor Immunotherapy Medical Research Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Clinical Vaccine R&D Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Vaxcell-Bio Therapeutics, Hwasun-gun 58141, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Joo-Hee Hwang
- Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Jeonbuk 54907, Republic of Korea.
| | - Kyung Min Chung
- Department of Microbiology and Immunology, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Jeonbuk 54907, Republic of Korea.
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14
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Rv2626c and Rv2032 activate TH1 response and downregulate regulatory T cells in peripheral blood mononuclear cells of tuberculosis patients. Comp Immunol Microbiol Infect Dis 2019; 62:46-53. [DOI: 10.1016/j.cimid.2018.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/24/2018] [Accepted: 11/27/2018] [Indexed: 12/19/2022]
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15
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Zhang L, Hu Q, Hang P, Zhou X, Jiang J. Characterization of an arylamidase from a newly isolated propanil-transforming strain of Ochrobactrum sp. PP-2. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 167:122-129. [PMID: 30317116 DOI: 10.1016/j.ecoenv.2018.09.127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/16/2018] [Accepted: 09/30/2018] [Indexed: 06/08/2023]
Abstract
Propanil, one of the most extensively used post-emergent contact herbicides, has also been reported to have adverse effect on environmental safety. A bacterial strain of Ochrobactrum sp. PP-2, which was capable of transforming propanil, was isolated from a propanil-contaminated soil collected from a chemical factory. An arylamidase gene mah responsible for transforming propanil to 3,4-dichloroaniline (3,4-DCA) was cloned from strain PP-2 by shotgun method and subsequently confirmed by function expression. The arylamidase Mah shares low amino acid sequence identity (27-50%) with other biochemically characterized amidases and shows less than 30% identities to other reported propanil hydrolytic enzymes. Mah was most active at pH 8 and 35 °C. Mah had a remarkable activity toward propanil (Km = 6.3 ± 1.2 µM), showing the highest affinity efficiency for propanil as compared with other reported propanil hydrolytic enzymes. Our study also provides a new arylamidase for the hydrolysis of propanil.
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Affiliation(s)
- Long Zhang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Qiang Hu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Ping Hang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Xiyi Zhou
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China.
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16
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Paolino M, Visintin M, Margotti E, Visentini M, Salvini L, Reale A, Razzano V, Giuliani G, Caselli G, Tavanti F, Menziani MC, Cappelli A. Functionalization of protein hexahistidine tags by functional nanoreactors. NEW J CHEM 2019. [DOI: 10.1039/c9nj03463c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The reactivity of functional nanoreactors was evaluated in CRB0137 as a model protein to develop a new methodology for the site-specific PEGylation of proteins bearing poly-histidine tags.
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Affiliation(s)
- Marco Paolino
- Dipartimento di Biotecnologie
- Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)
- Università di Siena
- 53100 Siena
- Italy
| | | | | | | | | | - Annalisa Reale
- Dipartimento di Biotecnologie
- Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)
- Università di Siena
- 53100 Siena
- Italy
| | - Vincenzo Razzano
- Dipartimento di Biotecnologie
- Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)
- Università di Siena
- 53100 Siena
- Italy
| | - Germano Giuliani
- Dipartimento di Biotecnologie
- Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)
- Università di Siena
- 53100 Siena
- Italy
| | | | - Francesco Tavanti
- Dipartimento di Scienze Chimiche e Geologiche
- Università di Modena e Reggio Emilia
- 41121 Modena
- Italy
| | - Maria Cristina Menziani
- Dipartimento di Scienze Chimiche e Geologiche
- Università di Modena e Reggio Emilia
- 41121 Modena
- Italy
| | - Andrea Cappelli
- Dipartimento di Biotecnologie
- Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)
- Università di Siena
- 53100 Siena
- Italy
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17
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Paolino M, Reale A, Razzano V, Giuliani G, Donati A, Bonechi C, Caselli G, Visintin M, Makovec F, Scialabba C, Licciardi M, Paccagnini E, Gentile M, Salvini L, Tavanti F, Menziani MC, Cappelli A. Nanoreactors for the multi-functionalization of poly-histidine fragments. NEW J CHEM 2019. [DOI: 10.1039/c9nj00279k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Water-soluble MBHA derivatives self-assemble to generate aggregates showing reactive core–shell architectures.
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18
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Gengenbach BB, Müschen CR, Buyel JF. Expression and purification of human phosphatase and actin regulator 1 (PHACTR1) in plant-based systems. Protein Expr Purif 2018; 151:46-55. [PMID: 29894805 DOI: 10.1016/j.pep.2018.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 05/31/2018] [Accepted: 06/07/2018] [Indexed: 12/21/2022]
Abstract
Cardiovascular diseases are a prevalent cause of morbidity and mortality especially in industrialized countries. The human phosphatase and actin regulator 1 (PHACTR1) may be involved in such diseases, but its precise regulatory function remains unclear due to the large number of potential interaction partners. The same phenomenon makes this protein difficult to express in mammalian cells, but it is also an intrinsically disordered protein that likely aggregates when expressed in bacteria due to the absence of chaperones. We therefore used a design of experiments approach to test the suitability of three plant-based systems for the expression of satisfactory quantities of recombinant PHACTR1, namely transient expression in tobacco (Nicotiana tabacum) BY-2 plant cell packs (PCPs), whole N. benthamiana leaves and BY-2 cell lysate (BYL). The highest yield was achieved using the BYL: up to 120 mg product kg-1 biomass equivalent within 48 h of translation. This was 1.3-fold higher than transient expression in N. benthamiana together with the silencing inhibitor p19, and 6-fold higher than the PCP system. The presence of Triton X-100 in the extraction buffer increased the recovery of PHACTR1 by 2-200-fold depending on the conditions. PHACTR1 was incompatible with biomass blanching and was stable for less than 16 h in raw plant extracts. Purification using a DDK-tag proved inefficient whereas 15% purity was achieved by immobilized metal affinity chromatography.
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Affiliation(s)
- B B Gengenbach
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, 52074, Aachen, Germany.
| | - C R Müschen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, 52074, Aachen, Germany.
| | - J F Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, 52074, Aachen, Germany; Institute for Molecular Biotechnology, Worringerweg 1, RWTH Aachen University, 52074, Aachen, Germany.
