1
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Yuan H, Prabhala SV, Coolbaugh MJ, Stimple SD, Wood DW. Improved self-cleaving precipitation tags for efficient column free bioseparations. Protein Expr Purif 2024; 224:106578. [PMID: 39153561 DOI: 10.1016/j.pep.2024.106578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/31/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
Current biological research requires simple protein bioseparation methods capable of purifying target proteins in a single step with high yields and purities. Conventional affinity tag-based approaches require specific affinity resins and expensive proteolytic enzymes for tag removal. Purification strategies based on self-cleaving aggregating tags have been previously developed to address these problems. However, these methods often utilize C-terminal cleaving contiguous inteins which suffer from premature cleavage, resulting in significant product loss during protein expression. In this work, we evaluate two novel mutants of the Mtu RecA ΔI-CM mini-intein obtained through yeast surface display for improved protein purification. When used with the elastin-like-polypeptide (ELP) precipitation tag, the novel mutants - ΔI-12 and ΔI-29 resulted in significantly higher precursor content, product purity and process yield compared to the original Mtu RecA ΔI-CM mini-intein. Product purities ranging from 68 % to 94 % were obtained in a single step for three model proteins - green fluorescent protein (GFP), maltose binding protein (MBP) and beta-galactosidase (beta-gal). Further, high cleaving efficiency was achieved after 5 h under most conditions. Overall, we have developed improved self-cleaving precipitation tags which can be used for purifying a wide range of proteins cheaply at laboratory scale.
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Affiliation(s)
- Hongyu Yuan
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Sai Vivek Prabhala
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Michael J Coolbaugh
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Samuel D Stimple
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - David W Wood
- William G. Lowrie Department of Chemical and Biomolecular Engineering, Ohio State University, Columbus, OH, 43210, USA.
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2
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Lima AJF, Hajdu KL, Abdo L, Batista-Silva LR, de Oliveira Andrade C, Correia EM, Aragão EAA, Bonamino MH, Lourenzoni MR. In silico and in vivo analysis reveal impact of c-Myc tag in FMC63 scFv-CD19 protein interface and CAR-T cell efficacy. Comput Struct Biotechnol J 2024; 23:2375-2387. [PMID: 38873646 PMCID: PMC11170440 DOI: 10.1016/j.csbj.2024.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024] Open
Abstract
Anti-CD19 CAR-T cell therapy represents a breakthrough in the treatment of B-cell malignancies, and it is expected that this therapy modality will soon cover a range of solid tumors as well. Therefore, a universal cheap and sensitive method to detect CAR expression is of foremost importance. One possibility is the use of epitope tags such as c-Myc, HA or FLAG tags attached to the CAR extracellular domain, however, it is important to determine whether these tags can influence binding of the CAR with its target molecule. Here, we conducted in-silico structural modelling of an FMC63-based anti-CD19 single-chain variable fragment (scFv) with and without a c-Myc peptide tag added to the N-terminus portion and performed molecular dynamics simulation of the scFv with the CD19 target. We show that the c-Myc tag presence in the N-terminus portion does not affect the scFv's structural equilibrium and grants more stability to the scFv. However, intermolecular interaction potential (IIP) analysis reveals that the tag can approximate the complementarity-determining regions (CDRs) present in the scFv and cause steric impediment, potentially disturbing interaction with the CD19 protein. We then tested this possibility with CAR-T cells generated from human donors in a Nalm-6 leukemia model, showing that CAR-T cells with the c-Myc tag have overall worse antitumor activity, which was also observed when the tag was added to the C-terminus position. Ultimately, our results suggest that tag addition is an important aspect of CAR design and can influence CAR-T cell function, therefore its use should be carefully considered.
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Affiliation(s)
- Ana Julia Ferreira Lima
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Oswaldo Cruz Foundation Ceará (Fiocruz-CE), São José, Precabura, 61773-270 Eusébio, Ceará, Brazil
- Federal University of Ceará (UFC), Pici campus (Building 873), 60440-970 Fortaleza, Ceará, Brazil
| | - Karina Lobo Hajdu
- Cell and Gene Therapy Program, Research coordination - Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Luiza Abdo
- Cell and Gene Therapy Program, Research coordination - Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | | | - Clara de Oliveira Andrade
- Cell and Gene Therapy Program, Research coordination - Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Eduardo Mannarino Correia
- Cell and Gene Therapy Program, Research coordination - Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | | | - Martín Hernán Bonamino
- Cell and Gene Therapy Program, Research coordination - Brazilian National Cancer Institute, Rio de Janeiro, Brazil
- Vice - Presidency of Research and Biological Collections (VPPCB), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Marcos Roberto Lourenzoni
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Oswaldo Cruz Foundation Ceará (Fiocruz-CE), São José, Precabura, 61773-270 Eusébio, Ceará, Brazil
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3
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Li X, Kuchinski LM, Park A, Murphy GS, Soto KC, Schuster BS. Enzyme purification and sustained enzyme activity for pharmaceutical biocatalysis by fusion with phase-separating intrinsically disordered protein. Biotechnol Bioeng 2024; 121:3155-3168. [PMID: 38951956 DOI: 10.1002/bit.28787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
In recent decades, biocatalysis has emerged as an important alternative to chemical catalysis in pharmaceutical manufacturing. Biocatalysis is attractive because enzymatic cascades can synthesize complex molecules with incredible selectivity, yield, and in an environmentally benign manner. Enzymes for pharmaceutical biocatalysis are typically used in their unpurified state, since it is time-consuming and cost-prohibitive to purify enzymes using conventional chromatographic processes at scale. However, impurities present in crude enzyme preparations can consume substrate, generate unwanted byproducts, as well as make the isolation of desired products more cumbersome. Hence, a facile, nonchromatographic purification method would greatly benefit pharmaceutical biocatalysis. To address this issue, here we have captured enzymes into membraneless compartments by fusing enzymes with an intrinsically disordered protein region, the RGG domain from LAF-1. The RGG domain can undergo liquid-liquid phase separation, forming liquid condensates triggered by changes in temperature or salt concentration. By centrifuging these liquid condensates, we have successfully purified enzyme-RGG fusions, resulting in significantly enhanced purity compared to cell lysate. Furthermore, we performed enzymatic reactions utilizing purified fusion proteins to assay enzyme activity. Results from the enzyme assays indicate that enzyme-RGG fusions purified by the centrifugation method retain enzymatic activity, with greatly reduced background activity compared to crude enzyme preparations. Our work focused on three different enzymes-a kinase, a phosphorylase, and an ATP-dependent ligase. The kinase and phosphorylase are components of the biocatalytic cascade for manufacturing molnupiravir, and we demonstrated facile co-purification of these two enzymes by co-phase separation. To conclude, enzyme capture by RGG tagging promises to overcome difficulties in bioseparations and biocatalysis for pharmaceutical synthesis.
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Affiliation(s)
- Xinyi Li
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Liam M Kuchinski
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Augene Park
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Grant S Murphy
- Department of Process Research and Development, Process Research and Development, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Karla Camacho Soto
- Department of Process Research and Development, Process Research and Development, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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4
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Wang C, Zheng M, Est C, Lawal R, Liang W, Korasick DA, Rau MJ, Saracco SA, Johnson V, Wang Y, White T, Li W, Zhang J, Gu X, Liu-Gontarek F. Production and characterization of homologous protoporphyrinogen IX oxidase (PPO) proteins: Evidence that small N-terminal amino acid changes do not impact protein function. PLoS One 2024; 19:e0311049. [PMID: 39325813 PMCID: PMC11426539 DOI: 10.1371/journal.pone.0311049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024] Open
Abstract
Transgenic soybean, cotton, and maize tolerant to protoporphyrinogen IX oxidase (PPO)-inhibiting herbicides have been developed by introduction of a bacterial-derived PPO targeted into the chloroplast. PPO is a membrane-associated protein with an intrinsic tendency for aggregation, making expression, purification, and formulation at high concentrations difficult. In this study, transgenic PPO expressed in three crops was demonstrated to exhibit up to a 13 amino acid sequence difference in the N-terminus due to differential processing of the chloroplast transit peptide (CTP). Five PPO protein variants were produced in and purified from E. coli, each displaying equivalent immunoreactivity and functional activity, with values ranging from 193 to 266 nmol min-1 mg-1. Inclusion of an N-terminal 6xHis-tag or differential processing of the CTP peptide does not impact PPO functional activity. Additionally, structural modeling by Alphafold, ESMfold, and Openfold indicates that these short N-terminal extensions are disordered and predicted to not interfere with the mature PPO structure. These results support the view that safety studies on PPO from various crops can be performed from a single representative variant. Herein, we report a novel and robust method for large-scale production of PPO, enabling rapid production of more than 200 g of highly active PPO protein at 99% purity and low endotoxin contamination. We also present a formulation that allows for concentration of active PPO to > 75 mg/mL in a buffer suitable for mammalian toxicity studies.
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Affiliation(s)
- Cunxi Wang
- Regulatory Science, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Meiying Zheng
- Regulatory Science, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Chandler Est
- Regulatory Science, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Remi Lawal
- Regulatory Science, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Wenguang Liang
- Plant Biotechnology, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - David A. Korasick
- Small Molecules, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Michael J. Rau
- Plant Biotechnology, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Scott A. Saracco
- Regulatory Science, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Virginia Johnson
- Regulatory Science, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Yanfei Wang
- Regulatory Science, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Tommi White
- Plant Biotechnology, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Wenze Li
- Regulatory Science, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Jun Zhang
- Regulatory Science, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Xin Gu
- Regulatory Science, Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Flora Liu-Gontarek
- Regulatory Science, Bayer Crop Science, Chesterfield, Missouri, United States of America
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5
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Seo Y, Zhou A, Nguyen TH, Wei N. Yeast Surface-Displayed Quenchbody as a Novel Whole-Cell Biosensor for One-Step Detection of Influenza A (H1N1) Virus. ACS Synth Biol 2024; 13:2926-2937. [PMID: 39256183 DOI: 10.1021/acssynbio.4c00317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Timely surveillance of airborne pathogens is essential to preventing the spread of infectious diseases and safeguard human health. Methods for sensitive, efficient, and cost-effective detection of airborne viruses are needed. With advances in synthetic biology, whole-cell biosensors have emerged as promising platforms for environmental monitoring and medical diagnostics. However, the current design paradigm of whole-cell biosensors is mostly based on intracellular detection of analytes that can transport across the cell membrane, which presents a critical challenge for viral pathogens and large biomolecules. To address this challenge, we developed a new type of whole-cell biosensor by expressing and displaying VHH-based quenchbody (Q-body) on the surface of the yeast Saccharomyces cerevisiae for simple one-step detection of influenza A (H1N1) virus. Seventeen VHH antibody fragments targeting the hemagglutinin protein H1N1-HA were displayed on the yeast cells and screened for the H1N1-HA binding affinity. The functionally displayed VHHs were selected to create surface-displayed Q-body biosensors. The surface-displayed Q-body exhibiting the highest quenching and dequenching efficiency was identified. The biosensor quantitatively detected H1N1-HA in a range from 0.5 to 16 μg/mL, with a half-maximal concentration of 2.60 μg/mL. The biosensor exhibited high specificity for H1N1-HA over other hemagglutinin proteins from various influenza A virus subtypes. Moreover, the biosensor succeeded in detecting the H1N1 virus at concentrations from 2.4 × 104 to 1.5 × 107 PFU/mL. The results from this study demonstrated a new whole-cell biosensor design that circumvents the need for transport of analytes into biosensor cells, enabling efficient detection of the target virus particles.
