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Weng D, Yang L, Xie Y. Engineering and characterization of GFP-targeting nanobody: Expression, purification, and post-translational modification analysis. Protein Expr Purif 2024; 221:106501. [PMID: 38782081 DOI: 10.1016/j.pep.2024.106501] [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: 02/21/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Nanobodies are single-variable domain antibodies with excellent properties, which are evolving as versatile tools to guide cognate antigens in vitro and in vivo for biological research, diagnosis, and treatment. Given their simple structure, nanobodies are readily produced in multiple systems. However, selecting an appropriate expression system is crucial because different conditions might cause proteins to produce different folds or post-translational modifications (PTMs), and these differences often result in different functions. At present, the strategies of PTMs are rarely reported. The GFP nanobody can specifically target the GFP protein. Here, we engineered a GFP nanobody fused with 6 × His tag and Fc tag, respectively, and expressed in bacteria and mammalian cells. The 6 × His-GFP-nanobody was produced from Escherichia coli at high yields and the pull-down assay indicated that it can precipitate the GFP protein. Meanwhile, the Fc-GFP-nanobody can be expressed in HEK293T cells, and the co-immunoprecipitation experiment can trace and target the GFP-tagged protein in vivo. Furthermore, some different PTMs in antigen-binding regions have been identified after using mass spectrometry (MS) to analyze the GFP nanobodies, which are expressed in prokaryotes and eukaryotes. In this study, a GFP nanobody was designed, and its binding ability was verified by using the eukaryotic and prokaryotic protein expression systems. In addition, this GFP nanobody was transformed into a useful instrument for more in-depth functional investigations of GFP fusion proteins. MS was further used to explore the reason for the difference in binding ability, providing a novel perspective for the study of GFP nanobodies and protein expression purification.
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Affiliation(s)
- Dunchu Weng
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Lin Yang
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yajun Xie
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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2
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Dilly JJ, Morgan AL, Bedding MJ, Low JKK, Mackay JP, Conibear AC, Bhusal RP, Stone MJ, Franck C, Payne RJ. Tyrosine Sulfation Modulates the Binding Affinity of Chemokine-Targeting Nanobodies. ACS Chem Biol 2024; 19:1426-1432. [PMID: 38941516 DOI: 10.1021/acschembio.4c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Chemokines are an important family of small proteins integral to leukocyte recruitment during inflammation. Dysregulation of the chemokine-chemokine receptor axis is implicated in many diseases, and both chemokines and their cognate receptors have been the targets of therapeutic development. Analysis of the antigen-binding regions of chemokine-binding nanobodies revealed a sequence motif suggestive of tyrosine sulfation. Given the well-established importance of post-translational tyrosine sulfation of receptors for chemokine affinity, it was hypothesized that the sulfation of these nanobodies may contribute to chemokine binding and selectivity. Four nanobodies (16C1, 9F1, 11B1, and 11F2) were expressed using amber codon suppression to incorporate tyrosine sulfation. The sulfated variant of 16C1 demonstrated significantly improved chemokine binding compared to the non-sulfated counterpart, while the other nanobodies displayed equipotent or reduced affinity upon sulfation. The ability of tyrosine sulfation to modulate chemokine binding, both positively and negatively, could be leveraged for chemokine-targeted sulfo-nanobody therapeutics in the future.
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Affiliation(s)
- Joshua J Dilly
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alexandra L Morgan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Max J Bedding
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anne C Conibear
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/163, Wien 1060, Austria
| | - Ram Prasad Bhusal
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Martin J Stone
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Cardiovascular Disease Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Charlotte Franck
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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3
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Tsukamoto A, Jae Man L, Oyama K, Masuda A, Mon H, Ueda T, Kusakabe T. Effective expression and characterization of the receptor binding domains in SARS-CoV-2 Spike proteins from original strain and variants of concern using Bombyx mori nucleopolyhedrovirus in silkworm. Protein Expr Purif 2024; 218:106450. [PMID: 38395208 DOI: 10.1016/j.pep.2024.106450] [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: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
A new coronavirus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the global pandemic of COVID-19 in 2020. Through structural analysis, it was found that several amino acid residues in the human angiotensin-converting enzyme-2 (hACE2) receptor directly interact with those in the receptor binding domain (RBD) of the spike glycoprotein (S-protein). Various cell lines, including HEK293, HeLa cells, and the baculovirus expression vector system (BEVS) with the insect cell line Sf9, have been utilized to produce the RBD. In this study, we investigated the use of Bombyx mori nucleopolyhedrovirus (BmNPV) and BEVS. For efficient production of a highly pure recombinant RBD protein, we designed it with two tags (His tag and STREP tag) at the C-terminus and a solubilizing tag (SUMO) at the N-terminus. After expressing the protein using BmNPV and silkworm and purifying it with a HisTrap excel column, the eluted protein was digested with SUMO protease and further purified using a Strep-Tactin Superflow column. As a result, we obtained the RBD as a monomer with a yield of 2.6 mg/10 mL serum (equivalent to 30 silkworms). The RBD showed an affinity for the hACE2 receptor. Additionally, the RBDs from the Alpha, Beta, Gamma, Delta, and Omicron variants were expressed and purified using the same protocol. It was found that the RBD from the Alpha, Beta, Gamma, and Delta variants could be obtained with yields of 1.4-2.6 mg/10 mL serum and had an affinity to the hACE2 receptor.