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19
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Zhou X, Zhou J, Xin F, Ma J, Zhang W, Wu H, Jiang M, Dong W. Heterologous expression of a novel d‑lactate dehydrogenase from Lactobacillus sp. ZX1 and its application for d‑phenyllactic acid production. Int J Biol Macromol 2018; 119:1171-1178. [DOI: 10.1016/j.ijbiomac.2018.08.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 01/07/2023]
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20
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Dual column approach for the purification of zinc finger proteins by immobilized metal affinity chromatography. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.08.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Jiang Y, Zhou J, Wu R, Xin F, Zhang W, Fang Y, Ma J, Dong W, Jiang M. Heterologous expression of cyclodextrin glycosyltransferase from Paenibacillus macerans in Escherichia coli and its application in 2-O-α-D-glucopyranosyl-L-ascorbic acid production. BMC Biotechnol 2018; 18:53. [PMID: 30170578 PMCID: PMC6119282 DOI: 10.1186/s12896-018-0463-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyclodextrin glucanotransferase (CGTase) can transform L-ascorbic acid (L-AA, vitamin C) to 2-O-α-D-glucopyranosyl-L-ascorbic acid (AA-2G), which shows diverse applications in food, cosmetic and pharmaceutical industries. RESULTS In this study, the cgt gene encoding α-CGTase from Paenibacillus macerans was codon-optimized (opt-cgt) and cloned into pET-28a (+) for intracellular expression in E. coli BL21 (DE3). The Opt-CGT was purified by Ni2+-NTA resin with a 55% recovery, and specific activity was increased significantly from 1.17 to 190.75 U·mg- 1. In addition, the enzyme was adopted to transform L-AA into 9.1 g/L of AA-2G. Finally, more economic substrates, including β-cyclodextrin, soluble starch, corn starch and cassava starch could also be used as glycosyl donors, and 4.9, 3.5, 1.3 and 1.5 g/L of AA-2G were obtained, respectively. CONCLUSIONS N-terminal amino acid is critical to the activity of CGTase suggested by its truncation study. Furthermore, when the Opt-CGT was flanked by His6-tags on the C- and N-terminal, the recovery of purification by Ni2+-NTA resin is appreciably enhanced. α-cyclodextrin was the ideal glycosyl donor for AA-2G production. In addition, the selection of low cost glycosyl donors would make the process of AA-2G production more economically competitive.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Ruofan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Wenming Zhang
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Yan Fang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
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22
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Bartoschik T, Galinec S, Kleusch C, Walkiewicz K, Breitsprecher D, Weigert S, Muller YA, You C, Piehler J, Vercruysse T, Daelemans D, Tschammer N. Near-native, site-specific and purification-free protein labeling for quantitative protein interaction analysis by MicroScale Thermophoresis. Sci Rep 2018; 8:4977. [PMID: 29563556 PMCID: PMC5862892 DOI: 10.1038/s41598-018-23154-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/05/2018] [Indexed: 12/21/2022] Open
Abstract
MicroScale Thermophoresis (MST) is a frequently used method for the quantitative characterization of intermolecular interactions with several advantages over other technologies. One of these is its capability to determine equilibrium constants in solution including complex biological matrices such as cell lysates. MST requires one binding partner to be fluorescent, which is typically achieved by labeling target proteins with a suitable fluorophore. Here, we present a near-native, site-specific in situ labeling strategy for MST experiments that enables reliable measurements in cell lysates and that has distinct advantages over routine covalent labeling techniques. To this end, we exploited the high-affinity interaction of tris-NTA with oligohistidine-tags, which are popular for purification, immobilization or detection of recombinant proteins. We used various DYE-tris-NTA conjugates to successfully label His-tagged proteins that were either purified or a component of cell lysate. The RED-tris-NTA was identified as the optimal dye conjugate with a high affinity towards oligohistidine-tags, a high fluorescence signal and an optimal signal-to-noise ratio in MST binding experiments. Owing to its emission in the red region of the spectrum, it also enables reliable measurements in complex biological matrices such as cell lysates allowing a more physiologically realistic assessment and eliminating the need for protein purification.
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Affiliation(s)
- Tanja Bartoschik
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany
| | - Stefanie Galinec
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany
| | - Christian Kleusch
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany
| | | | | | - Sebastian Weigert
- Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen, Nuremberg Henkestr 91, 91052, Erlangen, Germany
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen, Nuremberg Henkestr 91, 91052, Erlangen, Germany
| | - Changjiang You
- Division of Biophysics, Department of Biology, University Osnabrück, Barbarastr 11, 49076, Osnabrück, Germany
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University Osnabrück, Barbarastr 11, 49076, Osnabrück, Germany
| | - Thomas Vercruysse
- KU Leuven Department of Immunology and Microbiology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000, Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Immunology and Microbiology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000, Leuven, Belgium
| | - Nuska Tschammer
- NanoTemper Technologies GmbH, Floessergasse 4, 81069, München, Germany.
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23
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Chen S, Maini R, Bai X, Nangreave RC, Dedkova LM, Hecht SM. Incorporation of Phosphorylated Tyrosine into Proteins: In Vitro Translation and Study of Phosphorylated IκB-α and Its Interaction with NF-κB. J Am Chem Soc 2017; 139:14098-14108. [PMID: 28898075 PMCID: PMC5901656 DOI: 10.1021/jacs.7b05168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphorylated proteins play important roles in the regulation of many different cell networks. However, unlike the preparation of proteins containing unmodified proteinogenic amino acids, which can be altered readily by site-directed mutagenesis and expressed in vitro and in vivo, the preparation of proteins phosphorylated at predetermined sites cannot be done easily and in acceptable yields. To enable the synthesis of phosphorylated proteins for in vitro studies, we have explored the use of phosphorylated amino acids in which the phosphate moiety bears a chemical protecting group, thus eliminating the negative charges that have been shown to have a negative effect on protein translation. Bis-o-nitrobenzyl protection of tyrosine phosphate enabled its incorporation into DHFR and IκB-α using wild-type ribosomes, and the elaborated proteins could subsequently be deprotected by photolysis. Also investigated in parallel was the re-engineering of the 23S rRNA of Escherichia coli, guided by the use of a phosphorylated puromycin, to identify modified ribosomes capable of incorporating unprotected phosphotyrosine into proteins from a phosphotyrosyl-tRNACUA by UAG codon suppression during in vitro translation. Selection of a library of modified ribosomal clones with phosphorylated puromycin identified six modified ribosome variants having mutations in nucleotides 2600-2605 of 23S rRNA; these had enhanced sensitivity to the phosphorylated puromycin. The six clones demonstrated some sequence homology in the region 2600-2605 and incorporated unprotected phosphotyrosine into IκB-α using a modified gene having a TAG codon in the position corresponding to amino acid 42 of the protein. The purified phosphorylated protein bound to a phosphotyrosine specific antibody and permitted NF-κB binding to a DNA duplex sequence corresponding to its binding site in the IL-2 gene promoter. Unexpectedly, phosphorylated IκB-α also mediated the exchange of exogenous DNA into an NF-κB-cellular DNA complex isolated from the nucleus of activated Jurkat cells.