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Affiliation(s)
- Yoonjoo Seo
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, Urbana, Illinois 61801, United States
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, Urbana, Illinois 61801, United States
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, Urbana, Illinois 61801, United States
| | - Na Wei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, Urbana, Illinois 61801, United States
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6
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Bowlin MQ, Lieber AD, Long AR, Gray MJ. C-terminal Poly-histidine Tags Alter Escherichia coli Polyphosphate Kinase Activity and Susceptibility to Inhibition. J Mol Biol 2024; 436:168651. [PMID: 38866092 PMCID: PMC11297678 DOI: 10.1016/j.jmb.2024.168651] [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: 02/21/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
In Escherichia coli, many environmental stressors trigger polyphosphate (polyP) synthesis by polyphosphate kinase (PPK1), including heat, nutrient restriction, toxic compounds, and osmotic imbalances. PPK1 is essential for virulence in many pathogens and has been the target of multiple screens for small molecule inhibitors that might serve as new anti-virulence drugs. However, the mechanisms by which PPK1 activity and polyP synthesis are regulated are poorly understood. Our previous attempts to uncover PPK1 regulatory elements resulted in the discovery of PPK1* mutants, which accumulate more polyP in vivo, but do not produce more in vitro. In attempting to further characterize these mutant enzymes, we discovered that the most commonly-used PPK1 purification method - Ni-affinity chromatography using a C-terminal poly-histidine tag - altered intrinsic aspects of the PPK1 enzyme, including specific activity, oligomeric state, and kinetic values. We developed an alternative purification strategy using a C-terminal C-tag which did not have these effects. Using this strategy, we were able to demonstrate major differences in the in vitro response of PPK1 to 5-aminosalicylic acid, a known PPK1 inhibitor, and observed several key differences between the wild-type and PPK1* enzymes, including changes in oligomeric distribution, increased enzymatic activity, and increased resistance to both product (ADP) and substrate (ATP) inhibition, that help to explain their in vivo effects. Importantly, our results indicate that the C-terminal poly-histidine tag is inappropriate for purification of PPK1, and that any in vitro studies or inhibitor screens performed with such tags need to be reconsidered in that light.
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Affiliation(s)
- Marvin Q Bowlin
- Department of Microbiology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Avery D Lieber
- Department of Microbiology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Abagail R Long
- Department of Microbiology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Michael J Gray
- Department of Microbiology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA.
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7
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Sun JW, Thomas JS, Monkovic JM, Gibson H, Nagapurkar A, Frezzo JA, Katyal P, Punia K, Mahmoudinobar F, Renfrew PD, Montclare JK. Supercharged coiled-coil protein with N-terminal decahistidine tag boosts siRNA complexation and delivery efficiency of a lipoproteoplex. J Pept Sci 2024; 30:e3594. [PMID: 38499991 DOI: 10.1002/psc.3594] [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: 11/30/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
Short interfering RNA (siRNA) therapeutics have soared in popularity due to their highly selective and potent targeting of faulty genes, providing a non-palliative approach to address diseases. Despite their potential, effective transfection of siRNA into cells requires the assistance of an accompanying vector. Vectors constructed from non-viral materials, while offering safer and non-cytotoxic profiles, often grapple with lackluster loading and delivery efficiencies, necessitating substantial milligram quantities of expensive siRNA to confer the desired downstream effects. We detail the recombinant synthesis of a diverse series of coiled-coil supercharged protein (CSP) biomaterials systematically designed to investigate the impact of two arginine point mutations (Q39R and N61R) and decahistidine tags on liposomal siRNA delivery. The most efficacious variant, N8, exhibits a twofold increase in its affinity to siRNA and achieves a twofold enhancement in transfection activity with minimal cytotoxicity in vitro. Subsequent analysis unveils the destabilizing effect of the Q39R and N61R supercharging mutations and the incorporation of C-terminal decahistidine tags on α-helical secondary structure. Cross-correlational regression analyses reveal that the amount of helical character in these mutants is key in N8's enhanced siRNA complexation and downstream delivery efficiency.
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Affiliation(s)
- Jonathan W Sun
- Department of Chemistry, New York University, New York, New York, USA
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Joseph S Thomas
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Julia M Monkovic
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Halle Gibson
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Akash Nagapurkar
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Joseph A Frezzo
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Kamia Punia
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Farbod Mahmoudinobar
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Jin Kim Montclare
- Department of Chemistry, New York University, New York, New York, USA
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Department of Radiology, NYU Grossman School of Medicine, New York, New York, USA
- Department of Biomaterials, NYU College of Dentistry, New York, New York, USA
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8
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Doğru EK, Sakallı T, Liu G, Sayers Z, Surmeli NB. Small angle X-ray scattering analysis of thermophilic cytochrome P450 CYP119 and the effects of the N-terminal histidine tag. Int J Biol Macromol 2024; 265:131026. [PMID: 38522710 DOI: 10.1016/j.ijbiomac.2024.131026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Combining size exclusion chromatography-small angle X-ray scattering (SEC-SAXS) and molecular dynamics (MD) analysis is a promising approach to investigate protein behavior in solution, particularly for understanding conformational changes due to substrate binding in cytochrome P450s (CYPs). This study investigates conformational changes in CYP119, a thermophilic CYP from Sulfolobus acidocaldarius that exhibits structural flexibility similar to mammalian CYPs. Although the crystal structure of ligand-free (open state) and ligand-bound (closed state) forms of CYP119 is known, the overall structure of the enzyme in solution has not been explored until now. It was found that theoretical scattering profiles from the crystal structures of CYP119 did not align with the SAXS data, but conformers from MD simulations, particularly starting from the open state (46 % of all frames), agreed well. Interestingly, a small percentage of closed-state conformers also fit the data (9 %), suggesting ligand-free CYP119 samples ligand-bound conformations. Ab initio SAXS models for N-His tagged CYP119 revealed a tail-like unfolded structure impacting protein flexibility, which was confirmed by in silico modeling. SEC-SAXS analysis of N-His CYP119 indicated pentameric structures in addition to monomers in solution, affecting the stability and activity of the enzyme. This study adds insights into the conformational dynamics of CYP119 in solution.
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Affiliation(s)
- Ekin Kestevur Doğru
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye
| | - Tuğçe Sakallı
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye
| | - Goksin Liu
- Sabancı University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla 34956, Istanbul, Türkiye
| | - Zehra Sayers
- Sabancı University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla 34956, Istanbul, Türkiye
| | - Nur Basak Surmeli
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye.
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9
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Tarabarova A, Lopukhov A, Fedorov AN, Yurkova MS. Novel His-tag Variants for Insertion Inside Polypeptide Chain. ACS OMEGA 2024; 9:858-865. [PMID: 38222536 PMCID: PMC10785306 DOI: 10.1021/acsomega.3c06682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 01/16/2024]
Abstract
His-tags are protein affinity tags ubiquitously used due to their convenience and effectiveness. However, in some individual cases, the attachment of His-tags to a protein's N- or C-termini resulted in impairment of the protein's structure or function, which led to attempts to include His-tags inside of polypeptide chains. In this work, we describe newly designed internal His-tags, where two triplets of histidine residues are separated by glycine residues to avoid steric hindrances and consequently minimize their impact on the protein structure. The applicability of these His-tags was tested with eGFP, a multifaceted reference protein, and GrAD207, a modified apical domain of GroEL chaperone, designed to stabilize in soluble form initially insoluble proteins. Both proteins are used as fusion partners for different purposes, and providing them with His-tags introduced into their polypeptide chains should conveniently broaden their functionality without involving the termini. We conclude that the insertable tags may be adjusted for the purification of proteins belonging to different structural classes.
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Affiliation(s)
- Anastasiia
G. Tarabarova
- A
N Bach Institute of Biochemistry of the Russian Academy of Sciences, Leninskii prosp 33/2, Moscow 119071, Russian Federation
| | - Anton Lopukhov
- Chemistry
Department, Lomonosov Moscow State University, GSP-1, Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Alexey N. Fedorov
- FSI
Federal Research Centre Fundamentals of Biotechnology of the Russian
Academy of Sciences, Leninskii prosp 33/2, Moscow 119071, Russian Federation
| | - Maria S. Yurkova
- A
N Bach Institute of Biochemistry of the Russian Academy of Sciences, Leninskii prosp 33/2, Moscow 119071, Russian Federation
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10
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Jeje O, Pandian R, Sayed Y, Achilonu I. Obtaining high yield recombinant Enterococcus faecium nicotinate nucleotide adenylyltransferase for X-ray crystallography and biophysical studies. Int J Biol Macromol 2023; 250:126066. [PMID: 37544558 DOI: 10.1016/j.ijbiomac.2023.126066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/28/2023] [Accepted: 07/28/2023] [Indexed: 08/08/2023]
Abstract
Nicotinate nucleotide adenylyltransferase (NNAT) has been a significant research focus on druggable targets, given its indispensability in the biosynthesis of NAD+, which is crucial to the survival of bacterial pathogens. However, no information is available on the structure-function of Enterococcus faecium NNAT (EfNNAT). This study established the expression and purification protocol for obtaining a high-yield recombinant EfNNAT using the E. coli expression system and a single-step IMAC purification method. Approximately 101 mg of EfNNAT was obtained per 7.8 g of wet E. coli cells, estimated to be over 98 % pure. We further characterized the biophysical structure and determined the three-dimensional structure of the EfNNAT. Biophysical studies revealed a dimeric protein with a higher α-helical composition. The highly stable protein crystalizes in multiple conditions, yielding high-quality crystals diffracting between 1.78 and 2.80 Å. Two high-resolution crystal structures of EfNNAT in its native and adenine-bound forms were determined at 1.90 Å and 1.82 Å, respectively. The X-ray structures of the EfNNAT revealed the presence of phosphate and sulfate ions occupying and interacting with conserved amino acid residues within the putative substrate binding site, hence providing insight into the probable substrate preference of EfNNAT and, consequently, why EfNNAT may not prefer β-nicotinamide mononucleotide as a substrate. With the accessibility to high-resolution structures of EfNNAT, further structural evaluation and drug-based screening can be achieved. Hence, we anticipate that this study will provide the basis for the discovery of structure-based inhibitors against this enzyme.
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Affiliation(s)
- Olamide Jeje
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa.
| | - Ramesh Pandian
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa.
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa.
| | - Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa.