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Affiliation(s)
- Akira Tsukamoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Lee Jae Man
- Laboratory of Creative Science for Insect Industries, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kosuke Oyama
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Akitsu Masuda
- Laboratory of Creative Science for Insect Industries, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hiroaki Mon
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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4
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Nazir A, Shad M, Rehman HM, Azim N, Sajjad M. Application of SUMO fusion technology for the enhancement of stability and activity of lysophospholipase from Pyrococcus abyssi. World J Microbiol Biotechnol 2024; 40:183. [PMID: 38722449 DOI: 10.1007/s11274-024-03998-w] [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: 02/11/2024] [Accepted: 04/21/2024] [Indexed: 05/18/2024]
Abstract
Heterologous production of proteins in Escherichia coli has raised several challenges including soluble production of target proteins, high levels of expression and purification. Fusion tags can serve as the important tools to overcome these challenges. SUMO (small ubiquitin-related modifier) is one of these tags whose fusion to native protein sequence can enhance its solubility and stability. In current research, a simple, efficient and cost-effective method is being discussed for the construction of pET28a-SUMO vector. In order to improve the stability and activity of lysophospholipase from Pyrococcus abyssi (Pa-LPL), a 6xHis-SUMO tag was fused to N-terminal of Pa-LPL by using pET28a-SUMO vector. Recombinant SUMO-fused enzyme (6 H-S-PaLPL) works optimally at 35 °C and pH 6.5 with remarkable thermostability at 35-95 °C. Thermo-inactivation kinetics of 6 H-S-PaLPL were also studied at 35-95 °C with first order rate constant (kIN) of 5.58 × 10- 2 h-1 and half-life of 12 ± 0 h at 95 °C. Km and Vmax for the hydrolysis of 4-nitrophenyl butyrate were calculated to be 2 ± 0.015 mM and 3882 ± 22.368 U/mg, respectively. 2.4-fold increase in Vmax of Pa-LPL was observed after fusion of 6xHis-SUMO tag to its N-terminal. It is the first report on the utilization of SUMO fusion tag to enhance the overall stability and activity of Pa-LPL. Fusion of 6xHis-SUMO tag not only aided in the purification process but also played a crucial role in increasing the thermostability and activity of the enzyme. SUMO-fused enzyme, thus generated, can serve as an important candidate for degumming of vegetable oils at industrial scale.
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Affiliation(s)
- Arshia Nazir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mohsin Shad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Naseema Azim
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
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5
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Iwaï H, Beyer HM, Johansson JEM, Li M, Wlodawer A. The three-dimensional structure of the Vint domain from Tetrahymena thermophila suggests a ligand-regulated cleavage mechanism by the HINT fold. FEBS Lett 2024; 598:864-874. [PMID: 38351630 DOI: 10.1002/1873-3468.14817] [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: 11/12/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 04/23/2024]
Abstract
Vint proteins have been identified in unicellular metazoans as a novel hedgehog-related gene family, merging the von Willebrand factor type A domain and the Hedgehog/INTein (HINT) domains. We present the first three-dimensional structure of the Vint domain from Tetrahymena thermophila corresponding to the auto-processing domain of hedgehog proteins, shedding light on the unique features, including an adduct recognition region (ARR). Our results suggest a potential binding between the ARR and sulfated glycosaminoglycans like heparin sulfate. Moreover, we uncover a possible regulatory role of the ARR in the auto-processing by Vint domains, expanding our understanding of the HINT domain evolution and their use in biotechnological applications. Vint domains might have played a crucial role in the transition from unicellular to multicellular organisms.