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Affiliation(s)
- Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Rumit Maini
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Ryan C. Nangreave
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M. Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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24
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Functional Analysis of a Novel β-(1,3)-Glucanase from Corallococcus sp. Strain EGB Containing a Fascin-Like Module. Appl Environ Microbiol 2017. [PMID: 28625980 DOI: 10.1128/aem.01016-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A novel β-(1,3)-glucanase gene designated lamC, cloned from Corallococcus sp. strain EGB, contains a fascin-like module and a glycoside hydrolase family 16 (GH16) catalytic module. LamC displays broad hydrolytic activity toward various polysaccharides. Analysis of the hydrolytic products revealed that LamC is an exo-acting enzyme on β-(1,3)(1,3)- and β-(1,6)-linked glucan substrates and an endo-acting enzyme on β-(1,4)-linked glucan and xylan substrates. Site-directed mutagenesis of conserved catalytic Glu residues (E304A and E309A) demonstrated that these activities were derived from the same active site. Excision of the fascin-like module resulted in decreased activity toward β-(1,3)(1,3)-linked glucans. The carbohydrate-binding assay showed that the fascin-like module was a novel β-(1,3)-linked glucan-binding module. The functional characterization of the fascin-like module and catalytic module will help us better understand these enzymes and modules.IMPORTANCE In this report of a bacterial β-(1,3)(1,3)-glucanase containing a fascin-like module, we reveal the β-(1,3)(1,3)-glucan-binding function of the fascin-like module present in the N terminus of LamC. LamC displays exo-β-(1,3)/(1,6)-glucanase and endo-β-(1,4)-glucanase/xylanase activities with a single catalytic domain. Thus, LamC was identified as a novel member of the GH16 family.
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25
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Jamrichová D, Tišáková L, Jarábková V, Godány A. How to approach heterogeneous protein expression for biotechnological use: An overview. NOVA BIOTECHNOLOGICA ET CHIMICA 2017. [DOI: 10.1515/nbec-2017-0001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
AbstractProduction of recombinant proteins in Escherichia coli expression systems has shown many advantages, as well as disadvantages, especially for biotechnological and other down-stream applications. The choice of an appropriate vector depends on the gene, to be cloned for purification procedures and other analyses. Selection of a suitable production strain plays an important role in the preparation of recombinant proteins. The main criteria for the selection of the host organism are the properties of the recombinant produced protein, its subsequent use and the total amount desired. The most common problems in eukaryotic gene expression and recombinant proteins purification are, for instance, post-translational modifications, formation of disulphide bonds, or inclusion bodies. Obtaining a purified protein is a key step enabling further characterization of its role in the biological system. Moreover, methods of protein purification have been developed in parallel with the discovery of proteins and the need for their studies and applications. After protein purification, and also between the individual purification steps, it is necessary to test protein stability under different conditions over time. Shortly, all the essential points have been briefly discussed, which could be encountered during production and purification of a recombinant protein of interest, especially from eukaryotic source and expressed heterogeneously in prokaryotic production system.
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Schröder H, Fischer R, Sollfrank L, Paulsen F, Bräuer L, Schicht M. Expression of recombinant surfactant protein SFTA3 in the human kidney cell line HEK 293T. Ann Anat 2017; 211:149-157. [DOI: 10.1016/j.aanat.2017.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/17/2017] [Indexed: 10/20/2022]
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27
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Duret D, Haftek-Terreau Z, Carretier M, Ladavière C, Charreyre MT, Favier A. Fluorescent RAFT polymers bearing a nitrilotriacetic acid (NTA) ligand at the α-chain-end for the site-specific labeling of histidine-tagged proteins. Polym Chem 2017. [DOI: 10.1039/c6py02222g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Fluorescent polymer probes bearing a nitrilotriacetic acid ligand at the α−chain-end selectively labeled histidine-tagged recombinant proteins.
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Affiliation(s)
- Damien Duret
- Univ Lyon
- Université Lyon 1
- INSA de Lyon
- CNRS
- Laboratoire Ingénierie des Matériaux Polymères
| | - Zofia Haftek-Terreau
- Univ Lyon
- Ecole Normale Supérieure de Lyon
- CNRS
- Laboratoire Joliot-Curie
- F-69364 Lyon
| | - Matthieu Carretier
- Univ Lyon
- Université Lyon 1
- INSA de Lyon
- CNRS
- Laboratoire Ingénierie des Matériaux Polymères
| | - Catherine Ladavière
- Univ Lyon
- Université Lyon 1
- INSA de Lyon
- CNRS
- Laboratoire Ingénierie des Matériaux Polymères
| | | | - Arnaud Favier
- Univ Lyon
- Université Lyon 1
- INSA de Lyon
- CNRS
- Laboratoire Ingénierie des Matériaux Polymères
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28
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Pendimethalin Nitroreductase Is Responsible for the Initial Pendimethalin Degradation Step in Bacillus subtilis Y3. Appl Environ Microbiol 2016; 82:7052-7062. [PMID: 27694234 DOI: 10.1128/aem.01771-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/22/2016] [Indexed: 11/20/2022] Open
Abstract
Pendimethalin [N-(1-ethylpropyl)-2,6-dinitro-3,4-xylidine] is a selective preemergence dinitroaniline herbicide. Several fungi and bacteria have been reported to degrade pendimethalin, but the enzymes or genes involved in this process have not been characterized. Nitroreduction is the initial degradation and detoxification step for pendimethalin. In this study, a pendimethalin nitroreductase (PNR), responsible for the nitroreduction of pendimethalin, was purified from the pendimethalin-degrading strain Bacillus subtilis Y3. Based on a comparison of its mass fingerprints with all of the deduced proteins from the draft genome of strain Y3, a protein annotated as a nitroreductase was identified, and its corresponding encoding gene was termed pnr PNR was a functional homodimer with a subunit molecular mass of approximately 23 kDa. PNR reduced the C-6 nitro group of the aromatic ring of pendimethalin, yielding 2-nitro-6-amino-N-(1-ethylpropyl)-3,4-xylidine. PNR could also catalyze the nitroreduction of three other major varieties of dinitroaniline herbicides, including butralin, oryzalin, and trifluralin. However, the number of reduced nitro groups was two instead of one, which differed from the nitroreduction of pendimethalin by PNR and which may be due to the symmetry in the chemical structures of the two nitro groups. A detoxification assay revealed that 2-nitro-6-amino-N-(1-ethylpropyl)-3,4-xylidine (PNR-reduced pendimethalin) showed no inhibitory effect on the growth of Saccharomyces cerevisiae BY4741, whereas pendimethalin showed an obvious inhibitory effect on its growth, indicating the detoxification effect of pendimethalin by PNR. Therefore, PNR has potential in pendimethalin detoxification applications. This report describes an enzyme (and corresponding gene) involved in the biodegradation of pendimethalin and dinitroaniline herbicides. IMPORTANCE Pendimethalin [N-(1-ethylpropyl)-2,6-dinitro-3,4-xylidine] is a widely used selective preemergence dinitroaniline herbicide, and its residue has been frequently detected in the environment. The U.S. Environmental Protection Agency (EPA) has classified pendimethalin as a persistent bioaccumulative toxin. To date, no enzymes or genes involved in pendimethalin biodegradation have been reported. In the present study, the gene pnr, which encodes the nitroreductase PNR, responsible for the nitroreduction of pendimethalin, was cloned from the pendimethalin-degrading strain Bacillus subtilis Y3. PNR could also catalyze the nitroreduction of three other major varieties of dinitroaniline herbicides, including butralin, oryzalin, and trifluralin. The reduction of pendimethalin by PNR might eliminate its toxicity against Saccharomyces cerevisiae BY4741, indicating the application potential of PNR in the detoxification of pendimethalin.
