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Lamer T, Vederas JC. Simplified cloning and isolation of peptides from "sandwiched" SUMO-peptide-intein fusion proteins. BMC Biotechnol 2023; 23:11. [PMID: 37020212 PMCID: PMC10074672 DOI: 10.1186/s12896-023-00779-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/28/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Some peptides are targets for degradation when heterologously expressed as fusion proteins in E. coli, which can limit yields after isolation and purification. We recently reported that peptide degradation may be prevented by production of a "sandwiched" SUMO-peptide-intein (SPI) fusion protein, which protects the target peptide sequence from truncation and improves yield. This initial system required cloning with two commercially available vectors. It used an N-terminal polyhistidine tagged small ubiquitin-like modifier (SUMO) protein and a C-terminal engineered Mycobacterium xenopii DNA Gyrase A intein with an inserted chitin binding domain (CBD) to create "sandwiched" fusion proteins of the form: His6-SUMO-peptide-intein-CBD. However, the major drawback of this previously reported fusion protein "sandwich" approach is the increased time and number of steps required to complete the cloning and isolation procedures, relative to the simple procedures to produce recombinant peptides in E. coli from a single (non-"sandwiched") fusion protein system. RESULTS In this work we generate the plasmid pSPIH6, which improves upon the previous system by encoding both the SUMO and intein proteins and allows facile construction of a SPI protein in a single cloning step. Additionally, the Mxe GyrA intein encoded in pSPIH6 contains a C-terminal polyhistidine tag, resulting in SPI fusion proteins of the form: His6-SUMO-peptide-intein-CBD-His6. The dual polyhistidine tags greatly simplify isolation procedures compared to the original SPI system, which we have here demonstrated with two linear bacteriocin peptides: leucocin A and lactococcin A. The yields obtained for both peptides after purification were also improved compared to the previous SPI system as a result of this streamlined protocol. CONCLUSIONS This modified SPI system and its simplified cloning and purification procedures described here may be generally useful as a heterologous E. coli expression system to obtain pure peptides in high yield, especially when degradation of the target peptide is an issue.
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Affiliation(s)
- Tess Lamer
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
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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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Cabral ACS, Jakovleska J, Deb A, Penner-Hahn JE, Pecoraro VL, Freisinger E. Further insights into the metal ion binding abilities and the metalation pathway of a plant metallothionein from Musa acuminata. J Biol Inorg Chem 2018; 23:91-107. [PMID: 29218632 PMCID: PMC5756683 DOI: 10.1007/s00775-017-1513-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
The superfamily of metallothioneins (MTs) combines a diverse group of metalloproteins, sharing the characteristics of rather low molecular weight and high cysteine content. The latter provides MTs with the capability to coordinate thiophilic metal ions, in particular those with a d 10 electron configuration. The sub-family of plant MT3 proteins is only poorly characterized and there is a complete lack of three-dimensional structure information. Building upon our previous results on the Musa acuminata MT3 (musMT3) protein, the focus of the present work is to understand the metal cluster formation process, the role of the single histidine residue present in musMT3, and the metal ion binding affinity. We concentrate our efforts on the coordination of ZnII and CdII ions, using CoII as a spectroscopic probe for ZnII binding. The overall protein-fold is analysed with a combination of limited proteolytic digestion, mass spectrometry, and dynamic light scattering. Histidine coordination of metal ions is probed with extended X-ray absorption fine structure spectroscopy and CoII titration experiments. Initial experiments with isothermal titration calorimetry provide insights into the thermodynamics of metal ion binding.
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Affiliation(s)
- Augusto C S Cabral
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jovana Jakovleska
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
| | - James E Penner-Hahn
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
| | - Eva Freisinger
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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Putting the pieces into place: Properties of intact zinc metallothionein 1A determined from interaction of its isolated domains with carbonic anhydrase. Biochem J 2015; 471:347-56. [DOI: 10.1042/bj20150676] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Competitive metallation reactions between the isolated domain fragments and apo-carbonic anhydrase [CA; metal-free CA (apo-CA)] provided the binding affinities for each of the eight sites and showed that CA competed more efficiently for added zinc with the β-domain fragment. The combined effects of the number of sites, chain length and cysteine accessibility modulate the zinc-binding properties of mammalian metallothionein (MT).