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Affiliation(s)
- Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Finland
| | - Hannes M Beyer
- Institute of Biotechnology, University of Helsinki, Finland
| | | | - Mi Li
- Center for Structural Biology, National Cancer Institute, Frederick, MD, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, MD, USA
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD, USA
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6
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Melville KT, Kamran M, Yao J, Costa M, Holland M, Taylor NL, Fritz G, Flematti GR, Waters MT. Perception of butenolides by Bacillus subtilis via the α/β hydrolase RsbQ. Curr Biol 2024; 34:623-631.e6. [PMID: 38183985 DOI: 10.1016/j.cub.2023.12.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 01/08/2024]
Abstract
The regulation of behavioral and developmental decisions by small molecules is common to all domains of life. In plants, strigolactones and karrikins are butenolide growth regulators that influence several aspects of plant growth and development, as well as interactions with symbiotic fungi.1,2,3 DWARF14 (D14) and KARRIKIN INSENSITIVE2 (KAI2) are homologous enzyme-receptors that perceive strigolactones and karrikins, respectively, and that require hydrolase activity to effect signal transduction.4,5,6,7 RsbQ, a homolog of D14 and KAI2 from the gram-positive bacterium Bacillus subtilis, regulates growth responses to nutritional stress via the alternative transcription factor SigmaB (σB).8,9 However, the molecular function of RsbQ is unknown. Here, we show that RsbQ perceives butenolide compounds that are bioactive in plants. RsbQ is thermally destabilized by the synthetic strigolactone GR24 and its desmethyl butenolide equivalent dGR24. We show that, like D14 and KAI2, RsbQ is a functional butenolide hydrolase that undergoes covalent modification of the catalytic histidine residue. Exogenous application of both GR24 and dGR24 inhibited the endogenous signaling function of RsbQ in vivo, with dGR24 being 10-fold more potent. Application of dGR24 to B. subtilis phenocopied loss-of-function rsbQ mutations and led to a significant downregulation of σB-regulated transcripts. We also discovered that exogenous butenolides promoted the transition from planktonic to biofilm growth. Our results suggest that butenolides may serve as inter-kingdom signaling compounds between plants and bacteria to help shape rhizosphere communities.
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Affiliation(s)
- Kim T Melville
- School of Molecular Sciences, The University of Western Australia, Perth WA 6009, Australia
| | - Muhammad Kamran
- School of Molecular Sciences, The University of Western Australia, Perth WA 6009, Australia
| | - Jiaren Yao
- School of Molecular Sciences, The University of Western Australia, Perth WA 6009, Australia
| | - Marianne Costa
- School of Molecular Sciences, The University of Western Australia, Perth WA 6009, Australia
| | - Madeleine Holland
- School of Molecular Sciences, The University of Western Australia, Perth WA 6009, Australia
| | - Nicolas L Taylor
- School of Molecular Sciences, The University of Western Australia, Perth WA 6009, Australia; Institute of Agriculture, The University of Western Australia, Perth WA 6009, Australia
| | - Georg Fritz
- School of Molecular Sciences, The University of Western Australia, Perth WA 6009, Australia
| | - Gavin R Flematti
- School of Molecular Sciences, The University of Western Australia, Perth WA 6009, Australia
| | - Mark T Waters
- School of Molecular Sciences, The University of Western Australia, Perth WA 6009, Australia.
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7
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Sudarev VV, Gette MS, Bazhenov SV, Tilinova OM, Zinovev EV, Manukhov IV, Kuklin AI, Ryzhykau YL, Vlasov AV. Ferritin-based fusion protein shows octameric deadlock state of self-assembly. Biochem Biophys Res Commun 2024; 690:149276. [PMID: 38007906 DOI: 10.1016/j.bbrc.2023.149276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/28/2023]
Abstract
Ferritin is a universal protein complex responsible for iron perception in almost all living organisms and has applications from fundamental biophysics to drug delivery and structure-based immunogen design. Different platforms based on ferritin share similar technological challenges limiting their development - control of self-assembling processes of ferritin itself as well as ferritin-based chimeric recombinant protein complexes. In our research, we studied self-assembly processes of ferritin-based protein complexes under different expression conditions. We fused a ferritin subunit with a SMT3 protein tag, a homolog of human Small Ubiquitin-like Modifier (SUMO-tag), which was taken to destabilize ferritin 3-fold channel contacts and increase ferritin-SUMO subunits solubility. We first obtained the octameric protein complex of ferritin-SUMO (8xFer-SUMO) and studied its structural organization by small-angle X-ray scattering (SAXS). Obtained SAXS data correspond well with the high-resolution models predicted by AlphaFold and CORAL software of an octameric assembly around the 4-fold channel of ferritin without formation of 3-fold channels. Interestingly, three copies of 8xFer-SUMO do not assemble into 24-meric globules. Thus, we first obtained and structurally characterized ferritin-based self-assembling oligomers in a deadlock state. Deadlock oligomeric states of ferritin extend the known scheme of its self-assembly process, being new potential tools for a number of applications. Finally, our results might open new directions for various biotechnological platforms utilizing ferritin-based tools.