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Schröder H, Sollfrank L, Paulsen F, Bräuer L, Schicht M. Recombinant expression of surfactant protein H (SFTA3) in Escherichia coli. Ann Anat 2016; 208:129-134. [DOI: 10.1016/j.aanat.2016.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/11/2016] [Indexed: 11/15/2022]
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Yao VJ, D'Angelo S, Butler KS, Theron C, Smith TL, Marchiò S, Gelovani JG, Sidman RL, Dobroff AS, Brinker CJ, Bradbury ARM, Arap W, Pasqualini R. Ligand-targeted theranostic nanomedicines against cancer. J Control Release 2016; 240:267-286. [PMID: 26772878 PMCID: PMC5444905 DOI: 10.1016/j.jconrel.2016.01.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/17/2015] [Accepted: 01/02/2016] [Indexed: 02/06/2023]
Abstract
Nanomedicines have significant potential for cancer treatment. Although the majority of nanomedicines currently tested in clinical trials utilize simple, biocompatible liposome-based nanocarriers, their widespread use is limited by non-specificity and low target site concentration and thus, do not provide a substantial clinical advantage over conventional, systemic chemotherapy. In the past 20years, we have identified specific receptors expressed on the surfaces of tumor endothelial and perivascular cells, tumor cells, the extracellular matrix and stromal cells using combinatorial peptide libraries displayed on bacteriophage. These studies corroborate the notion that unique receptor proteins such as IL-11Rα, GRP78, EphA5, among others, are differentially overexpressed in tumors and present opportunities to deliver tumor-specific therapeutic drugs. By using peptides that bind to tumor-specific cell-surface receptors, therapeutic agents such as apoptotic peptides, suicide genes, imaging dyes or chemotherapeutics can be precisely and systemically delivered to reduce tumor growth in vivo, without harming healthy cells. Given the clinical applicability of peptide-based therapeutics, targeted delivery of nanocarriers loaded with therapeutic cargos seems plausible. We propose a modular design of a functionalized protocell in which a tumor-targeting moiety, such as a peptide or recombinant human antibody single chain variable fragment (scFv), is conjugated to a lipid bilayer surrounding a silica-based nanocarrier core containing a protected therapeutic cargo. The functionalized protocell can be tailored to a specific cancer subtype and treatment regimen by exchanging the tumor-targeting moiety and/or therapeutic cargo or used in combination to create unique, theranostic agents. In this review, we summarize the identification of tumor-specific receptors through combinatorial phage display technology and the use of antibody display selection to identify recombinant human scFvs against these tumor-specific receptors. We compare the characteristics of different types of simple and complex nanocarriers, and discuss potential types of therapeutic cargos and conjugation strategies. The modular design of functionalized protocells may improve the efficacy and safety of nanomedicines for future cancer therapy.
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Affiliation(s)
- Virginia J Yao
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131
| | - Sara D'Angelo
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131
| | - Kimberly S Butler
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131
| | - Christophe Theron
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131
| | - Tracey L Smith
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131
| | - Serena Marchiò
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131; Department of Oncology, University of Turin, Candiolo, 10060, Italy
| | - Juri G Gelovani
- Department of Biomedical Engineering, College of Engineering and School of Medicine, Wayne State University, Detroit, MI 48201
| | - Richard L Sidman
- Department of Neurology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215
| | - Andrey S Dobroff
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131
| | - C Jeffrey Brinker
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131; Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, NM 87131; Cancer Research and Treatment Center, Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131; Self-Assembled Materials Department, Sandia National Laboratories, Albuquerque, NM 87185
| | - Andrew R M Bradbury
- Bioscience Division, Los Alamos National Laboratories, Los Alamos, NM, 87545
| | - Wadih Arap
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Hematology/Oncology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131.
| | - Renata Pasqualini
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131.
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Saraav I, Pandey K, Misra R, Singh S, Sharma M, Sharma S. Characterization of MymA protein as a flavin-containing monooxygenase and as a target of isoniazid. Chem Biol Drug Des 2016; 89:152-160. [DOI: 10.1111/cbdd.12840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 05/12/2016] [Accepted: 08/06/2016] [Indexed: 01/29/2023]
Affiliation(s)
- Iti Saraav
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
| | - Kirti Pandey
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
| | - Richa Misra
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
| | - Swati Singh
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
| | - Monika Sharma
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
| | - Sadhna Sharma
- D S Kothari Centre for Research and Innovation in Science Education; Miranda House; Delhi India
- Department of Zoology; Miranda House, University of Delhi; Delhi India
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Su Q, Guo M, Jia Z, Qiu F, Lu X, Gao Y, Meng Q, Tian R, Bi S, Yi Y. Epitope-based recombinant diagnostic antigen to distinguish natural infection from vaccination with hepatitis A virus vaccines. J Virol Methods 2016; 233:41-5. [PMID: 26994964 DOI: 10.1016/j.jviromet.2016.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 02/20/2016] [Accepted: 02/21/2016] [Indexed: 11/25/2022]
Abstract
Hepatitis A virus (HAV) infection can stimulate the production of antibodies to structural and non-structural proteins of the virus. However, vaccination with an inactivated or attenuated HAV vaccine produces antibodies mainly against structural proteins, whereas no or very limited antibodies are produced against the non-structural proteins. Current diagnostic assays to determine exposure to HAV, such as the Abbott HAV AB test, detect antibodies only to the structural proteins and so are not able to distinguish a natural infection from vaccination with an inactivated or attenuated virus. Here, we constructed a recombinant tandem multi-epitope diagnostic antigen (designated 'H1') based on the immune-dominant epitopes of the non-structural proteins of HAV to distinguish the two situations. H1 protein expressed in Escherichia coli and purified by affinity and anion exchange chromatography was applied in a double-antigen sandwich ELISA for the detection of anti-non-structural HAV proteins, which was confirmed to distinguish a natural infection from vaccination with an inactivated or attenuated HAV vaccine.