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Peroza EA, dos Santos Cabral A, Wan X, Freisinger E. Metal ion release from metallothioneins: proteolysis as an alternative to oxidation. Metallomics 2013; 5:1204-14. [DOI: 10.1039/c3mt00079f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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De Rosa L, Cortajarena AL, Romanelli A, Regan L, D'Andrea LD. Site-specific protein double labeling by expressed protein ligation: applications to repeat proteins. Org Biomol Chem 2011; 10:273-80. [PMID: 22072074 DOI: 10.1039/c1ob06397a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the last few years, the use of labeled proteins has significantly expanded in the life sciences. Now, labeled proteins are indispensable tools for a wide spectrum of biophysical and chemical biology applications. In particular, the quest for more sophisticated experimental setups requires the development of new synthetic methodology, especially for multiple site-specific labeling. In this paper, we describe a synthetic strategy based on expressed protein ligation to prepare proteins in high purity and homogeneity, in which two different molecular probes are incorporated specifically at any desired position. Proteins are sequentially labeled in solution, with the advantage that a large excess of probes is not required and the labeled fragments are not restricted to peptide synthesis length limitations. This strategy was applied to selectively label a repeat protein with a fluorophores pair in different positions along the protein sequence. The doubly labeled proteins were prepared at high purity and homogeneity, as required for single molecule FRET studies. Remarkably, this approach can be adapted to the introduction of more than two molecular probes.
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Affiliation(s)
- Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134, Napoli, Italy
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Aranko AS, Volkmann G. Protein trans-splicing as a protein ligation tool to study protein structure and function. Biomol Concepts 2011; 2:183-98. [DOI: 10.1515/bmc.2011.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 03/10/2011] [Indexed: 01/21/2023] Open
Abstract
AbstractProtein trans-splicing (PTS) exerted by split inteins is a protein ligation reaction which enables overcoming the barriers of conventional heterologous protein production. We provide an overview of the current state-of-the-art in split intein engineering, as well as the achievements of PTS technology in the realm of protein structure-function analyses, including incorporation of natural and artificial protein modifications, controllable protein reconstitution, segmental isotope labeling and protein cyclization. We further discuss factors crucial for the successful implementation of PTS in these protein engineering approaches, and speculate on necessary future endeavours to make PTS a universally applicable protein ligation tool.
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Affiliation(s)
- A. Sesilja Aranko
- 1Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland
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Zhou X, Song Z, Liu X, Jia F, Wang Y. Production of Recombinant Porcine Interferon alpha Using PHB–Intein-Mediated Protein Purification Strategy. Appl Biochem Biotechnol 2010; 163:981-93. [DOI: 10.1007/s12010-010-9101-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2010] [Accepted: 09/28/2010] [Indexed: 01/01/2023]
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Blindauer CA, Leszczyszyn OI. Metallothioneins: unparalleled diversity in structures and functions for metal ion homeostasis and more. Nat Prod Rep 2010; 27:720-41. [PMID: 20442962 DOI: 10.1039/b906685n] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Metallothioneins have been the subject of intense study for five decades, and have greatly inspired the development of bio-analytical methodologies including multi-dimensional and multi-nuclear NMR.With further advancements in molecular biology, protein science, and instrumental techniques, recent years have seen a renaissance of research into metallothioneins. The current report focuses on in vitro studies of so-called class II metallothioneins from a variety of phyla, highlighting the diversity of metallothioneins in terms of structure, biological functions, and molecular functions such as metal ion specificity, thermodynamic stabilities, and kinetic reactivity. We are still far from being able to predict any of these properties, and further efforts will be required to generate the knowledge that will enable a better understanding of what governs the biological and chemical properties of these unusual and intriguing small proteins.