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Affiliation(s)
- V V Sudarev
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - M S Gette
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - S V Bazhenov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - O M Tilinova
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - E V Zinovev
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - I V Manukhov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation
| | - A I Kuklin
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, 141980, Russian Federation
| | - Yu L Ryzhykau
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, 141980, Russian Federation.
| | - A V Vlasov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russian Federation; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, 141980, Russian Federation.
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8
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Syngkli S, Das B. Purification and characterization of human glycerol 3-phosphate dehydrogenases (mitochondrial and cytosolic) by NAD +/NADH redox method. Biochimie 2023; 214:199-215. [PMID: 37481063 DOI: 10.1016/j.biochi.2023.07.015] [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: 06/29/2023] [Accepted: 07/20/2023] [Indexed: 07/24/2023]
Abstract
Glycerol 3-phosphate (G3P) shuttle is composed of mGPDH and cGPDH and serves as the interface between carbohydrate- and lipid-metabolism. Recently, these metabolic enzymes have been implicated in type II diabetes mellitus but the detailed kinetic parameters and crystal structure of human mGPDH is unknown, though fewer studies on cGPDH are available. To characterize these enzymes, the human mGPDH and cGPDH genes were optimized and cloned into the pET-SUMO vector and pET-24a(+) vector, respectively, and over-expressed in Escherichia coli BL21 (DE3). However, SUMO-mGPDH was expressed as inclusion bodies. Hence, various culture parameters, solubilizing agents and expression vectors were used to solubilize the protein but they did not produce functional SUMO-mGPDH. Over-expression of SUMO-mGPDH along with molecular chaperone (pG-KJE8) produced a functional SUMO-mGPDH. The functional SUMO-mGPDH was purified and characterized using NAD+/NADH redox method. cGPDH was also over-expressed and purified for its characterization. DLS analysis and CD spectra of the purified proteins were performed. The mGPDH was a monomeric enzyme with MW of ∼74 kDa and displayed optimal activity in the Tris-HCl buffer (pH 7.4); while, cGPDH was a homodimer with a monomeric MW of ∼37 kDa and showed optimal activity in imidazole buffer (pH 8.0). The Kmapp was 0.475 mM for G3P, and 0.734 mM for DHAP. These methods may be used to characterize these enzymes to understand their role in metabolic disorders.
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Affiliation(s)
- Superior Syngkli
- Biological Chemistry Laboratory, Department of Zoology, North-Eastern Hill University, Shillong, 793022, India
| | - Bidyadhar Das
- Biological Chemistry Laboratory, Department of Zoology, North-Eastern Hill University, Shillong, 793022, India.