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11
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Wang K, Huai S, Tan Z, Ngea GLN, Godana EA, Shi J, Yang Q, Zhang X, Zhao L, Zhang H. A First Expression, Purification and Characterization of Endo-β-1,3-Glucanase from Penicillium expansum. J Fungi (Basel) 2023; 9:961. [PMID: 37888217 PMCID: PMC10608044 DOI: 10.3390/jof9100961] [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: 08/26/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
β-1,3-glucanase plays an important role in the biodegradation, reconstruction, and development of β-1,3-glucan. An endo-β-1,3-glucanase which was encoded by PeBgl1 was expressed, purified and characterized from Penicillium expansum for the first time. The PeBgl1 gene was amplified and transformed into the competent cells of E. coli Rosetta strain with the help of the pET-30a cloning vector. The recombinant protein PeBgl1 was expressed successfully at the induction conditions of 0.8 mmol/L IPTG at 16 °C for 16 h and then was purified by nickel ion affinity chromatography. The optimum reaction temperature of PeBgl1 was 55 °C and it had maximal activity at pH 6.0 according to the enzymatic analysis. Na2HPO4-NaH2PO4 buffer (pH 6.0) and NaCl have inhibitory and enhancing effects on the enzyme activities, respectively. SDS, TritonX-100 and some metal ions (Mg2+, Ca2+, Ba2+, Cu2+, and Zn2+) have an inhibitory effect on the enzyme activity. The results showed that PeBgl1 protein has good enzyme activity at 50-60 °C and at pH 5.0-9.0, and it is not a metal dependent enzyme, which makes it robust for storage and transportation, ultimately holding great promise in green biotechnology and biorefining.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (K.W.); (S.H.); (Z.T.); (G.L.N.N.); (E.A.G.); (J.S.); (Q.Y.); (X.Z.); (L.Z.)
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12
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Antos-Krzeminska N, Kicinska A, Nowak W, Jarmuszkiewicz W. Acanthamoeba castellanii Uncoupling Protein: A Complete Sequence, Activity, and Role in Response to Oxidative Stress. Int J Mol Sci 2023; 24:12501. [PMID: 37569876 PMCID: PMC10419851 DOI: 10.3390/ijms241512501] [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: 06/26/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Uncoupling proteins (UCPs) are mitochondrial inner membrane transporters that mediate free-fatty-acid-induced, purine-nucleotide-inhibited proton leak into the mitochondrial matrix, thereby uncoupling respiratory substrate oxidation from ATP synthesis. The aim of this study was to provide functional evidence that the putative Acucp gene of the free-living protozoan amoeba, A. castellanii, encodes the mitochondrial protein with uncoupling activity characteristic of UCPs and to investigate its role during oxidative stress. We report the sequencing and cloning of a complete Acucp coding sequence, its phylogenetic analysis, and the heterologous expression of AcUCP in the S. cerevisiae strain InvSc1. Measurements of mitochondrial respiratory activity and membrane potential indicate that the heterologous expression of AcUCP causes AcUCP-mediated uncoupling activity. In addition, in a model of oxidative stress with increased reactive oxygen species levels (superoxide dismutase 1 knockout yeasts), AcUCP expression strongly promotes cell survival and growth. The level of superoxide anion radicals is greatly reduced in the ΔSOD1 strain expressing AcUCP. These results suggest that AcUCP targeted to yeast mitochondria causes uncoupling and may act as an antioxidant system. Phylogenetic analysis shows that the A. castellanii UCP diverges very early from other UCPs, but clearly locates within the UCP subfamily rather than among other mitochondrial anion carrier proteins.
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Affiliation(s)
- Nina Antos-Krzeminska
- Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (A.K.); (W.J.)
| | - Anna Kicinska
- Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (A.K.); (W.J.)
| | - Witold Nowak
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland;
| | - Wieslawa Jarmuszkiewicz
- Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (A.K.); (W.J.)
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13
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Tsimbalyuk S, Shornikov A, Srivastava P, Le VTB, Warren I, Khandokar YB, Kuhn ML, Forwood JK. Structural and Kinetic Characterization of the SpeG Spermidine/Spermine N-acetyltransferase from Methicillin-Resistant Staphylococcus aureus USA300. Cells 2023; 12:1829. [PMID: 37508494 PMCID: PMC10378331 DOI: 10.3390/cells12141829] [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: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Polyamines are simple yet critical molecules with diverse roles in numerous pathogenic and non-pathogenic organisms. Regulating polyamine concentrations affects the transcription and translation of genes and proteins important for cell growth, stress, and toxicity. One way polyamine concentrations are maintained within the cell is via spermidine/spermine N-acetyltransferases (SSATs) that acetylate intracellular polyamines so they can be exported. The bacterial SpeG enzyme is an SSAT that exhibits a unique dodecameric structure and allosteric site compared to other SSATs that have been previously characterized. While its overall 3D structure is conserved, its presence and role in different bacterial pathogens are inconsistent. For example, not all bacteria have speG encoded in their genomes; in some bacteria, the speG gene is present but has become silenced, and in other bacteria, it has been acquired on mobile genetic elements. The latter is the case for methicillin-resistant Staphylococcus aureus (MRSA) USA300, where it appears to aid pathogenesis. To gain a greater understanding of the structure/function relationship of SpeG from the MRSA USA300 strain (SaSpeG), we determined its X-ray crystal structure in the presence and absence of spermine. Additionally, we showed the oligomeric state of SaSpeG is dynamic, and its homogeneity is affected by polyamines and AcCoA. Enzyme kinetic assays showed that pre-incubation with polyamines significantly affected the positive cooperativity toward spermine and spermidine and the catalytic efficiency of the enzyme. Furthermore, we showed bacterial SpeG enzymes do not have equivalent capabilities to acetylate aminopropyl versus aminbutyl ends of spermidine. Overall, this study provides new insight that will assist in understanding the SpeG enzyme and its role in pathogenic and non-pathogenic bacteria at a molecular level.
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Affiliation(s)
- Sofiya Tsimbalyuk
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| | - Aleksander Shornikov
- Deparment of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Parul Srivastava
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| | - Van Thi Bich Le
- Deparment of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Imani Warren
- Deparment of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Yogesh B Khandokar
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| | - Misty L Kuhn
- Deparment of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
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14
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Bijak V, Szczygiel M, Lenkiewicz J, Gucwa M, Cooper DR, Murzyn K, Minor W. The current role and evolution of X-ray crystallography in drug discovery and development. Expert Opin Drug Discov 2023; 18:1221-1230. [PMID: 37592849 PMCID: PMC10620067 DOI: 10.1080/17460441.2023.2246881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
INTRODUCTION Macromolecular X-ray crystallography and cryo-EM are currently the primary techniques used to determine the three-dimensional structures of proteins, nucleic acids, and viruses. Structural information has been critical to drug discovery and structural bioinformatics. The integration of artificial intelligence (AI) into X-ray crystallography has shown great promise in automating and accelerating the analysis of complex structural data, further improving the efficiency and accuracy of structure determination. AREAS COVERED This review explores the relationship between X-ray crystallography and other modern structural determination methods. It examines the integration of data acquired from diverse biochemical and biophysical techniques with those derived from structural biology. Additionally, the paper offers insights into the influence of AI on X-ray crystallography, emphasizing how integrating AI with experimental approaches can revolutionize our comprehension of biological processes and interactions. EXPERT OPINION Investing in science is crucially emphasized due to its significant role in drug discovery and advancements in healthcare. X-ray crystallography remains an essential source of structural biology data for drug discovery. Recent advances in biochemical, spectroscopic, and bioinformatic methods, along with the integration of AI techniques, hold the potential to revolutionize drug discovery when effectively combined with robust data management practices.
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Affiliation(s)
- Vanessa Bijak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Michal Szczygiel
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Joanna Lenkiewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
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15
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Ghasemian K, Broer I, Schön J, Kolp N, Killisch R, Mikkat S, Huckauf J. Immunogenicity and contraceptive efficacy of plant-produced putative mouse-specific contraceptive peptides. FRONTIERS IN PLANT SCIENCE 2023; 14:1191640. [PMID: 37448868 PMCID: PMC10337994 DOI: 10.3389/fpls.2023.1191640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023]
Abstract
Rodent population control through contraception requires species-specific oral contraceptive vaccines. Therefore, in this study, we produced putative mouse-specific contraceptive peptides, mZP2 (from oocyte) and mIzumo1 (from sperm), in plants using Agrobacterium-mediated transient expression. Peptides were produced separately in Nicotiana benthamiana using constructs encoding antigens containing three copies of each peptide. We also determined the immunogenicity and contraceptive effects of the plant-produced antigens in female BALB/c mice. Mice immunized subcutaneously with a relatively low amount of antigen (5 µg/dose of each peptide in a mixture) showed systemic immune responses against mZP2-3 and mIzumo1-3 antigens. Moreover, the mean litter size of mice treated with the plant-produced antigens was reduced by 39% compared to that of the control mice. Notably, there was a significant negative correlation between the number of pups born and individual antibody levels against both antigens. Immunofluorescence assays demonstrated the binding of induced antibodies to the oocytes of BALB/c and wild-type mice in vivo and in vitro, respectively. Our study demonstrate the feasibility of producing small contraceptive peptides in plants that can be further used to develop oral contraceptive vaccines against mouse populations.
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Affiliation(s)
- Khadijeh Ghasemian
- Department of Agrobiotechnology and Risk Assessment for Bio and Gene Technology, Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Inge Broer
- Department of Agrobiotechnology and Risk Assessment for Bio and Gene Technology, Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Jennifer Schön
- Department of Reproduction Biology, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Nadine Kolp
- BIOSERV, Analytik und Medizinprodukte GmbH, Rostock, Germany
| | | | - Stefan Mikkat
- Core Facility Proteome Analysis, Rostock University Medical Center, Rostock, Germany
| | - Jana Huckauf
- Department of Agrobiotechnology and Risk Assessment for Bio and Gene Technology, Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
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16
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Calil Brondani J, Afful D, Nune H, Hart J, Cook S, Momany C. Overproduction, purification, and transcriptional activity of recombinant Acinetobacter baylyi ADP1 RNA polymerase holoenzyme. Protein Expr Purif 2023; 206:106254. [PMID: 36804950 DOI: 10.1016/j.pep.2023.106254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
Acinetobacter baylyi is an interesting model organism to investigate bacterial metabolism due to its vast repertoire of metabolic enzymes and ease of genetic manipulation. However, the study of gene expression in vitro is dependent on the availability of its RNA polymerase (RNAp), an essential enzyme in transcription. In this work, we developed a convenient method of producing the recombinant A. baylyi ADP1 RNA polymerase holoenzyme (RNApholo) in E. coli that yields 22 mg of a >96% purity protein from a 1-liter shake flask culture. We further characterized the A. baylyi ADP1 RNApholo kinetic profile using T7 Phage DNA as template and demonstrated that it is a highly transcriptionally active enzyme with an elongation rate of 24 nt/s and a termination efficiency of 94%. Moreover, the A. baylyi ADP1 RNApholo has a substantial sequence identity (∼95%) with the RNApholo from the human pathogen Acinetobacter baumannii. This protein can serve as a source of material for structural and biological studies towards advancing our understanding of genome expression and regulation in Acinetobacter species.
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Affiliation(s)
- Juliana Calil Brondani
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Derrick Afful
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Hanna Nune
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Jesse Hart
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Shelby Cook
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Cory Momany
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA.