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Affiliation(s)
- Qiudong Su
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Minzhuo Guo
- Beijing International Travel Healthcare Center, Beijing, China
| | - Zhiyuan Jia
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Feng Qiu
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuexin Lu
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yan Gao
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qingling Meng
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiguang Tian
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengli Bi
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yao Yi
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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Farsad AS, Malekzadeh-Shafaroudi S, Moshtaghi N, Fotouhi F, Zibaee S. Expression of HA1 antigen of H5N1 influenza virus as a potent candidate for vaccine in bacterial system. IRANIAN JOURNAL OF VETERINARY RESEARCH 2016; 17:237-242. [PMID: 28224006 PMCID: PMC5309454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The impending influenza virus pandemic requires global vaccination to prevent large-scale mortality and morbidity, but traditional influenza virus vaccine production is too slow for rapid responses. In this study, bacterial system has been developed for expression and purification of properly folded HA1 antigen as a rapid response to emerging pandemic strains. Here, a recombinant H5N1 (A/Indonesia/05/05) hemagglutinin globular domain, the synthesized HA1 (1-320 amino acids), was amplified and cloned into pET-28a bacterial expression vector. Then, his-tagged HA1 protein was expressed in Escherichia coli BL21 under 1 mM IPTG induction. The protein expression was optimized under a time-course induction study and further purified using Ni-NTA chromatography. Migration size of protein was detected at 40 KDa by Western blot using anti-His tag monoclonal antibody and demonstrated no discrepancy compared to its calculated molecular weight. Since most antigenic sites are in the HA1 domain of HA, using this domain of influenza virus as antigen is of great importance in vaccine development. The ability of the antibody stimulation against HA1 expressed in bacterial cells is also examined using enzyme-linked immunosorbent assay (ELISA) analysis. Upon immunization of rabbits, oligomeric HA1 elicited potent neutralizing antibodies and high levels of serum antibody binding to HA1. Our findings suggest that HA1-based vaccines can be produced efficiently in bacterial systems and can be easily upscaled in response to a pandemic influenza virus threat.
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Affiliation(s)
- A. S. Farsad
- Ph.D. Student in Plant Biotechnology, Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran;
| | - S. Malekzadeh-Shafaroudi
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran; ,Correspondence: S. Malekzadeh-Shafaroudi, Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran. E-mail:
| | - N. Moshtaghi
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran;
| | - F. Fotouhi
- Influenza Research Lab, Pasteur Institute of Iran, Tehran, Iran;
| | - S. Zibaee
- Razi Vaccine and Serum Research Institute, Mashhad, Iran
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Wang X, Xu H, Chen X, Tian Y, Wang F, Lin X. Cloning, expression and cytotoxicity of granulin A, a novel polypeptide contained in human progranulin. Biosci Trends 2016; 10:181-7. [DOI: 10.5582/bst.2016.01036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Xuan Wang
- Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University
- SDU-ZB Biomedical R&D Institute
| | - Huanli Xu
- Department of Pharmacology, Capital Medical University
| | | | - Ye Tian
- Department of Pharmacology, Capital Medical University
| | - Fengshan Wang
- Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University
- SDU-ZB Biomedical R&D Institute
| | - Xiukun Lin
- SDU-ZB Biomedical R&D Institute
- Department of Pharmacology, Capital Medical University
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Chen Q, Chen K, Ni H, Zhuang W, Wang H, Zhu J, He Q, He J. A novel amidohydrolase (DmhA) from Sphingomonas sp. that can hydrolyze the organophosphorus pesticide dimethoate to dimethoate carboxylic acid and methylamine. Biotechnol Lett 2015; 38:703-10. [DOI: 10.1007/s10529-015-2027-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/23/2015] [Indexed: 11/28/2022]
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Talukder P, Chen S, Roy B, Yakovchuk P, Spiering MM, Alam MP, Madathil MM, Bhattacharya C, Benkovic SJ, Hecht SM. Cyanotryptophans as Novel Fluorescent Probes for Studying Protein Conformational Changes and DNA–Protein Interaction. Biochemistry 2015; 54:7457-69. [DOI: 10.1021/acs.biochem.5b01085] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Poulami Talukder
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Basab Roy
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Petro Yakovchuk
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Michelle M. Spiering
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mohammad P. Alam
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Manikandadas M. Madathil
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Chandrabali Bhattacharya
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Stephen J. Benkovic
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sidney M. Hecht
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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Bartnicki F, Kowalska E, Pels K, Strzalka W. Imidazole-free purification of His3-tagged recombinant proteins using ssDNA aptamer-based affinity chromatography. J Chromatogr A 2015; 1418:130-139. [PMID: 26427325 DOI: 10.1016/j.chroma.2015.09.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/11/2015] [Accepted: 09/16/2015] [Indexed: 02/07/2023]
Abstract
Immobilized metal ion affinity chromatography (IMAC) is widely used for the purification of many different His6-tagged recombinant proteins. On the one hand, it is a powerful technique but on the other hand it has its disadvantages. In this report, we present the development of a unique ssDNA aptamer for the purification of His3-tagged recombinant proteins. Our study shows that stability of the His3-tag/H3T aptamer complex can be controlled by the sodium ion concentration. Based on this feature, we demonstrate that H3T aptamer resin was successfully employed for the purification of three out of four tested His3-tagged recombinant proteins from an E. coli total protein extract using imidazole-free buffers. Finally, we show that the purity of His3-tagged proteins is superior when purified with the help of the H3T aptamer in comparison with Ni-NTA resin.