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9
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Tapela K, Opurum PC, Nuokpem FY, Tetteh B, Siaw GK, Humbert MV, Tawiah-Eshun S, Barakisu AI, Asiedu K, Arhin SK, Manu AA, Appiedu-Addo SNA, Obbeng L, Quansah D, Languon S, Anyigba C, Dosoo D, Edu NKO, Oduro-Mensah D, Ampofo W, Tagoe E, Quaye O, Donkor IO, Akorli J, Aniweh Y, Christodoulides M, Mutungi J, Bediako Y, Rayner JC, Awandare GA, McCormick CJ, Quashie PK. Development of an Affordable ELISA Targeting the SARS-CoV-2 Nucleocapsid and Its Application to Samples from the Ongoing COVID-19 Epidemic in Ghana. Mol Diagn Ther 2023; 27:583-592. [PMID: 37462793 PMCID: PMC10435612 DOI: 10.1007/s40291-023-00655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2023] [Indexed: 08/18/2023]
Abstract
INTRODUCTION The true nature of the population spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in populations is often not fully known as most cases, particularly in Africa, are asymptomatic. Finding the true magnitude of SARS-CoV-2 spread is crucial to provide actionable data about the epidemiological progress of the disease for researchers and policymakers. This study developed and optimized an antibody enzyme-linked immunosorbent assay (ELISA) using recombinant nucleocapsid antigen expressed in-house using a simple bacterial expression system. METHODS Nucleocapsid protein from SARS-CoV-2 was expressed and purified from Escherichia coli. Plasma samples used for the assay development were obtained from Ghanaian SARS-CoV-2 seropositive individuals during the pandemic, while seronegative controls were plasma samples collected from blood donors before the coronavirus disease 2019 (COVID-19) pandemic. Another set of seronegative controls was collected during the COVID-19 pandemic. Antibody detection and levels within the samples were validated using commercial kits and Luminex. Analyses were performed using GraphPad Prism, and the sensitivity, specificity and background cut-off were calculated. RESULTS AND DISCUSSION This low-cost ELISA (£0.96/test) assay has a high prediction of 98.9%, and sensitivity and specificity of 97% and 99%, respectively. The assay was subsequently used to screen plasma from SARS-CoV-2 RT-PCR-positive Ghanaians. The assay showed no significant difference in nucleocapsid antibody levels between symptomatic and asymptomatic, with an increase of the levels over time. This is in line with our previous publication. CONCLUSION This study developed a low-cost and transferable assay that enables highly sensitive and specific detection of human anti-SARS-CoV-2 IgG antibodies. This assay can be modified to include additional antigens and used for continuous monitoring of sero-exposure to SARS-CoV-2 in West Africa.
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Affiliation(s)
- Kesego Tapela
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Precious C Opurum
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Franklin Y Nuokpem
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Becky Tetteh
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Godfred K Siaw
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Maria V Humbert
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Sylvia Tawiah-Eshun
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Anna Ibrahim Barakisu
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Kwame Asiedu
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Samuel Kojo Arhin
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Aaron A Manu
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Sekyibea N A Appiedu-Addo
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Louisa Obbeng
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Darius Quansah
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Sylvester Languon
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Claudia Anyigba
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Daniel Dosoo
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Nelson K O Edu
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Daniel Oduro-Mensah
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - William Ampofo
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Emmanuel Tagoe
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Irene Owusu Donkor
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Jewelna Akorli
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Yaw Aniweh
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Myron Christodoulides
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Joe Mutungi
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- Yemaachi Biotech Inc., 222 Swaniker St, Accra, Ghana
| | - Julian C Rayner
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Christopher J McCormick
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Peter Kojo Quashie
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana.
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.
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10
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Singh AK, Krężel A. Calcium-assisted sortase A cleavage of SUMOylated metallothionein constructs leads to high-yield production of human MT3. Microb Cell Fact 2023; 22:125. [PMID: 37434134 DOI: 10.1186/s12934-023-02134-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/24/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Mammalian metallothioneins (MTs) are small (6-7 kDa), intracellular, cysteine-rich, metal-binding proteins involved, inter alia, in the homeostasis of zinc and copper, detoxification of heavy metals, antioxidation against reactive oxygen species, and protection against DNA damage. The high cysteine content (~ 30%) in MTs makes them toxic to bacterial cells during protein production, resulting in low yield. To address this issue, we present for the first time a combinatorial approach using the small ubiquitin-like modifier (SUMO) and/or sortase as fusion tags for high-level expression of human MT3 in E. coli and its purification by three different strategies. RESULTS Three different plasmids were generated using SUMO, sortase A pentamutant (eSrtA), and sortase recognition motif (LPETG) as removable fusion tags for high-level expression and purification of human MT3 from the bacterial system. In the first strategy, SUMOylated MT3 was expressed and purified using Ulp1-mediated cleavage. In the second strategy, SUMOylated MT3 with a sortase recognition motif at the N-terminus of MT3 was expressed and purified using sortase-mediated cleavage. In the final strategy, the fusion protein His6-SUMO-eSrtA-LPETG-MT3 was expressed and purified by one-step sortase-mediated inducible on-bead autocleavage. Using these three strategies the apo-MT3 was purified in a yield of 11.5, 11, and 10.8 mg/L, respectively, which is the highest yield achieved for MT expression and purification to date. No effect of MT3 on Ni2+-containing resin was observed. CONCLUSION The SUMO/sortase-based strategy used as the production system for MT3 resulted in a very high expression level and protein production yield. The apo-MT3 purified by this strategy contained an additional glycine residue and had similar metal binding properties as WT-MT3. This SUMO-sortase fusion system is a simple, robust, and inexpensive one-step purification approach for various MTs as well as other toxic proteins with very high yield via immobilized metal affinity chromatography (IMAC).