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17
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Zhang Y, Zhao L, Wang Q, Zhang Z, Ren X, Yang X, Zeng S, Lv L, Zhao L, Su S, Chen X, Fu B. A novel epitope tag from rabies virus has versatile in vitro applications. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12546-9. [PMID: 37166480 DOI: 10.1007/s00253-023-12546-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023]
Abstract
Fusion tag technology is an important tool for rapid separation, purification, and characterization of proteins. Combined with monoclonal antibodies, tag epitope systems can be rapidly adapted to many assay systems. A monoclonal antibody that reacts with the matrix protein of the rabies virus CVS-11 strain was reported. The epitope (termed M) targeted by this antibody contains only six amino acids. We examine whether this specific sequence epitope can be applied as a protein tag. We show ectopic expression of M-tagged proteins has little impact on cell viability or major signaling pathways. The M tag system can be used for western blotting, immunoprecipitation, immunofluorescence staining, and flow cytometry assays. The results indicate the specificity, sensitivity, and versatility of this novel epitope tag system are comparable to the widely used FLAG tag system, providing researchers with an additional tool for molecular analysis. KEY POINTS: • A short peptide (Pro Pro Tyr Asp Asp Asp) can be applied as a new tag. • The new epitope-tagging fusion system has no effect on the main cellular signaling pathway. • The epitope-tagging fusion system can be widely used for western blotting, immunoprecipitation, immunofluorescence, flow cytometry, etc.
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Affiliation(s)
- Yuelan Zhang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Lin Zhao
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Qinyang Wang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Zhuyou Zhang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Xiaoyan Ren
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Xue Yang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Shaowei Zeng
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Linyue Lv
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural Universitygrid, 35155.37, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoqi Chen
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Bishi Fu
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China.
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18
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Bijak V, Gucwa M, Lenkiewicz J, Murzyn K, Cooper DR, Minor W. Continuous Validation Across Macromolecular Structure Determination Process. NIHON KESSHO GAKKAI SHI 2023; 65:10-16. [PMID: 37416056 PMCID: PMC10321142 DOI: 10.5940/jcrsj.65.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The overall quality of the experimentally determined structures contained in the PDB is exceptionally high, mainly due to the continuous improvement of model building and structural validation programs. Improving reproducibility on a large scale requires expanding the concept of validation in structural biology and all other disciplines to include a broader framework that encompasses the entire project. A successful approach to science requires diligent attention to detail and a focus on the future. An earnest commitment to data availability and reuse is essential for scientific progress, be that by human minds or artificial intelligence.
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Affiliation(s)
- Vanessa Bijak
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University
| | - Joanna Lenkiewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University
| | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia
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19
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Bubić A, Narczyk M, Petek A, Wojtyś MI, Maksymiuk W, Wielgus-Kutrowska B, Winiewska-Szajewska M, Pavkov-Keller T, Bertoša B, Štefanić Z, Luić M, Bzowska A, Leščić Ašler I. The pursuit of new alternative ways to eradicate Helicobacter pylori continues: Detailed characterization of interactions in the adenylosuccinate synthetase active site. Int J Biol Macromol 2023; 226:37-50. [PMID: 36470440 DOI: 10.1016/j.ijbiomac.2022.12.001] [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: 06/15/2022] [Revised: 11/11/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Purine nucleotide synthesis is realised only through the salvage pathway in pathogenic bacterium Helicobacter pylori. Therefore, the enzymes of this pathway, among them also the adenylosuccinate synthetase (AdSS), present potential new drug targets. This paper describes characterization of His6-tagged AdSS from H. pylori. Thorough analysis of 3D-structures of fully ligated AdSS (in a complex with guanosine diphosphate, 6-phosphoryl-inosine monophosphate, hadacidin and Mg2+) and AdSS in a complex with inosine monophosphate (IMP) only, enabled identification of active site interactions crucial for ligand binding and enzyme activity. Combination of experimental and molecular dynamics (MD) simulations data, particularly emphasized the importance of hydrogen bond Arg135-IMP for enzyme dimerization and active site formation. The synergistic effect of substrates (IMP and guanosine triphosphate) binding was suggested by MD simulations. Several flexible elements of the structure (loops) are stabilized by the presence of IMP alone, however loops comprising residues 287-293 and 40-44 occupy different positions in two solved H. pylori AdSS structures. MD simulations discovered the hydrogen bond network that stabilizes the closed conformation of the residues 40-50 loop, only in the presence of IMP. Presented findings provide a solid basis for the design of new AdSS inhibitors as potential drugs against H. pylori.
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Affiliation(s)
- Ante Bubić
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Marta Narczyk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Ana Petek
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10000 Zagreb, Croatia
| | - Marta Ilona Wojtyś
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Weronika Maksymiuk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Maria Winiewska-Szajewska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/III, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, Graz 8010, Austria; BioHealth Field of Excellence, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10000 Zagreb, Croatia
| | - Zoran Štefanić
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Marija Luić
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Ivana Leščić Ašler
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
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20
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Gucwa M, Lenkiewicz J, Zheng H, Cymborowski M, Cooper DR, Murzyn K, Minor W. CMM-An enhanced platform for interactive validation of metal binding sites. Protein Sci 2023; 32:e4525. [PMID: 36464767 PMCID: PMC9794025 DOI: 10.1002/pro.4525] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
Metal ions bound to macromolecules play an integral role in many cellular processes. They can directly participate in catalytic mechanisms or be essential for the structural integrity of proteins and nucleic acids. However, their unique nature in macromolecules can make them difficult to model and refine, and a substantial portion of metal ions in the PDB are misidentified or poorly refined. CheckMyMetal (CMM) is a validation tool that has gained widespread acceptance as an essential tool for researchers working on metal-macromolecule complexes. CMM can be used during structure determination or to validate metal binding sites in structural models within the PDB. The functionalities of CMM have recently been greatly enhanced and provide researchers with additional information that can guide modeling decisions. The new version of CMM shows metals in the context of electron density maps and allows for on-the-fly refinement of metal binding sites. The improvements should increase the reproducibility of biomedical research. The web server is available at https://cmm.minorlab.org.
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Affiliation(s)
- Michal Gucwa
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA,Department of Computational Biophysics and BioinformaticsJagiellonian UniversityKrakowPoland
| | - Joanna Lenkiewicz
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Heping Zheng
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA,Present address:
Hunan University College of BiologyBioinformatics CenterHunanPeople's Republic of China
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - David R. Cooper
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Krzysztof Murzyn
- Department of Computational Biophysics and BioinformaticsJagiellonian UniversityKrakowPoland
| | - Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
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21
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A novel broad spectrum venom metalloproteinase autoinhibitor in the rattlesnake Crotalus atrox evolved via a shift in paralog function. Proc Natl Acad Sci U S A 2022; 119:e2214880119. [PMID: 36508672 PMCID: PMC9907073 DOI: 10.1073/pnas.2214880119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The complexity of snake venom composition reflects adaptation to the diversity of prey and may be driven at times by a coevolutionary arms race between snakes and venom-resistant prey. However, many snakes are also resistant to their own venom due to serum-borne inhibitors of venom toxins, which raises the question of how snake autoinhibitors maintain their efficacy as venom proteins evolve. To investigate this potential three-way arms race among venom, prey, and autoinhibitors, we have identified and traced the evolutionary origin of serum inhibitors of snake venom metalloproteinases (SVMPs) in the Western Diamondback rattlesnake Crotalus atrox which possesses the largest known battery of SVMP genes among crotalids examined. We found that C. atrox expresses five members of a Fetuin A-related metalloproteinase inhibitor family but that one family member, FETUA-3, is the major SVMP inhibitor that binds to approximately 20 different C. atrox SVMPs and inhibits activities of all three SVMP classes. We show that the fetua-3 gene arose deep within crotalid evolution before the origin of New World species but, surprisingly, fetua-3 belongs to a different paralog group than previously identified SVMP inhibitors in Asian and South American crotalids. Conversely, the C. atrox FETUA-2 ortholog of previously characterized crotalid SVMP inhibitors shows limited activity against C. atrox SVMPs. These results reveal that there has been a functional evolutionary shift in the major SVMP inhibitor in the C. atrox lineage as the SVMP family expanded and diversified in the Crotalus lineage. This broad-spectrum inhibitor may be of potential therapeutic interest.
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22
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Bromberg R, Cai K, Guo Y, Plymire D, Emde T, Puzio M, Borek D, Otwinowski Z. The His-tag as a decoy modulating preferred orientation in cryoEM. Front Mol Biosci 2022; 9:912072. [PMID: 36325274 PMCID: PMC9619061 DOI: 10.3389/fmolb.2022.912072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/19/2022] [Indexed: 12/02/2022] Open
Abstract
The His-tag is a widely used affinity tag that facilitates purification by means of affinity chromatography of recombinant proteins for functional and structural studies. We show here that His-tag presence affects how coproheme decarboxylase interacts with the air-water interface during grid preparation for cryoEM. Depending on His-tag presence or absence, we observe significant changes in patterns of preferred orientation. Our analysis of particle orientations suggests that His-tag presence can mask the hydrophobic and hydrophilic patches on a protein’s surface that mediate the interactions with the air-water interface, while the hydrophobic linker between a His-tag and the coding sequence of the protein may enhance other interactions with the air-water interface. Our observations suggest that tagging, including rational design of the linkers between an affinity tag and a protein of interest, offer a promising approach to modulating interactions with the air-water interface.
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Affiliation(s)
- Raquel Bromberg
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Ligo Analytics, Dallas, TX, United States
| | - Kai Cai
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yirui Guo
- Ligo Analytics, Dallas, TX, United States
| | - Daniel Plymire
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Ligo Analytics, Dallas, TX, United States
| | - Tabitha Emde
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Maciej Puzio
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Dominika Borek
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Center for Structural Genomics of Infectious Diseases, Dallas, TX, United States
- *Correspondence: Dominika Borek, ; Zbyszek Otwinowski,
| | - Zbyszek Otwinowski
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Center for Structural Genomics of Infectious Diseases, Dallas, TX, United States
- *Correspondence: Dominika Borek, ; Zbyszek Otwinowski,
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23
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Zhang W, Xie M, Eleftherianos I, Mohamed A, Cao Y, Song B, Zang LS, Jia C, Bian J, Keyhani NO, Xia Y. An odorant binding protein is involved in counteracting detection-avoidance and Toll-pathway innate immunity. J Adv Res 2022:S2090-1232(22)00194-1. [PMID: 36064181 DOI: 10.1016/j.jare.2022.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/10/2022] [Accepted: 08/20/2022] [Indexed: 10/14/2022] Open
Abstract
INTRODUCTION Odorant-binding proteins (OBPs) are a class of small molecular weight soluble proteins that exist as expanded gene families in all insects, acting as ligand carriers mediating olfaction and other physiological processes. During fungal infection, a subset of insect OBPs were shown to be differentially expressed. OBJECTIVES We tested whether the altered expression of insect OBPs during pathogenic infection plays a role in behavioral or immune interactions between insect hosts and their pathogens. METHODS A wide range of techniques including RNAi-directed knockdown, heterologous protein expression, electrophysiological/behavioral analyses, transcriptomics, gut microbiome analyses, coupled with tandem mass spectrometry ion monitoring, were used to characterize the function of a locust OBP in host behavioral and immune responses. RESULTS The entomopathogenic fungus Metarhizium anisopliae produces the volatile compound phenylethyl alcohol (PEA) that causes behavioral avoidance in locusts. This is mediated by the locust odorant binding protein 11 (LmOBP11). Expression of LmOBP11 is induced by M. anisopliae infection and PEA treatment. LmOBP11 participates in insect detection of the fungal-produced PEA and avoidance of PEA-contaminated food, but the upregulation of LmOBP11 upon M. anisopliae infection negatively affects the insect immune responses to ultimately benefit successful mycosis by the pathogen. RNAi knockdown of LmOBP11 increases the production of antimicrobial peptides and enhances locust resistance to M. anisopliae infection, while reducing host antennal electrophysiological responses to PEA and locust avoidance of PEA treated food. Also, transcriptomic and gut microbiome analyses reveal microbiome dysbiosis and changes in host genes involved in behavior and immunity. These results are consistent with the elevated expression of LmOBP11 leading to enhanced volatile detection and suppression of immune responses. CONCLUSION These findings suggest a crosstalk between olfaction and immunity, indicating manipulation of host OBPs as a novel target exploited by fungal pathogens to alter immune activation and thus promote the successful infection of the host.