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Gäb J, John H, Melzer M, Blum MM. Stable adducts of nerve agents sarin, soman and cyclosarin with TRIS, TES and related buffer compounds--characterization by LC-ESI-MS/MS and NMR and implications for analytical chemistry. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:1382-90. [PMID: 20172768 DOI: 10.1016/j.jchromb.2010.01.043] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 01/25/2010] [Accepted: 01/26/2010] [Indexed: 11/27/2022]
Abstract
Buffering compounds like TRIS are frequently used in chemical, biochemical and biomedical applications to control pH in solution. One of the prerequisites of a buffer compound, in addition to sufficient buffering capacity and pH stability over time, is its non-reactivity with other constituents of the solution. This is especially important in the field of analytical chemistry where analytes are to be determined quantitatively. Investigating the enzymatic hydrolysis of G-type nerve agents sarin, soman and cyclosarin in buffered solution we have identified stable buffer adducts of TRIS, TES and other buffer compounds with the nerve agents. We identified the molecular structure of these adducts as phosphonic diesters using 1D (1)H-(31)P HSQC NMR and LC-ESI-MS/MS techniques. Reaction rates with TRIS and TES are fast enough to compete with spontaneous hydrolysis in aqueous solution and to yield substantial amounts (up to 20-40%) of buffer adduct over the course of several hours. A reaction mechanism is proposed in which the amino function of the buffer serves as an intramolecular proton acceptor rendering the buffer hydroxyl groups nucleophilic enough for attack on the phosphorus atom of the agents. Results show that similar buffer adducts are formed with a range of hydroxyl and amino function containing buffers including TES, BES, TRIS, BIS-TRIS, BIS-TRIS propane, Tricine, Bicine, HEPES and triethanol amine. It is recommended to use alternative buffers like MOPS, MES and CHES when working with G-type nerve agents especially at higher concentrations and over prolonged times.
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Affiliation(s)
- Jürgen Gäb
- Blum - Scientific Services, Ledererstrasse 23, 80331 Munich, Germany
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Leszczyszyn OI, Blindauer CA. Zinc transfer from the embryo-specific metallothionein EC from wheat: a case study. Phys Chem Chem Phys 2010; 12:13408-18. [DOI: 10.1039/c0cp00680g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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12
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13
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The two distinctive metal ion binding domains of the wheat metallothionein Ec-1. J Inorg Biochem 2009; 103:342-53. [DOI: 10.1016/j.jinorgbio.2008.11.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 11/12/2008] [Accepted: 11/18/2008] [Indexed: 11/23/2022]
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Wan X, Freisinger E. The plant metallothionein 2 from Cicer arietinum forms a single metal–thiolate cluster. Metallomics 2009; 1:489-500. [DOI: 10.1039/b906428a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy has emerged as one of the principle techniques of structural biology. It is not only a powerful method for elucidating the three-dimensional structures under near physiological conditions but also a convenient method for studying protein-ligand interactions and protein dynamics. A major drawback of macromolecular NMR is its size limitation, caused by slower tumbling rates and greater complexity of the spectra as size increases. Segmental isotopic labeling allows for specific segment(s) within a protein to be selectively examined by NMR, thus significantly reducing the spectral complexity for large proteins and allowing for the application of a variety of solution-based NMR strategies. Two related approaches are generally used in the segmental isotopic labeling of proteins: expressed protein ligation and protein trans-splicing. Here, we describe the methodology and recent application of expressed protein ligation and protein trans-splicing for NMR structural studies of proteins and protein complexes. We also describe the protocol used in our lab for the segmental isotopic labeling of a 50-kDa protein Csk (C-terminal Src kinase) using expressed protein ligation methods.
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Freisinger E. Plant MTs—long neglected members of the metallothionein superfamily. Dalton Trans 2008:6663-75. [DOI: 10.1039/b809789e] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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