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Affiliation(s)
- Filip Bartnicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Ewa Kowalska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Katarzyna Pels
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Wojciech Strzalka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
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Synthesis of fluorescent dipeptidomimetics and their ribosomal incorporation into green fluorescent protein. Bioorg Med Chem Lett 2015; 25:4715-4718. [PMID: 26351043 DOI: 10.1016/j.bmcl.2015.08.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/24/2015] [Accepted: 08/27/2015] [Indexed: 12/12/2022]
Abstract
The synthesis and incorporation into position 66 of green fluorescent protein (GFP) by in vitro protein translation of novel oxazole and thiazole based dipeptidomimetics are described. The compounds may be regarded as GFP chromophore analogues, and are strongly fluorescent. An α-amido-β-ketoester intermediate was obtained via bisacylation of a protected glycine. The intermediate underwent dehydrative cyclization to afford the 1,3-oxazole and was treated with Lawesson's reagent to furnish the 1,3-thiazole. When these fluorophores were introduced into position 66 of GFP in place of Tyr66, the resulting GFP analogues exhibited fluorescence emission several-fold greater than wild-type GFP; the emission was also shifted to shorter wavelength. It may be noted that compared to the typical fluorophores formed in the natural and modified fluorescent proteins, the oxazole and thiazole fluorophores are completely stable and do not require activation by posttranslational modification to exhibit fluorescence.
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Lim JH, Park GC, Lee SM, Lee JH, Lim B, Hwang SM, Kim JH, Park H, Joo J, Kim YP. Surface-Tunable Bioluminescence Resonance Energy Transfer via Geometry-Controlled ZnO Nanorod Coordination. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:3469-3475. [PMID: 25802061 DOI: 10.1002/smll.201403700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/24/2015] [Indexed: 06/04/2023]
Abstract
The use of ZnO nanorods (NRs) as an effective coordinator and biosensing platform to create bioluminescence resonance energy transfer (BRET) is reported. Herein, a hydrothermal approach is applied to obtain morphologically controlled ZnO NRs, which are directly bound to luciferase (Luc) and carboxy-modified quantum dot (QD) acting as a donor-acceptor pair for BRET. BRET efficiency varies significantly with the geometry of ZnO NRs, which modulates the coordination between hexahistidine-tagged Luc (Luc-His6 ) and QD, owing to the combined effect of the total surface area consisting of (001) and (100) planes and their surface polarities. Unlike typical QD-BRET reactions with metal ions (e.g., zinc ions), a geometry-controlled ZnO NR platform can facilitate the design of surface-initiated BRET sensors without being supplemented by copious metal ions: the geometry-controlled ZnO NR platform can therefore pave the way for nanostructure-based biosensors with enhanced analytical performance.
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Affiliation(s)
- Jun Hyung Lim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Republic of Korea
| | - Geun Chul Park
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Republic of Korea
| | - Seung Muk Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Republic of Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Republic of Korea
| | - Butaek Lim
- Department of Life Science and Institute of Nano Science and Technology, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Soo Min Hwang
- Institute for Superconducting and Electronic Materials, University of Wollongong, North Wollongong, NSW, 2500, Australia
| | - Jung Ho Kim
- Institute for Superconducting and Electronic Materials, University of Wollongong, North Wollongong, NSW, 2500, Australia
| | - Hansoo Park
- School of Integrative Engineering, Chung-Ang University, Seoul, 156-756, Korea
| | - Jinho Joo
- School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Republic of Korea
| | - Young-Pil Kim
- Department of Life Science and Institute of Nano Science and Technology, Hanyang University, Seoul, 133-791, Republic of Korea
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Dong W, Jiang S, Shi K, Wang F, Li S, Zhou J, Huang F, Wang Y, Zheng Y, Hou Y, Huang Y, Cui Z. Biodegradation of fenoxaprop-P-ethyl (FE) by Acinetobacter sp. strain DL-2 and cloning of FE hydrolase gene afeH. BIORESOURCE TECHNOLOGY 2015; 186:114-121. [PMID: 25812814 DOI: 10.1016/j.biortech.2015.03.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/04/2015] [Accepted: 03/07/2015] [Indexed: 06/04/2023]
Abstract
Fenoxaprop-P-ethyl (FE) is widely used as a post-emergence aryloxyphenoxy propionate (AOPP) herbicide in agriculture. An efficient FE-degrading strain DL-2 was isolated from the enrichment culture and identified as Acinetobacter sp. and the metabolite fenoxaprop acid (FA) was identified by HPLC/MS analysis. The strain DL-2 could also degrade a wide range of other AOPP herbicides. A novel FE hydrolase esterase gene afeH was cloned from strain DL-2 and functionally expressed in Escherichia coli BL21(DE3). The specific activities of recombinant AfeH was 216.39 U mg(-1) for FE with Km and Vmax values of 0.82 μM and 7.94 μmol min(-1) mg(-1). AfeH could also hydrolyze various AOPP herbicides, p-nitrophenyl esters and triglycerides. The optimal pH and temperature for recombinant AfeH were 9.0 and 50°C, respectively; the enzyme was activated by Co(2+) and inhibited by Ca(2+), Zn(2+), Ba(2+). AfeH was inhibited strongly by phenylmethylsulfonyl and SDS and weakly by dimethyl sulfoxide.
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Affiliation(s)
- Weiliang Dong
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China
| | - Sheng Jiang
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China
| | - Kaiwen Shi
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China
| | - Fei Wang
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China; College of Bioscience and Bioengineering, Jiangxi Agriculture University, 330045 Nanchang, China
| | - Shuhuan Li
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China
| | - Jie Zhou
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China
| | - Fei Huang
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China
| | - Yicheng Wang
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China
| | - Yuxiao Zheng
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China
| | - Ying Hou
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China; College of Food and Bioengineering, Henan University of Science and Technology, 471003 Luoyang, China
| | - Yan Huang
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China
| | - Zhongli Cui
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, 210095 Nanjing, China.
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41
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Purification, cloning, expression, and biochemical characterization of a monofunctional catalase, KatP, from Pigmentiphaga sp. DL-8. Protein Expr Purif 2015; 108:54-61. [PMID: 25665507 DOI: 10.1016/j.pep.2015.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 11/20/2022]
Abstract
Catalases are essential components of the cellular equipment used to cope with oxidative stress. The monofunctional catalase KatP was purified from Pigmentiphaga sp. using ammonium sulfate precipitation (ASP), diethylaminoethyl ion exchange chromatography (IEC), and hydrophobic interaction chromatography (HIC). The purified catalase formed polymer with an estimated monomer molecular mass of 54kDa, which were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and zymogram analysis. KatP exhibited a specific catalytic activity of 73,000U/mg, which was higher than that of catalase-1 of Comamonas terrigena N3H (55,900U/mg). Seven short tryptic fragments of this catalase were obtained by electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-Q-TOF MS/MS), and the gene, katP, was cloned by PCR amplification and overexpressed in Escherichia coli BL21 (DE3). Based on the complete amino acid sequence, KatP was identified as a clade 3 monofunctional catalase. The specific activities of recombinant KatP for hydrogen peroxide (690,000U/mg) increased 9-fold over that of the parent strain. The Km and Vmax of recombinant KatP were 9.48mM and 81.2mol/minmg, respectively. The optimal pH and temperature for KatP were 7.0 and 37°C, respectively, and the enzyme displayed abroad pH-stable range of 4.0-11.0. The enzyme was inhibited by Zn(2+), Cu(2+), Cr(2+), and Mn(2+), whereas Fe(3+) and Mg(2+) stimulated KatP enzymatic activity. Interestingly, the catalase activity of recombinant KatP displayed high stability under different temperature and pH conditions, suggesting that KatP is a potential candidate for the production of catalase.