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Affiliation(s)
- Wei Zhang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China.
| | - Mushan Xie
- School of Life Science, Chongqing University, Chongqing 401331, China
| | - Ioannis Eleftherianos
- Infection and Innate Immunity Laboratory, Department of Biological Sciences, Institute for Biomedical Sciences, The George Washington University, Washington, DC 20052, USA
| | - Amr Mohamed
- Department of Entomology, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Yueqing Cao
- School of Life Science, Chongqing University, Chongqing 401331, China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Lian-Sheng Zang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Chen Jia
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Jing Bian
- School of Life Science, Chongqing University, Chongqing 401331, China
| | - Nemat O Keyhani
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
| | - Yuxian Xia
- School of Life Science, Chongqing University, Chongqing 401331, China.
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24
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Macnar JM, Brzezinski D, Chruszcz M, Gront D. Analysis of protein structures containing
HEPES
and
MES
molecules. Protein Sci 2022. [PMCID: PMC9601878 DOI: 10.1002/pro.4415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
X‐ray crystallography is the main experimental method behind ligand–macromolecule complexes found in the Protein Data Bank (PDB). Applying bioinformatics methods to such structural data can fuel drug discovery, albeit under the condition that the information is correct. Regrettably, a small number of structures in the PDB are of suboptimal quality due to incorrectly identified and modeled ligands in protein–ligand complexes. In this paper, we combine a theoretical‐graph approach, nuclear density estimates, bioinformatics methods, and prior chemical knowledge to analyze two non‐physiological ligands, HEPES and MES, that are frequent components of crystallization and purifications buffers. Our analysis includes quantum mechanics calculations and Cambridge Structure Database (CSD) queries to define the ideal conformation of these ligands, geometry analysis of PDB deposits regarding several quality factors, and a search for homologous structures to identify other small molecules that could bind in place of the parasitic ligand. Our results highlight the need for careful refinement of macromolecule–ligand complexes and better validation tools that integrate results from all relevant resources. PDB Code(s): 3K4L, 3PYI, 5T6L, 6BB0, 1PJX, 3O4P, 6WCF, 3DKE, 3E10, 6G38, 4E8R, 4Z91, 3E9F, 1MOS, 1MOQ, 2ESB, 1VHR, 4P66 and 6NNI;
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Affiliation(s)
- Joanna Magdalena Macnar
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia USA
- College of Inter‐Faculty Individual Studies in Mathematics and Natural Sciences University of Warsaw Warsaw Poland
- Faculty of Chemistry, Biological and Chemical Research Center University of Warsaw Warsaw Poland
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia USA
- Institute of Computing Science Poznan University of Technology Poznan Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry University of South Carolina Columbia South Carolina USA
| | - Dominik Gront
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia USA
- Faculty of Chemistry, Biological and Chemical Research Center University of Warsaw Warsaw Poland
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25
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Mei Y, Li X, Yang B, Zhao J, Zhang H, Chen H, Chen W. Heterologous expression of a novel linoleic acid isomerase BBI, and effect of fusion tags on its performance. Curr Res Food Sci 2022; 5:2053-2060. [DOI: 10.1016/j.crfs.2022.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/18/2022] [Accepted: 07/27/2022] [Indexed: 10/14/2022] Open
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26
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Lu L, Liu X, Zuo C, Zhou J, Zhu C, Zhang Z, Fillet M, Crommen J, Jiang Z, Wang Q. In vitro/in vivo degradation analysis of trastuzumab by combining specific capture on HER2 mimotope peptide modified material and LC-QTOF-MS. Anal Chim Acta 2022; 1225:340199. [DOI: 10.1016/j.aca.2022.340199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
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27
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Gallego Del Sol F, Quiles-Puchalt N, Brady A, Penadés JR, Marina A. Insights into the mechanism of action of the arbitrium communication system in SPbeta phages. Nat Commun 2022; 13:3627. [PMID: 35750663 PMCID: PMC9232636 DOI: 10.1038/s41467-022-31144-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/01/2022] [Indexed: 11/09/2022] Open
Abstract
The arbitrium system is employed by phages of the SPbeta family to communicate with their progeny during infection to decide either to follow the lytic or the lysogenic cycle. The system is controlled by a peptide, AimP, that binds to the regulator AimR, inhibiting its DNA-binding activity and expression of aimX. Although the structure of AimR has been elucidated for phages SPβ and phi3T, there is still controversy regarding the molecular mechanism of AimR function, with two different proposed models for SPβ. In this study, we deepen our understanding of the system by solving the structure of an additional AimR that shows chimerical characteristics with the SPβ receptor. The crystal structures of this AimR (apo, AimP-bound and DNA-bound) together with in vitro and in vivo analyses confirm a mechanism of action by AimP-induced conformational restriction, shedding light on peptide specificity and cross regulation with relevant biological implications.
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Affiliation(s)
- Francisca Gallego Del Sol
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Nuria Quiles-Puchalt
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Aisling Brady
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - José R Penadés
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
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28
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Adhikari B, Narain A, Wolf E. Generation of auxin inducible degron (AID) knock-in cell lines for targeted protein degradation in mammalian cells. STAR Protoc 2021; 2:100949. [PMID: 34849487 PMCID: PMC8609061 DOI: 10.1016/j.xpro.2021.100949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Targeted protein degradation using degrons, such as the mini-Auxin-inducible degron (mAID), has an advantage over genetic silencing/knockout. However, the efficiency of sgRNA, homologous recombination, tedious expansion, and screening single clones makes the process of tagging endogenous proteins long and laborious. This protocol describes a practical and economical way to obtain AID-tagged endogenous proteins using CRISPR/Cas9-mediated homology-directed repair (HDR). We use the generation of endogenously AID-tagged SPT6 in U2OS cells as an example but provide sufficient details for usage in other cell types. For complete details on the use and execution of this protocol, please refer to Narain et al. (2021).
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Affiliation(s)
- Bikash Adhikari
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ashwin Narain
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Mildred Scheel Early Career Center, University of Würzburg, Beethovenstraße 1A, 97080 Würzburg, Germany
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29
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Flores SS, Clop PD, Barra JL, Argaraña CE, Perillo MA, Nolan V, Sánchez JM. His-tag β-galactosidase supramolecular performance. Biophys Chem 2021; 281:106739. [PMID: 34923392 DOI: 10.1016/j.bpc.2021.106739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/05/2021] [Accepted: 12/05/2021] [Indexed: 11/02/2022]
Abstract
β-Galactosidase is an important biotechnological enzyme used in the dairy industry, pharmacology and in molecular biology. In our laboratory we have overexpressed a recombinant β-galactosidase in Escherichia coli (E. coli). This enzyme differs from its native version (β-GalWT) in that 6 histidine residues have been added to the carboxyl terminus in the primary sequence (β-GalHis), which allows its purification by immobilized metal affinity chromatography (IMAC). In this work we compared the functionality and structure of both proteins and evaluated their catalytic behavior on the kinetics of lactose hydrolysis. We observed a significant reduction in the enzymatic activity of β-GalHis with respect to β-GalWT. Although, both enzymes showed a similar catalytic profile as a function of temperature, β-GalHis presented a higher resistance to the thermal inactivation compared to β-GalWT. At room temperature, β-GalHis showed a fluorescence spectrum compatible with a partially unstructured protein, however, it exhibited a lower tendency to the thermal-induced unfolding with respect to β-GalWT. The distinctively supramolecular arranges of the proteins would explain the effect of the presence of His-tag on the enzymatic activity and thermal stability.
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Affiliation(s)
- Sandra S Flores
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sarsfield 1611, 5016 Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Pedro D Clop
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sarsfield 1611, 5016 Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - José L Barra
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica "Ranwel Caputto", Av. Haya de la Torre s/N° Ciudad Universitaria CP, X5000HUA Córdoba, Argentina; CONICET, Centro de Investigaciones en Química Biológicas de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Carlos E Argaraña
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica "Ranwel Caputto", Av. Haya de la Torre s/N° Ciudad Universitaria CP, X5000HUA Córdoba, Argentina; CONICET, Centro de Investigaciones en Química Biológicas de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - María A Perillo
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sarsfield 1611, 5016 Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Verónica Nolan
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sarsfield 1611, 5016 Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina.
| | - Julieta M Sánchez
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sarsfield 1611, 5016 Córdoba, Argentina; CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina.
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30
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Zou J, Cai Z, Liang Z, Liang Y, Zhang G, Yang J, Zhang Y, Lin H, Tan M. Different fusion tags affect the activity of ubiquitin overexpression on spastin protein stability. Eur J Histochem 2021; 65. [PMID: 34873900 PMCID: PMC8678624 DOI: 10.4081/ejh.2021.3352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/23/2021] [Indexed: 11/23/2022] Open
Abstract
Spastin is one of the proteins which lead to hereditary spastic paraplegia (HSP), whose dysfunction towards microtubule severing and membrane transporting is critically important. The present study is to elucidate the mechanisms of the protein stability regulation of spastin. The ubiquitin encoding plasmids were transfected into COS-7 cells with different fusion tags including Green Fluorescent Protein (GFP), mCherry and Flag. The expression level of spastin was detected, microtubule severing activity and neurite outgrowth were quantified. The data showed that ubiquitin overexpression significantly induced the decreased expression of spastin, suppressed the activity of microtubule severing in COS-7 cells and inhibited the promoting effect on neurite outgrowth in cultured hippocampal neurons. Furthermore, when modulating the overexpression experiments of ubiquitin, it was found that relatively small tag like Flag, but not large tags such as GFP or mCherry fused with ubiquitin, retained the activity on spastin stability. The present study investigated the effects of small/large tags addition to ubiquitin and the novel mechanisms of post-transcriptional modifications of spastin on regulating neurite outgrowth, in the attempt to experimentally elucidate the mechanisms that control the level or stability of spastin in hereditary spastic paraplegia.