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Affiliation(s)
- Avinash Kumar Singh
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383, Wrocław, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383, Wrocław, Poland.
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11
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Tovar-Ramírez ME, Schuth N, Rodríguez O, Kroll T, Saab-Rincon G, Costas M, Lampi K, Quintanar L. ATCUN-like Copper Site in βB2-Crystallin Plays a Protective Role in Cataract-Associated Aggregation. Inorg Chem 2023; 62:10592-10604. [PMID: 37379524 PMCID: PMC11156493 DOI: 10.1021/acs.inorgchem.3c00794] [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] [Indexed: 06/30/2023]
Abstract
Cataract is the leading cause of blindness worldwide, and it is caused by crystallin damage and aggregation. Senile cataractous lenses have relatively high levels of metals, while some metal ions can directly induce the aggregation of human γ-crystallins. Here, we evaluated the impact of divalent metal ions in the aggregation of human βB2-crystallin, one of the most abundant crystallins in the lens. Turbidity assays showed that Pb2+, Hg2+, Cu2+, and Zn2+ ions induce the aggregation of βB2-crystallin. Metal-induced aggregation is partially reverted by a chelating agent, indicating the formation of metal-bridged species. Our study focused on the mechanism of copper-induced aggregation of βB2-crystallin, finding that it involves metal-bridging, disulfide-bridging, and loss of protein stability. Circular dichroism and electron paramagnetic resonance (EPR) revealed the presence of at least three Cu2+ binding sites in βB2-crystallin, one of them with spectroscopic features typical for Cu2+ bound to an amino-terminal copper and nickel (ATCUN) binding motif, which is found in Cu transport proteins. The ATCUN-like Cu binding site is located at the unstructured N-terminus of βB2-crystallin, and it could be modeled by a peptide with the first six residues in the protein sequence (NH2-ASDHQF-). Isothermal titration calorimetry indicates a nanomolar Cu2+ binding affinity for the ATCUN-like site. An N-truncated form of βB2-crystallin is more susceptible to Cu-induced aggregation and is less thermally stable, indicating a protective role for the ATCUN-like site. EPR and X-ray absorption spectroscopy studies reveal the presence of a copper redox active site in βB2-crystallin that is associated with metal-induced aggregation and formation of disulfide-bridged oligomers. Our study demonstrates metal-induced aggregation of βB2-crystallin and the presence of putative copper binding sites in the protein. Whether the copper-transport ATCUN-like site in βB2-crystallin plays a functional/protective role or constitutes a vestige from its evolution as a lens structural protein remains to be elucidated.
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Affiliation(s)
- Martin E. Tovar-Ramírez
- Department of Chemistry, Centro de Investigación y de Estudios Avanzados (Cinvestav), Mexico City, 07360, Mexico
| | - Nils Schuth
- Department of Chemistry, Centro de Investigación y de Estudios Avanzados (Cinvestav), Mexico City, 07360, Mexico
| | - Oscar Rodríguez
- Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City, 04510, Mexico
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA
| | - Gloria Saab-Rincon
- Department of Biocatalysis and Cellular Engineering, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, 62210, Mexico
| | - Miguel Costas
- Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City, 04510, Mexico
| | - Kirsten Lampi
- Integrative Biosciences, Oregon Health & Science University, Portland, Oregon, 97239, United States
| | - Liliana Quintanar
- Department of Chemistry, Centro de Investigación y de Estudios Avanzados (Cinvestav), Mexico City, 07360, Mexico
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12
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Mani S, Kaur A, Jakhar K, Kumari G, Sonar S, Kumar A, Das S, Kumar S, Kumar V, Kundu R, Pandey AK, Singh UP, Majumdar T. Targeting DPP4-RBD interactions by sitagliptin and linagliptin delivers a potential host-directed therapy against pan-SARS-CoV-2 infections. Int J Biol Macromol 2023; 245:125444. [PMID: 37385308 PMCID: PMC10293653 DOI: 10.1016/j.ijbiomac.2023.125444] [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: 02/15/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023]
Abstract
Highly mutated SARS-CoV-2 is known aetiological factor for COVID-19. Here, we have demonstrated that the receptor binding domain (RBD) of the spike protein can interact with human dipeptidyl peptidase 4 (DPP4) to facilitate virus entry, in addition to the usual route of ACE2-RBD binding. Significant number of residues of RBD makes hydrogen bonds and hydrophobic interactions with α/β-hydrolase domain of DPP4. With this observation, we created a strategy to combat COVID-19 by circumventing the catalytic activity of DPP4 using its inhibitors. Sitagliptin, linagliptin or in combination disavowed RBD to establish a heterodimer complex with both DPP4 and ACE2 which is requisite strategy for virus entry into the cells. Both gliptins not only impede DPP4 activity, but also prevent ACE2-RBD interaction, crucial for virus growth. Sitagliptin, and linagliptin alone or in combination have avidity to impede the growth of pan-SARS-CoV-2 variants including original SARS-CoV-2, alpha, beta, delta, and kappa in a dose dependent manner. However, these drugs were unable to alter enzymatic activity of PLpro and Mpro. We conclude that viruses hijack DPP4 for cell invasion via RBD binding. Impeding RBD interaction with both DPP4 and ACE2 selectively by sitagliptin and linagliptin is an potential strategy for efficiently preventing viral replication.