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42
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AmyM, a Novel Maltohexaose-Forming α-Amylase from Corallococcus sp. strain EGB. Appl Environ Microbiol 2015; 81:1977-87. [PMID: 25576603 DOI: 10.1128/aem.03934-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel α-amylase, AmyM, was purified from the culture supernatant of Corallococcus sp. strain EGB. AmyM is a maltohexaose-forming exoamylase with an apparent molecular mass of 43 kDa. Based on the results of matrix-assisted laser desorption ionization-time of flight mass spectrometry and peptide mass fingerprinting of AmyM and by comparison to the genome sequence of Corallococcus coralloides DSM 2259, the AmyM gene was identified and cloned into Escherichia coli. amyM encodes a secretory amylase with a predicted signal peptide of 23 amino acid residues, which showed no significant identity with known and functionally verified amylases. amyM was expressed in E. coli BL21(DE3) cells with a hexahistidine tag. The signal peptide efficiently induced the secretion of mature AmyM in E. coli. Recombinant AmyM (rAmyM) was purified by Ni-nitrilotriacetic acid (NTA) affinity chromatography, with a specific activity of up to 14,000 U/mg. rAmyM was optimally active at 50°C in Tris-HCl buffer (50 mM; pH 7.0) and stable at temperatures of <50°C. rAmyM was stable over a wide range of pH values (from pH 5.0 to 10.0) and highly tolerant to high concentrations of salts, detergents, and various organic solvents. Its activity toward starch was independent of calcium ions. The Km and Vmax of recombinant AmyM for soluble starch were 6.61 mg ml(-1) and 44,301.5 μmol min(-1) mg(-1), respectively. End product analysis showed that maltohexaose accounted for 59.4% of the maltooligosaccharides produced. These characteristics indicate that AmyM has great potential in industrial applications.
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43
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Wiesler SC, Weinzierl ROJ. Robotic high-throughput purification of affinity-tagged recombinant proteins. Methods Mol Biol 2015; 1286:97-106. [PMID: 25749949 DOI: 10.1007/978-1-4939-2447-9_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Affinity purification of recombinant proteins has become the method of choice to obtain good quantities and qualities of proteins for a variety of downstream biochemical applications. While manual or FPLC-assisted purification techniques are generally time-consuming and labor-intensive, the advent of high-throughput technologies and liquid handling robotics has simplified and accelerated this process significantly. Additionally, without the human factor as a potential source of error, automated purification protocols allow for the generation of large numbers of proteins simultaneously and under directly comparable conditions. The delivered material is ideal for activity comparisons of different variants of the same protein. Here, we present our strategy for the simultaneous purification of up to 24 affinity-tagged proteins for activity measurements in biochemical assays. The protocol described is suitable for the scale typically required in individual research laboratories.
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Affiliation(s)
- Simone C Wiesler
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London, SW7 2AZ, UK
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44
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Talukder P, Chen S, Liu CT, Baldwin EA, Benkovic SJ, Hecht SM. Tryptophan-based fluorophores for studying protein conformational changes. Bioorg Med Chem 2014; 22:5924-34. [PMID: 25284250 PMCID: PMC4254292 DOI: 10.1016/j.bmc.2014.09.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/03/2014] [Accepted: 09/08/2014] [Indexed: 11/19/2022]
Abstract
With the continuing interest in deciphering the interplay between protein function and conformational changes, small fluorescence probes will be especially useful for tracking changes in the crowded protein interior space. Presently, we describe the potential utility of six unnatural amino acid fluorescence donors structurally related to tryptophan and show how they can be efficiently incorporated into a protein as fluorescence probes. We also examine the various photophysical properties of the new Trp analogues, which are significantly redshifted in their fluorescence spectra relative to tryptophan. In general, the Trp analogues were well tolerated when inserted into Escherichia coli DHFR, and did not perturb enzyme activity, although substitution for Trp22 did result in a diminution in DHFR activity. Further, it was demonstrated that D and E at position 37 formed efficient FRET pairs with acridon-2-ylalanine (Acd) at position 17. The same was also true for a DHFR construct containing E at position 79 and Acd at position 17. Together, these findings demonstrate that these tryptophan analogues can be introduced into DHFR with minimal disruption of function, and that they can be employed for the selective study of targeted conformational changes in proteins, even in the presence of unmodified tryptophans.
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Affiliation(s)
- Poulami Talukder
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - C Tony Liu
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Edwin A Baldwin
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
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45
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Purification of an amide hydrolase DamH from Delftia sp. T3-6 and its gene cloning, expression, and biochemical characterization. Appl Microbiol Biotechnol 2014; 98:7491-9. [DOI: 10.1007/s00253-014-5710-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 03/17/2014] [Indexed: 11/26/2022]
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46
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Kirk WR. Thermodynamics of imidazole-ligand binding to Ni-nitrilotriacetate in solution and covalently attached to agarose beads: Imidazole, his-6 (his-tag) peptide and a new bis-imidazolo-dithiane. Protein Expr Purif 2014; 95:1-7. [DOI: 10.1016/j.pep.2013.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/06/2013] [Accepted: 11/18/2013] [Indexed: 11/30/2022]
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47
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Pina AS, Lowe CR, Roque ACA. Challenges and opportunities in the purification of recombinant tagged proteins. Biotechnol Adv 2014; 32:366-81. [PMID: 24334194 PMCID: PMC7125906 DOI: 10.1016/j.biotechadv.2013.12.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/04/2013] [Accepted: 12/08/2013] [Indexed: 01/05/2023]
Abstract
The purification of recombinant proteins by affinity chromatography is one of the most efficient strategies due to the high recovery yields and purity achieved. However, this is dependent on the availability of specific affinity adsorbents for each particular target protein. The diversity of proteins to be purified augments the complexity and number of specific affinity adsorbents needed, and therefore generic platforms for the purification of recombinant proteins are appealing strategies. This justifies why genetically encoded affinity tags became so popular for recombinant protein purification, as these systems only require specific ligands for the capture of the fusion protein through a pre-defined affinity tag tail. There is a wide range of available affinity pairs "tag-ligand" combining biological or structural affinity ligands with the respective binding tags. This review gives a general overview of the well-established "tag-ligand" systems available for fusion protein purification and also explores current unconventional strategies under development.