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Affiliation(s)
- Jianyu Zou
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Zhenbin Cai
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Zhi Liang
- Department of Orthopaedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen.
| | - Yaozhong Liang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Guowei Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Jie Yang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Yunlong Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Hongsheng Lin
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Minghui Tan
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
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31
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Mompeán M, Treviño MÁ, Laurents DV. Partial structure, dampened mobility, and modest impact of a His tag in the SARS-CoV-2 Nsp2 C-terminal region. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:1129-1137. [PMID: 34633480 PMCID: PMC8503394 DOI: 10.1007/s00249-021-01575-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/10/2021] [Accepted: 10/03/2021] [Indexed: 11/30/2022]
Abstract
Intrinsically disordered proteins (IDPs) play essential roles in regulating physiological processes in eukaryotic cells. Many viruses use their own IDPs to "hack" these processes to deactivate host defenses and promote viral growth. Thus, viral IDPs are attractive drug targets. While IDPs are hard to study by X-ray crystallography or cryo-EM, atomic level information on their conformational preferences and dynamics can be obtained using NMR spectroscopy. SARS-CoV-2 Nsp2, whose C-terminal region (CtR) is predicted to be disordered, interacts with human proteins that regulate translation initiation and endosome vesicle sorting. Molecules that block these interactions could be valuable leads for drug development. The 13Cβ and backbone 13CO, 1HN, 13Cα, and 15N nuclei of Nsp2's 45-residue CtR were assigned and used to characterize its structure and dynamics in three contexts; namely: (1) retaining an N-terminal His tag, (2) without the His tag and with an adventitious internal cleavage, and (3) lacking both the His tag and the internal cleavage. Two five-residue segments adopting a minor extended population were identified. Overall, the dynamic behavior is midway between a completely rigid and a fully flexible chain. Whereas the presence of an N-terminal His tag and internal cleavage stiffen and loosen, respectively, neighboring residues, they do not affect the tendency of two regions to populate extended conformations.
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Affiliation(s)
- Miguel Mompeán
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Miguel Á Treviño
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain
| | - Douglas V Laurents
- "Rocasolano" Institute for Physical Chemistry, Spanish National Research Council, Serrano 119, 28006, Madrid, Spain.
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32
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Tietze L, Lale R. Importance of the 5' regulatory region to bacterial synthetic biology applications. Microb Biotechnol 2021; 14:2291-2315. [PMID: 34171170 PMCID: PMC8601185 DOI: 10.1111/1751-7915.13868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/02/2023] Open
Abstract
The field of synthetic biology is evolving at a fast pace. It is advancing beyond single-gene alterations in single hosts to the logical design of complex circuits and the development of integrated synthetic genomes. Recent breakthroughs in deep learning, which is increasingly used in de novo assembly of DNA components with predictable effects, are also aiding the discipline. Despite advances in computing, the field is still reliant on the availability of pre-characterized DNA parts, whether natural or synthetic, to regulate gene expression in bacteria and make valuable compounds. In this review, we discuss the different bacterial synthetic biology methodologies employed in the creation of 5' regulatory regions - promoters, untranslated regions and 5'-end of coding sequences. We summarize methodologies and discuss their significance for each of the functional DNA components, and highlight the key advances made in bacterial engineering by concentrating on their flaws and strengths. We end the review by outlining the issues that the discipline may face in the near future.
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Affiliation(s)
- Lisa Tietze
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| | - Rahmi Lale
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
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33
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McCartan AJS, Curran DW, Mrsny RJ. Evaluating parameters affecting drug fate at the intramuscular injection site. J Control Release 2021; 336:322-335. [PMID: 34153375 DOI: 10.1016/j.jconrel.2021.06.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022]
Abstract
Intramuscular (IM) injections are a well-established method of delivering a variety of therapeutics formulated for parenteral administration. While the wide range of commercial IM pharmaceuticals provide a wealth of pharmacokinetic (PK) information following injection, there remains an inadequate understanding of drug fate at the IM injection site that could dictate these PK outcomes. An improved understanding of injection site events could improve approaches taken by formulation scientists to identify therapeutically effective and consistent drug PK outcomes. Interplay between the typically non-physiological aspects of drug formulations and the homeostatic IM environment may provide insights into the fate of drugs at the IM injection site, leading to predictions of how a drug will behave post-injection in vivo. Immune responses occur by design after e.g. vaccine administration, however immune responses post-injection are not in the scope of this article. Taking cues from existing in vitro modelling technologies, the purpose of this article is to propose "critical parameters" of the IM environment that could be examined in hypothesis-driven studies. Outcomes of such studies might ultimately be useful in predicting and improving in vivo PK performance of IM injected drugs.
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Affiliation(s)
- Adam J S McCartan
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, Avon BA2 7AY, UK
| | - David W Curran
- CMC Analytical, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Randall J Mrsny
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, Avon BA2 7AY, UK.
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Le VTB, Tsimbalyuk S, Lim EQ, Solis A, Gawat D, Boeck P, Lim EQ, Renolo R, Forwood JK, Kuhn ML. The Vibrio cholerae SpeG Spermidine/Spermine N-Acetyltransferase Allosteric Loop and β6-β7 Structural Elements Are Critical for Kinetic Activity. Front Mol Biosci 2021; 8:645768. [PMID: 33928120 PMCID: PMC8076852 DOI: 10.3389/fmolb.2021.645768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 11/27/2022] Open
Abstract
Polyamines regulate many important biological processes including gene expression, intracellular signaling, and biofilm formation. Their intracellular concentrations are tightly regulated by polyamine transport systems and biosynthetic and catabolic pathways. Spermidine/spermine N-acetyltransferases (SSATs) are catabolic enzymes that acetylate polyamines and are critical for maintaining intracellular polyamine homeostasis. These enzymes belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily and adopt a highly conserved fold found across all kingdoms of life. SpeG is an SSAT protein found in a variety of bacteria, including the human pathogen Vibrio cholerae. This protein adopts a dodecameric structure and contains an allosteric site, making it unique compared to other SSATs. Currently, we have a limited understanding of the critical structural components of this protein that are required for its allosteric behavior. Therefore, we explored the importance of two key regions of the SpeG protein on its kinetic activity. To achieve this, we created various constructs of the V. cholerae SpeG protein, including point mutations, a deletion, and chimeras with residues from the structurally distinct and non-allosteric human SSAT protein. We measured enzyme kinetic activity toward spermine for ten constructs and crystallized six of them. Ultimately, we identified specific portions of the allosteric loop and the β6-β7 structural elements that were critical for enzyme kinetic activity. These results provide a framework for further study of the structure/function relationship of SpeG enzymes from other organisms and clues toward the structural evolution of members of the GNAT family across domains of life.
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Affiliation(s)
- Van Thi Bich Le
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Sofiya Tsimbalyuk
- School of Biomedical Science, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Ee Qi Lim
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Allan Solis
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Darwin Gawat
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Paloma Boeck
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Ee Qing Lim
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Rosselini Renolo
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Jade K. Forwood
- School of Biomedical Science, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Misty L. Kuhn
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States
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Zhu W, Fang T, Zhang W, Liang A, Zhang H, Zhang ZP, Zhang XE, Li F. A ROS scavenging protein nanocage for in vitro and in vivo antioxidant treatment. NANOSCALE 2021; 13:4634-4643. [PMID: 33616146 DOI: 10.1039/d0nr08878a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Elevated levels of reactive oxygen species (ROS) are implicated in the onset and progression of many diseases, e.g., virus infection, ischemic stroke and neurodegenerative diseases. ROS-scavenging nanomaterials have attracted particular interest. Here, we report the development of a natural protein nanocage named Dps for in vitro and in vivo antioxidant treatment by inhibiting the Fenton reaction, a critical step in ROS generation and interconversion. Systematic surface engineering enabled cell penetration, good colloidal stability, and facile purification of Dps. With its intrinsic ferroxidase activity consuming both H2O2 and Fe2+, Dps not only protects human cells from oxidative stress but also effectively alleviates ROS-induced inflammation in a mouse dermatitis model. The protection is triggered by elevated H2O2 and thereby, in principle, avoids ROS imbalances. Thus, Dps has potential as a new bionano platform for different purposes, such as antiaging, anti-inflammation and cosmetics.
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Affiliation(s)
- Weiwei Zhu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ti Fang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Wenjing Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ao Liang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Zhi-Ping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Xian-En Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Feng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 100049, China
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State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and in Vitro Biochemical Experiments. Methods Mol Biol 2021; 2199:209-236. [PMID: 33125653 PMCID: PMC8019398 DOI: 10.1007/978-1-0716-0892-0_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Efficient and comprehensive data management is an indispensable component of modern scientific research and requires effective tools for all but the most trivial experiments. The LabDB system developed and used in our laboratory was originally designed to track the progress of a structure determination pipeline in several large National Institutes of Health (NIH) projects. While initially designed for structural biology experiments, its modular nature makes it easily applied in laboratories of various sizes in many experimental fields. Over many years, LabDB has transformed into a sophisticated system integrating a range of biochemical, biophysical, and crystallographic experimental data, which harvests data both directly from laboratory instruments and through human input via a web interface. The core module of the system handles many types of universal laboratory management data, such as laboratory personnel, chemical inventories, storage locations, and custom stock solutions. LabDB also tracks various biochemical experiments, including spectrophotometric and fluorescent assays, thermal shift assays, isothermal titration calorimetry experiments, and more. LabDB has been used to manage data for experiments that resulted in over 1200 deposits to the Protein Data Bank (PDB); the system is currently used by the Center for Structural Genomics of Infectious Diseases (CSGID) and several large laboratories. This chapter also provides examples of data mining analyses and warnings about incomplete and inconsistent experimental data. These features, together with its capabilities for detailed tracking, analysis, and auditing of experimental data, make the described system uniquely suited to inspect potential sources of irreproducibility in life sciences research.
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Napiorkowska M, Pestalozzi L, Panke S, Held M, Schmitt S. High-Throughput Optimization of Recombinant Protein Production in Microfluidic Gel Beads. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005523. [PMID: 33325637 DOI: 10.1002/smll.202005523] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/31/2020] [Indexed: 06/12/2023]
Abstract
Efficient production hosts are a key requirement for bringing biopharmaceutical and biotechnological innovations to the market. In this work, a truly universal high-throughput platform for optimization of microbial protein production is described. Using droplet microfluidics, large genetic libraries of strains are encapsulated into biocompatible gel beads that are engineered to selectively retain any protein of interest. Bead-retained products are then fluorescently labeled and strains with superior production titers are isolated using flow cytometry. The broad applicability of the platform is demonstrated by successfully culturing several industrially relevant bacterial and yeast strains and detecting peptides or proteins of interest that are secreted or released from the cell via autolysis. Lastly, the platform is applied to optimize cutinase secretion in Komagataella phaffii (Pichia pastoris) and a strain with 5.7-fold improvement is isolated. The platform permits the analysis of >106 genotypes per day and is readily applicable to any protein that can be equipped with a His6 -tag. It is envisioned that the platform will be useful for large screening campaigns that aim to identify improved hosts for large-scale production of biotechnologically relevant proteins, thereby accelerating the costly and time-consuming process of strain engineering.
