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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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2
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Dang B, Mravic M, Hu H, Schmidt N, Mensa B, DeGrado WF. SNAC-tag for sequence-specific chemical protein cleavage. Nat Methods 2019; 16:319-322. [PMID: 30923372 DOI: 10.1038/s41592-019-0357-353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/06/2019] [Indexed: 05/28/2023]
Abstract
Site-specific protein cleavage is essential for many protein-production protocols and typically requires proteases. We report the development of a chemical protein-cleavage method that is achieved through the use of a sequence-specific nickel-assisted cleavage (SNAC)-tag. We demonstrate that the SNAC-tag can be inserted before both water-soluble and membrane proteins to achieve fusion protein cleavage under biocompatible conditions with efficiency comparable to that of enzymes, and that the method works even when enzymatic cleavages fail.
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Affiliation(s)
- Bobo Dang
- School of Life Sciences, Westlake University, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
| | - Marco Mravic
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Hailin Hu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Nathan Schmidt
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
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3
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SNAC-tag for sequence-specific chemical protein cleavage. Nat Methods 2019; 16:319-322. [PMID: 30923372 PMCID: PMC6443254 DOI: 10.1038/s41592-019-0357-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/06/2019] [Indexed: 11/25/2022]
Abstract
Biocompatible chemical protein cleavage methods have been long-sought to replace enzymatic cleavages, but have yet to be realized. Here, we report the development of the SNAC-tag (Sequence-specific Nickel Assisted Cleavage) to achieve sequence-specific chemical protein cleavage under biocompatible conditions with comparable efficiency to enzymes. We demonstrate that the SNAC-tag can be inserted before both water-soluble and membrane proteins to achieve fusion protein cleavage, even when enzymatic cleavages fail.
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4
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Abd Elhameed HAH, Hajdu B, Balogh RK, Hermann E, Hunyadi-Gulyás É, Gyurcsik B. Purification of proteins with native terminal sequences using a Ni(II)-cleavable C-terminal hexahistidine affinity tag. Protein Expr Purif 2019; 159:53-59. [PMID: 30905870 DOI: 10.1016/j.pep.2019.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 11/26/2022]
Abstract
The role of the termini of protein sequences is often perturbed by remnant amino acids after the specific protease cleavage of the affinity tags and/or by the amino acids encoded by the plasmid at/around the restriction enzyme sites used to insert the genes. Here we describe a method for affinity purification of a metallonuclease with its precisely determined native termini. First, the gene encoding the target protein is inserted into a newly designed cloning site, which contains two self-eliminating BsmBI restriction enzyme sites. As a consequence, the engineered DNA code of Ni(II)-sensitive Ser-X-His-X motif is fused to the 3'-end of the inserted gene followed by the gene of an affinity tag for protein purification purpose. The C-terminal segment starting from Ser mentioned above is cleaved off from purified protein by a Ni(II)-induced protease-like action. The success of the purification and cleavage was confirmed by gel electrophoresis and mass spectrometry, while structural integrity of the purified protein was checked by circular dichroism spectroscopy. Our new protein expression DNA construct is an advantageous tool for protein purification, when the complete removal of affinity or other tags, without any remaining amino acid residue is essential. The described procedure can easily be generalized and combined with various affinity tags at the C-terminus for chromatographic applications.
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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
| | - Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary
| | - Enikő Hermann
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720, Szeged, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 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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5
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Belczyk-Ciesielska A, Csipak B, Hajdu B, Sparavier A, Asaka MN, Nagata K, Gyurcsik B, Bal W. Nickel(ii)-promoted specific hydrolysis of zinc finger proteins. Metallomics 2018; 10:1089-1098. [DOI: 10.1039/c8mt00098k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The (S/T)XH sequence in Cys2His2zinc fingers can be hydrolytically cleaved by Ni(ii) ions. This reaction can be applied for purification, inhibition or activation of designed zinc finger fusion proteins.
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Affiliation(s)
| | - Brigitta Csipak
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | - Bálint Hajdu
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | | | - Masamitsu N. Asaka
- Nagata Special Laboratory
- Faculty of Medicine
- University of Tsukuba
- Tsukuba 305-8575
- Japan
| | - Kyosuke Nagata
- Nagata Special Laboratory
- Faculty of Medicine
- University of Tsukuba
- Tsukuba 305-8575
- Japan
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics
- Polish Academy of Sciences
- Warsaw
- Poland
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6
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Metal assisted peptide bond hydrolysis: Chemistry, biotechnology and toxicological implications. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.02.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Cabrera-Muñoz A, Rojas L, Gil DF, González-González Y, Mansur M, Camejo A, Pires JR, Alonso-Del-Rivero Antigua M. Heterologous expression of Cenchritis muricatus protease inhibitor II (CmPI-II) in Pichia pastoris system: Purification, isotopic labeling and preliminary characterization. Protein Expr Purif 2016; 126:127-136. [PMID: 27353494 DOI: 10.1016/j.pep.2016.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 10/21/2022]
Abstract
Cenchritis muricatus protease inhibitor II (CmPI-II) is a tight-binding serine protease inhibitor of the Kazal family with an atypical broad specificity, being active against several proteases such as bovine pancreatic trypsin, human neutrophil elastase and subtilisin A. CmPI-II 3D structures are necessary for understanding the molecular basis of its activity. In the present work, we describe an efficient and straightforward recombinant expression strategy, as well as a cost-effective procedure for isotope labeling for NMR structure determination purposes. The vector pCM101 containing the CmPI-II gene, under the control of Pichia pastoris AOX1 promoter was constructed. Methylotrophic Pichia pastoris strain KM71H was then transformed with the plasmid and the recombinant protein (rCmPI-II) was expressed in benchtop fermenter in unlabeled or (15)N-labeled forms using ammonium chloride ((15)N, 99%) as the sole nitrogen source. Protein purification was accomplished by sequential cation exchange chromatography in STREAMLINE DirectHST, anion exchange chromatography on Hitrap Q-Sepharose FF and gel filtration on Superdex 75 10/30, yielding high quantities of pure rCmPI-II and (15)N rCmPI-II. Recombinant proteins displayed similar functional features as compared to the natural inhibitor and NMR spectra indicated folded and homogeneously labeled samples, suitable for further studies of structure and protease-inhibitor interactions.
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Affiliation(s)
- Aymara Cabrera-Muñoz
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
| | - Laritza Rojas
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
| | - Dayrom F Gil
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
| | - Yamile González-González
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
| | - Manuel Mansur
- Institut de Biotecnología i de Biomedicina, Universitat Autònoma de Barcelona, Campus Universitari, 08193, Bellaterra, Cerdanyola del Vallès, Barcelona, Spain.
| | - Ayamey Camejo
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
| | - José R Pires
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Bloco E, Sala 10, 21941-902, Rio de Janeiro, RJ, Brazil.
| | - Maday Alonso-Del-Rivero Antigua
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de La Habana, Ciudad de La Habana-Cuba, Calle 25 No 455, Vedado, La Habana, Cuba.
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8
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Deller MC, Kong L, Rupp B. Protein stability: a crystallographer's perspective. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2016; 72:72-95. [PMID: 26841758 PMCID: PMC4741188 DOI: 10.1107/s2053230x15024619] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 12/21/2015] [Indexed: 12/18/2022]
Abstract
Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.
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Affiliation(s)
- Marc C Deller
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Shriram Center, 443 Via Ortega, Room 097, MC5082, Stanford, CA 94305-4125, USA
| | - Leopold Kong
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 8, Room 1A03, 8 Center Drive, Bethesda, MD 20814, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 91 Audrey Place, Vista, CA 92084, USA
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