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Affiliation(s)
- Shailendra Mani
- Translational Health Science and Technology Institute, Faridabad, India
| | | | - Kamini Jakhar
- Translational Health Science and Technology Institute, Faridabad, India
| | | | - Sudipta Sonar
- Translational Health Science and Technology Institute, Faridabad, India
| | - Amit Kumar
- National Institute of Immunology, New Delhi, India
| | - Sudesna Das
- CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | | | - Vijay Kumar
- National Institute of Immunology, New Delhi, India
| | - Rakesh Kundu
- Department of Zoology, Visva-Bharati University, Santiniketan, West Bengal, India
| | - Anil Kumar Pandey
- Department of Physiology, ESIC Medical College & Hospital, Faridabad, India
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13
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Demay F, Hallier M, Georgeault S, Com E, Cattoir V, Goude R, Gillet R. Simple purification and characterization of soluble and homogenous ABC-F translation factors from Enterococcus faecium. Protein Expr Purif 2023:106325. [PMID: 37354924 DOI: 10.1016/j.pep.2023.106325] [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: 12/05/2022] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023]
Abstract
The family of ATP-binding cassette F proteins (ABC-F) is mainly made up of cytosolic proteins involved in regulating protein synthesis, and they are often part of a mechanism that confers resistance to ribosome-targeting antibiotics. The existing literature has emphasized the difficulty of purifying these recombinant proteins because of their very low solubility and stability. Here, we describe a rapid and efficient three-step purification procedure that allows for the production of untagged ABC-F proteins from Enterococcus faecium in the heterologous host Escherichia coli. After four purified ABC-F proteins were produced using this protocol, their biological activities were validated by in vitro experiment. In conclusion, our study provides an invaluable tool for obtaining large amounts of untagged and soluble ABC-F proteins that can then be used for in vitro experiments.
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Affiliation(s)
- Fanny Demay
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Marc Hallier
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Sylvie Georgeault
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000, Rennes, France; Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, F-35000, Rennes, France
| | - Vincent Cattoir
- Department of Clinical Microbiology, Rennes University Hospital, Rennes, France; Univ. Rennes, Inserm, UMR 1230 BRM, Rennes, France
| | - Renan Goude
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Reynald Gillet
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France.
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14
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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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15
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Philipp M, Müller L, Andrée M, Hussnaetter KP, Schaal H, Feldbrügge M, Schipper K. Efficient virus detection utilizing chitin-immobilized nanobodies synthesized in Ustilago maydis. J Biotechnol 2023; 366:72-84. [PMID: 36948402 PMCID: PMC10028217 DOI: 10.1016/j.jbiotec.2023.03.005] [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: 12/12/2022] [Revised: 02/08/2023] [Accepted: 03/16/2023] [Indexed: 03/24/2023]
Abstract
The COVID-19 pandemic has greatly impacted the global economy and health care systems, illustrating the urgent need for timely and inexpensive responses to pandemic threats in the form of vaccines and antigen tests. Currently, antigen testing is mostly conducted by qualitative flow chromatography or via quantitative ELISA-type assays. The latter mostly utilize materials like protein-adhesive polymers and gold or latex particles. Here we present an alternative ELISA approach using inexpensive, biogenic materials and permitting quick detection based on components produced in the microbial model Ustilago maydis. In this fungus, heterologous proteins like biopharmaceuticals can be exported by fusion to unconventionally secreted chitinase Cts1. As a unique feature, the carrier chitinase binds to chitin allowing its additional use as a purification or immobilization tag. Recent work has demonstrated that nanobodies are suitable target proteins. These proteins represent a very versatile alternative antibody format and can quickly be adapted to detect novel antigens by camelidae immunization or synthetic libraries. In this study, we exemplarily produced different mono- and bivalent SARS-CoV-2 nanobodies directed against the spike protein receptor binding domain (RBD) as Cts1 fusions and screened their antigen binding affinity in vitro and in vivo. Functional nanobody-Cts1 fusions were immobilized on chitin forming an RBD tethering surface. This provides a solid base for future development of inexpensive antigen tests utilizing unconventionally secreted nanobodies as antigen trap and a matching ubiquitous and biogenic surface for immobilization.