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Affiliation(s)
- Marta Napiorkowska
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, CB2 1GA, UK
| | - Luzius Pestalozzi
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Martin Held
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Steven Schmitt
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
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Tang S, Han T, Wang Z, Yue N, Liu Z, Tang S, Yang X, Zhang Z, Zhou Y, Yuan W, Hao H, Sleman S, Pan D, Xuan B, Zhou W, Qian Z. Facile and Modular Pipeline for Protein-Specific Antibody Customization. ACS APPLIED BIO MATERIALS 2020; 3:4380-4387. [DOI: 10.1021/acsabm.0c00385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Shubing Tang
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
- Shanghai Public Health Clinical Center, Fudan University, 201058 Shanghai, China
| | - Tian Han
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Zewei Wang
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Nan Yue
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Zhi Liu
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Shuhua Tang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, 300134 Tianjin, China
| | - Xiaoqi Yang
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
| | - Zhe Zhang
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
| | - Yan Zhou
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
| | - Weiming Yuan
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
| | - Hongyun Hao
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Sirwan Sleman
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Deng Pan
- Shanghai Public Health Clinical Center, Fudan University, 201058 Shanghai, China
| | - Baoqin Xuan
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
| | - Wei Zhou
- Guangzhou Institute of Pediatrics, Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, 510623 Guangzhou, China
| | - Zhikang Qian
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, 200031 Shanghai, China
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Ferenc-Mrozek A, Bojarska E, Stepinski J, Darzynkiewicz E, Lukaszewicz M. Effect of the His-Tag Location on Decapping Scavenger Enzymes and Their Hydrolytic Activity toward Cap Analogs. ACS OMEGA 2020; 5:10759-10766. [PMID: 32455195 PMCID: PMC7240826 DOI: 10.1021/acsomega.0c00304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/08/2020] [Indexed: 05/11/2023]
Abstract
Decapping scavenger enzymes (DcpSs) are important players in mRNA degradation machinery and conserved in eukaryotes. Importantly, human DcpS is the recognized target for spinal muscular atrophy (SMA) and acute myeloid leukemia (AML) therapy, and has recently been connected to development of intellectual disability. Most recombinant DcpSs used in biochemical and biophysical studies are prepared as tagged proteins, with polyhistidine (His-tag) at the N-terminus or C-terminus. Our work is the first report on the parallel characterization of three versions of DcpSs (native and N- or C-terminally tagged) of three species (humans, Caenorhabditis elegans , and Ascaris suum). The native forms of all three enzymes were prepared by N-(His)10 tag cleavage. Protein thermal stability, measured by differential scanning fluorimetry (DSF), was unaffected in the case of native and tagged versions of human and A. suum DcpS; however, the melting temperature (T m) of C. elagans DcpS of was significantly influenced by the presence of the additional N- or C-tag. To investigate the impact of the tag positioning on the catalytic properties of DcpS, we tested the hydrolytic activity of native DcpS and their His-tagged counterparts toward cap dinucleotides (m7GpppG and m3 2,2,7GpppG) and m7GDP. The kinetic data indicate that dinucleotide substrates are hydrolyzed with comparable efficiency by native human and A. suum DcpS and their His-tagged forms. In contrast, both His-tagged C. elegans DcpSs exhibited higher activity toward m7GpppG than the native enzyme. m7GDP is resistant to enzymatic cleavage by all three forms of human and nematode DcpS.
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Affiliation(s)
- Aleksandra Ferenc-Mrozek
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
- Centre
of New Technologies, University of Warsaw, 02-093 Warsaw, Poland
| | - Elzbieta Bojarska
- Centre
of New Technologies, University of Warsaw, 02-093 Warsaw, Poland
| | - Janusz Stepinski
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
- Centre
of New Technologies, University of Warsaw, 02-093 Warsaw, Poland
| | - Maciej Lukaszewicz
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
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Yılmaz H, Özdemir Fİ, Ergenekon P, Özkan M. Affinity tag effect on the salt rejection potential of Halomonas elongata aquaporin incorporated in thin film nanocomposite membrane. Protein Expr Purif 2020; 173:105664. [PMID: 32380098 DOI: 10.1016/j.pep.2020.105664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/03/2020] [Indexed: 11/18/2022]
Abstract
In this study, effect of affinity tags, Histidine (His) and Glutathione-S-Transferase (GST), on the activity of halophilic aquaporin was analyzed. The gene coding for H. elongata aquaporin was cloned into pET28a vector and expressed in E. coli BL21 successfully. Stopped flow light scattering measurements showed that His-tagged aquaporin is functional. The difference in the filtration parameters caused by affinity tags were determined by using thin film composite nano-filtration (NFC) membranes prepared with the aquaporins. At 100 mM salt concentration, water permeability (L/m2.h) and the % salt rejection of NFC membranes produced with the His-tagged aquaporin was found to be higher than that of the membrane with GST-tagged aquaporin. Salt rejection of His-tagged aquaporin-membrane was found to be 53% with a lower solute permeability value (B). Use of short affinity tag (His tag) for cloning resulted in higher solute rejection ability of TFC membranes prepared with H. elongata aquaporins.
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Affiliation(s)
- Hilal Yılmaz
- Gebze Technical University, Department of Environmental Engineering, 41400, Gebze Kocaeli, Turkey
| | - Fatma İnci Özdemir
- Gebze Technical University, Department of Molecular Biology and Genetics, 41400, Gebze Kocaeli, Turkey
| | - Pınar Ergenekon
- Gebze Technical University, Department of Environmental Engineering, 41400, Gebze Kocaeli, Turkey
| | - Melek Özkan
- Gebze Technical University, Department of Environmental Engineering, 41400, Gebze Kocaeli, Turkey.
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Hirschi S, Kalbermatter D, Ucurum Z, Fotiadis D. Cryo-electron microscopic and X-ray crystallographic analysis of the light-driven proton pump proteorhodopsin reveals a pentameric assembly. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100024. [PMID: 32647827 PMCID: PMC7337067 DOI: 10.1016/j.yjsbx.2020.100024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 11/30/2022]
Abstract
Affinity tag-free isolation of proteorhodopsin (PR) by ion exchange and size exclusion chromatography. Biochemical and computational analysis indicate a single, pentameric PR population. Highly pure and homogeneous PR enables growth of 3D crystals. X-ray crystallography and cryo-electron microscopy reveal pentameric assembly of PR.
The green-light absorbing proteorhodopsin (GPR) is the prototype of bacterial light-driven proton pumps. It has been the focus of continuous research since its discovery 20 years ago and has sparked the development and application of various biophysical techniques. However, a certain controversy and ambiguity about the oligomeric assembly of GPR still remains. We present here the first tag-free purification of pentameric GPR. The combination of ion exchange and size exclusion chromatography yields homogeneous and highly pure untagged pentamers from GPR overexpressing Escherichia coli. The presented purification procedure provides native-like protein and excludes the need for affinity purification tags. Importantly, three-dimensional protein crystals of GPR were successfully grown and analyzed by X-ray crystallography. These results together with data from single particle cryo-electron microscopy provide direct evidence for the pentameric stoichiometry of purified GPR.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - David Kalbermatter
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
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42
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Abd Elhameed HAH, Hajdu B, Jancsó A, Kéri A, Galbács G, Hunyadi-Gulyás É, Gyurcsik B. Modulation of the catalytic activity of a metallonuclease by tagging with oligohistidine. J Inorg Biochem 2020; 206:111013. [PMID: 32088594 DOI: 10.1016/j.jinorgbio.2020.111013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 11/19/2022]
Abstract
Peptide tags are extensively used for affinity purification of proteins. In an optimal case, these tags can be completely removed from the purified protein by a specific protease mediated hydrolysis. However, the interactions of these tags with the target protein may also be utilized for the modulation of the protein function. Here we show that the C-terminal hexahistidine (6 × His) tag can influence the catalytic activity of the nuclease domain of the Colicin E7 metallonuclease (NColE7) used by E. coli to kill competing bacteria under stress conditions. This enzyme non-specifically cleaves the DNA that results in cytotoxicity. We have successfully cloned the genes of NColE7 protein and its R447G mutant into a modified pET-21a DNA vector fusing the affinity tag to the protein upon expression, which would be otherwise not possible in the absence of the gene of the Im7 inhibitory protein. This reflects the inhibitory effect of the 6 × His fusion tag on the nuclease activity, which proved to be a complex process via both coordinative and non-specific steric interactions. The modulatory effect of Zn2+ ion was observed in the catalytic activity experiments. The DNA cleavage ability of the 6 × His tagged enzyme was first enhanced by an increase of metal ion concentration, while high excess of Zn2+ ions caused a lower rate of the DNA cleavage. Modelling of the coordinative effect of the fusion tag by external chelators suggested ternary complex formation instead of removal of the metal ion from the active center.
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Affiliation(s)
- Heba A H Abd Elhameed
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Bálint Hajdu
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Albert Kéri
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Gábor Galbács
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Centre, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary.
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Liang S, Fuchs S, Mymrikov EV, Stulz A, Kaiser M, Heerklotz H, Hunte C. Calcium affects CHP1 and CHP2 conformation and their interaction with sodium/proton exchanger 1. FASEB J 2020; 34:3253-3266. [DOI: 10.1096/fj.201902093r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/10/2019] [Accepted: 12/23/2019] [Indexed: 01/27/2023]
Affiliation(s)
- Shuo Liang
- Institute for Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine University of Freiburg Freiburg Germany
- Faculty of Biology University of Freiburg Freiburg Germany
| | - Simon Fuchs
- Institute for Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine University of Freiburg Freiburg Germany
- Faculty of Biology University of Freiburg Freiburg Germany
| | - Evgeny V. Mymrikov
- Institute for Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine University of Freiburg Freiburg Germany
- CIBSS ‐ Centre for Integrative Biological Signalling Studies University of Freiburg Freiburg Germany
| | - Anja Stulz
- Department of Pharmaceutical Technology and Biopharmacy University of Freiburg Freiburg Germany
| | - Michael Kaiser
- Department of Pharmaceutical Technology and Biopharmacy University of Freiburg Freiburg Germany
| | - Heiko Heerklotz
- CIBSS ‐ Centre for Integrative Biological Signalling Studies University of Freiburg Freiburg Germany
- Department of Pharmaceutical Technology and Biopharmacy University of Freiburg Freiburg Germany
- Leslie Dan Faculty of Pharmacy University of Toronto Toronto Canada
- BIOSS Centre for Biological Signalling Studies University of Freiburg Freiburg Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology ZBMZ, Faculty of Medicine University of Freiburg Freiburg Germany
- CIBSS ‐ Centre for Integrative Biological Signalling Studies University of Freiburg Freiburg Germany
- BIOSS Centre for Biological Signalling Studies University of Freiburg Freiburg Germany
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Munadziroh E, Ulfa EU, Labiqah A, Asmarani O, Puspaningsih NNT. Effect of Poly-Histidine Tag Position toward Inhibition Activity of Secretory Leukocyte Protease Inhibitor as Candidate for Material Wound Healing. Avicenna J Med Biotechnol 2020; 12:32-36. [PMID: 32153736 PMCID: PMC7035463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The Secretory Leukocyte Protease Inhibitors (SLPI) has many biological functions including anti-bacterial, anti-fungal, anti-viral, anti-inflammatory, and immuno-modulatory. Previous studies have shown that gene-encoding human SLPI have successfully been expressed in Escherichia coli (E. coli) with a C-terminal poly-histidine tag (His-tag). The aim of this research was to investigate the inhibition activity of N-terminal His-tag position (NSLPI) and C-terminal His-tag position (CSLPI). We hypothesized that a His-tag close to an active site SLPI domain may interfere with the inhibition activity of SLPIs. METHODS A NSLPI and CSLPI were constructed with polymerase chain reaction (PCR) amplification. The PCR products were then ligated into pET-30a plasmid and transformed into E. coli TOP10. Recombinant plasmids were verified by using restriction analysis and nucleotide sequence analysis. pET-NSLPI and pET-CSLPI were then subcloned in E. coli BL21(DE3) for its expression. The SLPI protein was expressed using Isopropyl β-D-1-thiogalactopyranoside induction (IPTG). The inhibition effect of both SLPI against Porcine Pancreatic Elastase (PPE) enzyme was tested using the N-succinyil-alanyl-L-alanyl-L-prolyl-L-phenylalanyl-4-nitroanalide (NPN) substrate. RESULTS The SLPI gene was successfully cloned and expressed in E. coli BL21. Fusion proteins of NSLPI and CSLPI were generated with His-tag in the N-terminal and C-terminal position, respectively. The inhibition effect of NSLPI and CSLPI on PPE indicated that both SLPI were active. The inhibition activity of NSLPI was 66.7%, higher than CSLPI by 44.4%. CONCLUSION The His-tag position on the C-terminal of SLPI reduced the inhibition activity of SLPI.