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Affiliation(s)
- Ana Sofia Pina
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; IBET-Instituto de Biologia Experimental Tecnológica, Oeiras, Portugal
| | - Christopher R Lowe
- Institute of Biotechnology, Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, CB2 1QT Cambridge, UK
| | - Ana Cecília A Roque
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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48
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Travas-Sejdic J, Aydemir N, Kannan B, Williams DE, Malmström J. Intrinsically conducting polymer nanowires for biosensing. J Mater Chem B 2014; 2:4593-4609. [DOI: 10.1039/c4tb00598h] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The fabrication of conductive polymer nanowires and their sensing of nucleic acids, proteins and pathogens is reviewed in this feature article.
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Affiliation(s)
- J. Travas-Sejdic
- School of Chemical Sciences
- University of Auckland
- Auckland 1142, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology
- Wellington 6140, New Zealand
| | - N. Aydemir
- School of Chemical Sciences
- University of Auckland
- Auckland 1142, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology
- Wellington 6140, New Zealand
| | - B. Kannan
- Revolution Fibres Ltd
- , New Zealand
- School of Chemical Sciences
- University of Auckland
- Auckland 1142, New Zealand
| | - D. E. Williams
- School of Chemical Sciences
- University of Auckland
- Auckland 1142, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology
- Wellington 6140, New Zealand
| | - J. Malmström
- School of Chemical Sciences
- University of Auckland
- Auckland 1142, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology
- Wellington 6140, New Zealand
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49
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Chen S, Fahmi NE, Bhattacharya C, Wang L, Jin Y, Benkovic SJ, Hecht SM. Fluorescent biphenyl derivatives of phenylalanine suitable for protein modification. Biochemistry 2013; 52:8580-9. [PMID: 24152169 PMCID: PMC3875372 DOI: 10.1021/bi401275v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In a recent study, we demonstrated that structurally compact fluorophores incorporated into the side chains of amino acids could be introduced into dihydrofolate reductase from Escherichia coli (ecDHFR) with minimal disruption of protein structure or function, even when the site of incorporation was within a folded region of the protein. The modified proteins could be employed for FRET measurements, providing sensitive monitors of changes in protein conformation. The very favorable results achieved in that study encouraged us to prepare additional fluorescent amino acids of potential utility for studying protein dynamics. Presently, we describe the synthesis and photophysical characterization of four positional isomers of biphenyl-phenylalanine, all of which were found to exhibit potentially useful fluorescent properties. All four phenylalanine derivatives were used to activate suppressor tRNA transcripts and incorporated into multiple positions of ecDHFR. All phenylalanine derivatives were incorporated with good efficiency into position 16 of ecDHFR and afforded modified proteins that consumed NADPH at rates up to about twice the rate measured for wild type. This phenomenon has been noted on a number of occasions previously and shown to be due to an increase in the off-rate of tetrahydrofolate from the enzyme, altering a step that is normally rate limiting. When introduced into sterically accessible position 49, the four phenylalanine derivatives afforded DHFRs having catalytic function comparable to wild type. The four phenylalanine derivatives were also introduced into position 115 of ecDHFR, which is known to be a folded region of the protein less tolerant of structural alteration. As anticipated, significant differences were noted in the catalytic efficiencies of the derived proteins. The ability of two of the sizable biphenyl-phenylalanine derivatives to be accommodated at position 115 with minimal perturbation of DHFR function is attributed to rotational flexibility about the biphenyl bonds.
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Affiliation(s)
- Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Nour Eddine Fahmi
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Chandrabali Bhattacharya
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Lin Wang
- Department of Chemistry, the Pennsylvania State University, University Park, PA 106802, USA
| | - Yuguang Jin
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Stephen J. Benkovic
- Department of Chemistry, the Pennsylvania State University, University Park, PA 106802, USA
| | - Sidney M. Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
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50
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Shoji M, Takahashi E, Hatakeyama D, Iwai Y, Morita Y, Shirayama R, Echigo N, Kido H, Nakamura S, Mashino T, Okutani T, Kuzuhara T. Anti-influenza activity of c60 fullerene derivatives. PLoS One 2013; 8:e66337. [PMID: 23785493 PMCID: PMC3681905 DOI: 10.1371/journal.pone.0066337] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 05/03/2013] [Indexed: 11/24/2022] Open
Abstract
The H1N1 influenza A virus, which originated in swine, caused a global pandemic in 2009, and the highly pathogenic H5N1 avian influenza virus has also caused epidemics in Southeast Asia in recent years. Thus, the threat from influenza A remains a serious global health issue, and novel drugs that target these viruses are highly desirable. Influenza A RNA polymerase consists of the PA, PB1, and PB2 subunits, and the N-terminal domain of the PA subunit demonstrates endonuclease activity. Fullerene (C60) is a unique carbon molecule that forms a sphere. To identify potential new anti-influenza compounds, we screened 12 fullerene derivatives using an in vitro PA endonuclease inhibition assay. We identified 8 fullerene derivatives that inhibited the endonuclease activity of the PA N-terminal domain or full-length PA protein in vitro. We also performed in silico docking simulation analysis of the C60 fullerene and PA endonuclease, which suggested that fullerenes can bind to the active pocket of PA endonuclease. In a cell culture system, we found that several fullerene derivatives inhibit influenza A viral infection and the expression of influenza A nucleoprotein and nonstructural protein 1. These results indicate that fullerene derivatives are possible candidates for the development of novel anti-influenza drugs.
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Affiliation(s)
- Masaki Shoji
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Etsuhisa Takahashi
- Division of Enzyme Chemistry, Institute for Enzyme Research, The University of Tokushima, Tokushima, Japan
| | - Dai Hatakeyama
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Yuma Iwai
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Yuka Morita
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Riku Shirayama
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Noriko Echigo
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Hiroshi Kido
- Division of Enzyme Chemistry, Institute for Enzyme Research, The University of Tokushima, Tokushima, Japan
| | - Shigeo Nakamura
- Department of Chemistry, Nippon Medical School, Nakahara-ku, Kawasaki, Kanagawa, Japan
| | - Tadahiko Mashino
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Keio University, Minato-ku, Tokyo, Japan
| | - Takeshi Okutani
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Takashi Kuzuhara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
- * E-mail:
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