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Affiliation(s)
- Elly Munadziroh
- Department of Dental Material and Technology, Faculty of Dentistry, Universitas Airlangga, Surabaya, Indonesia
| | - Evi Umayah Ulfa
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Universitas Jember, Jember, Indonesia, Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - Amaliah Labiqah
- Department of Health Analysis, Stikes Kesetiakawanan Sosial Indonesia, Jakarta, Indonesia
| | - One Asmarani
- Proteomic Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Ni Nyoman Tri Puspaningsih
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia, Proteomic Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia,*Corresponding author: Ni Nyoman Tri Puspaningsih, Ph.D., Laboratory of Proteomic, Research center for Bio-Molecule Engineering, Universitas Airlangga, Surabaya, Indonesia and Department of Bioinformatics & Medical Engineering, Asia University, Taiwan, Tel: +62 31 5936501, Fax: +62 31 5936501, E-mail:
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45
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Alcala A, Ramirez G, Solis A, Kim Y, Tan K, Luna O, Nguyen K, Vazquez D, Ward M, Zhou M, Mulligan R, Maltseva N, Kuhn ML. Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species. Protein Sci 2019; 29:695-710. [PMID: 31762145 DOI: 10.1002/pro.3793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022]
Abstract
Chloramphenicol acetyltransferases (CATs) were among the first antibiotic resistance enzymes identified and have long been studied as model enzymes for examining plasmid-mediated antibiotic resistance. These enzymes acetylate the antibiotic chloramphenicol, which renders it incapable of inhibiting bacterial protein synthesis. CATs can be classified into different types: Type A CATs are known to be important for antibiotic resistance to chloramphenicol and fusidic acid. Type B CATs are often called xenobiotic acetyltransferases and adopt a similar structural fold to streptogramin acetyltransferases, which are known to be critical for streptogramin antibiotic resistance. Type C CATs have recently been identified and can also acetylate chloramphenicol, but their roles in antibiotic resistance are largely unknown. Here, we structurally and kinetically characterized three Vibrio CAT proteins from a nonpathogenic species (Aliivibrio fisheri) and two important human pathogens (Vibrio cholerae and Vibrio vulnificus). We found all three proteins, including one in a superintegron (V. cholerae), acetylated chloramphenicol, but did not acetylate aminoglycosides or dalfopristin. We also determined the 3D crystal structures of these CATs alone and in complex with crystal violet and taurocholate. These compounds are known inhibitors of Type A CATs, but have not been explored in Type B and Type C CATs. Based on sequence, structure, and kinetic analysis, we concluded that the V. cholerae and V. vulnificus CATs belong to the Type B class and the A. fisheri CAT belongs to the Type C class. Ultimately, our results provide a framework for studying the evolution of antibiotic resistance gene acquisition and chloramphenicol acetylation in Vibrio and other species.
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Affiliation(s)
- Ashley Alcala
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Guadalupe Ramirez
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Allan Solis
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois.,Structural Biology Center X-ray Science Division Argonne National Laboratory, Argonne, Illinois
| | - Kemin Tan
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois.,Structural Biology Center X-ray Science Division Argonne National Laboratory, Argonne, Illinois
| | - Oscar Luna
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Karen Nguyen
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Daniel Vazquez
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Michael Ward
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
| | - Min Zhou
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois.,Structural Biology Center X-ray Science Division Argonne National Laboratory, Argonne, Illinois
| | - Rory Mulligan
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois.,Structural Biology Center X-ray Science Division Argonne National Laboratory, Argonne, Illinois
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois.,Structural Biology Center X-ray Science Division Argonne National Laboratory, Argonne, Illinois
| | - Misty L Kuhn
- San Francisco State University, Department of Chemistry and Biochemistry, San Francisco, California
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Effects of N-Terminal and C-Terminal Polyhistidine Tag on the Stability and Function of the Thermophilic P450 CYP119. Bioinorg Chem Appl 2019; 2019:8080697. [PMID: 31320891 PMCID: PMC6610755 DOI: 10.1155/2019/8080697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/05/2019] [Accepted: 03/18/2019] [Indexed: 01/01/2023] Open
Abstract
Biocatalysts are sought-after in synthesis of pharmaceuticals and agrochemicals due to their high regioselectivity and enantioselectivity. Among biocatalysts, heme-containing cytochrome P450 (P450) oxygenases are an attractive target since they catalyze oxidation of "unactivated" carbon-hydrogen bonds with high efficiency. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius, which has the potential to be widely used as a biocatalyst since it shows activity at high temperatures and low pH. Polyhistidine tags (His-tags) are widely used to simplify purification of proteins. However, His-tags can cause changes to protein structure and function. Here, we demonstrate the effects of His-tags on CYP119. To this end, the His-tags were cloned at the N-terminus or C-terminus of the CYP119, and His-tagged proteins were expressed and isolated. The thermostability and peroxidase activity of His-tagged CYP119s were tested and compared to wild type CYP119. Results indicated that while addition of His-tags increased the yield and simplified isolation of CYP119, they also influenced the electronic structure of active site and the activity of the protein. We show that N-terminal His-tagged CYP119 has desirable properties and potential to be used in industrial applications, but mechanistic studies using this protein need careful interpretation since the His-tag affects electronic properties of the active site heme iron.
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47
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Pick a Tag and Explore the Functions of Your Pet Protein. Trends Biotechnol 2019; 37:1078-1090. [PMID: 31036349 DOI: 10.1016/j.tibtech.2019.03.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 01/01/2023]
Abstract
Protein tags have been essential for advancing our knowledge of the function of proteins, their localization, and the mapping of their interaction partners. Expressing epitope-tagged proteins has become a standard practice in every life science laboratory and, thus, continues to enable new studies. In recent years, several new tagging moieties have entered the limelight, many of them bringing new functionalities, such as targeted protein degradation, accurate quantification, and proximity labeling. Other novel tags aim at tackling research questions in challenging niches. In this review, we elaborate on recently introduced tags and the opportunities they provide for future research endeavors. In addition, we highlight how the genome-engineering revolution may boost the field of protein tags.
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48
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Khairil Anuar INA, Banerjee A, Keeble AH, Carella A, Nikov GI, Howarth M. Spy&Go purification of SpyTag-proteins using pseudo-SpyCatcher to access an oligomerization toolbox. Nat Commun 2019; 10:1734. [PMID: 30988307 PMCID: PMC6465384 DOI: 10.1038/s41467-019-09678-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
Peptide tags are a key resource, introducing minimal change while enabling a consistent process to purify diverse proteins. However, peptide tags often provide minimal benefit post-purification. We previously designed SpyTag, forming an irreversible bond with its protein partner SpyCatcher. SpyTag provides an easy route to anchor, bridge or multimerize proteins. Here we establish Spy&Go, enabling protein purification using SpyTag. Through rational engineering we generated SpyDock, which captures SpyTag-fusions and allows efficient elution. Spy&Go enabled sensitive purification of SpyTag-fusions from Escherichia coli, giving superior purity than His-tag/nickel-nitrilotriacetic acid. Spy&Go allowed purification of mammalian-expressed, N-terminal, C-terminal or internal SpyTag. As an oligomerization toolbox, we established a panel of SpyCatcher-linked coiled coils, so SpyTag-fusions can be dimerized, trimerized, tetramerized, pentamerized, hexamerized or heptamerized. Assembling oligomers for Death Receptor 5 stimulation, we probed multivalency effects on cancer cell death. Spy&Go, combined with simple oligomerization, should have broad application for exploring multivalency in signaling.
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Affiliation(s)
| | - Anusuya Banerjee
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anthony H Keeble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Alberto Carella
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Georgi I Nikov
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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Conroy F, Rossi T, Ashmead H, Crowther JM, Mitra AK, Gerrard JA. Engineering peroxiredoxin 3 to facilitate control over self-assembly. Biochem Biophys Res Commun 2019; 512:263-268. [PMID: 30885432 DOI: 10.1016/j.bbrc.2019.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/11/2022]
Abstract
Oligomeric proteins are abundant in nature and are useful for a range of nanotechnological applications; however, a key requirement in using these proteins is controlling when and how they form oligomeric assemblies. Often, protein oligomerisation is triggered by various cellular signals, allowing for controllable oligomerisation. An example of this is human peroxiredoxin 3 (Prx), a stable protein that natively forms dimers, dodecameric rings, stacks, and tubes in response to a range of environmental stimuli. Although we know the key environmental stimuli for switching between different oligomeric states of Prx, we still have limited molecular knowledge and control over the formation and size of the protein's stacks and tubes. Here, we have generated a range of Prx mutants with either a decreased or knocked out ability to stack, and used both imaging and solution studies to show that Prx stacks through electrostatic interactions that are stabilised by a hydrogen bonding network. Furthermore, we show that altering the length of the polyhistidine tag will alter the length of the Prx stacks, with longer polyhistidine tags giving longer stacks. Finally, we have analysed the effect a variety of heavy metals have on the oligomeric state of Prx, wherein small transition metals like nickel enhances Prx stacking, while larger positively charged metals like tungstate ions can prevent Prx stacking. This work provides further structural characterisation of Prx, to enhance its use as a platform from which to build protein nanostructures for a variety of applications.
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Affiliation(s)
- Frankie Conroy
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand.
| | - Tatiana Rossi
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Helen Ashmead
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand; Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand
| | - Jennifer M Crowther
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand
| | - Alok K Mitra
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Juliet A Gerrard
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand.
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50
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Kutyshenko VP, Mikoulinskaia GV, Chernyshov SV, Yegorov AY, Prokhorov DA, Uversky VN. Effect of C-terminal His-tag and purification routine on the activity and structure of the metalloenzyme, l-alanyl-d-glutamate peptidase of the bacteriophage T5. Int J Biol Macromol 2019; 124:810-818. [DOI: 10.1016/j.ijbiomac.2018.11.219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/07/2018] [Accepted: 11/24/2018] [Indexed: 02/01/2023]
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