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Affiliation(s)
- Magnus Philipp
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Marcel Andrée
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Kai P Hussnaetter
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Kerstin Schipper
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany.
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16
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Ashraf QF, Quilates EJ, Olaoye OO, de Araujo ED, Gunning PT. Fluorescence Polarization-Based Competition Assays to Evaluate Histone Deacetylase 6 Inhibitors. Methods Mol Biol 2023; 2589:481-492. [PMID: 36255644 DOI: 10.1007/978-1-0716-2788-4_31] [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: 06/16/2023]
Abstract
Histone deacetylase 6 (HDAC6) is an emerging clinical target for the treatment of several hematological cancers and central nervous system disorders. HDAC6 catalyzes the deacetylation of lysine residues on substrates such as tubulin, with profound implications in key cellular processes, including cellular motility and migration. This critical deacetylation activity occurs at the catalytic domain 2 (CD2) of HDAC6, and small molecule inhibitors of HDAC6 are designed to target CD2. We briefly highlight previously reported strategies for recombinant bacterial expression and purification of the HDAC6 CD2. We aim to discuss competition assays that have been used to evaluate the potency of potential HDAC6 inhibitors against CD2 via displacement of pre-bound fluorescent HDAC-probes. Moreover, we elaborate on previous protocols that have been employed in inhibitor screening and present an HDAC6-selective probe that also enables rapid and reliable high-throughput screening of new chemical entities designed to target the HDAC6 CD2.
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Affiliation(s)
- Qirat F Ashraf
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Erica J Quilates
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Olasunkanmi O Olaoye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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17
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Guhathakurta P, Carter AL, Thompson AR, Kurila D, LaFrence J, Zhang L, Trask JR, Vanderheyden B, Muretta JM, Ervasti JM, Thomas DD. Enhancing interaction of actin and actin-binding domain 1 of dystrophin with modulators: Toward improved gene therapy for Duchenne muscular dystrophy. J Biol Chem 2022; 298:102675. [PMID: 36372234 PMCID: PMC9731851 DOI: 10.1016/j.jbc.2022.102675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Duchenne muscular dystrophy is a lethal muscle disease, caused by mutations in the gene encoding dystrophin, an actin-binding cytoskeletal protein. Absence of functional dystrophin results in muscle weakness and degeneration, eventually leading to cardiac and respiratory failure. Strategies to replace the missing dystrophin via gene therapy have been intensively pursued. However, the dystrophin gene is too large for current gene therapy approaches. Currently available micro-dystrophin constructs lack the actin-binding domain 2 and show decreased actin-binding affinity in vitro compared to full-length dystrophin. Thus, increasing the actin-binding affinity of micro-dystrophin, using small molecules, could be a beneficial therapeutic approach. Here, we have developed and validated a novel high-throughput screening (HTS) assay to discover small molecules that increase the binding affinity of dystrophin's actin-binding domain 1 (ABD1). We engineered a novel FRET biosensor, consisting of the mClover3, fluorescent protein (donor) attached to the C-terminus of dystrophin ABD1, and Alexa Fluor 568 (acceptor) attached to the C-terminal cysteine of actin. We used this biosensor in small-molecule screening, using a unique high-precision, HTS fluorescence lifetime assay, identifying several compounds from an FDA-approved library that significantly increase the binding between actin and ABD1. This HTS assay establishes feasibility for the discovery of small-molecule modulators of the actin-dystrophin interaction, with the ultimate goal of developing therapies for muscular dystrophy.
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18
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Optimized method for the recombinant production of a sea anemone’s peptide. MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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A Novel Tandem-Tag Purification Strategy for Challenging Disordered Proteins. Biomolecules 2022; 12:biom12111566. [DOI: 10.3390/biom12111566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) lack well-defined 3D structures and can only be described as ensembles of different conformations. This high degree of flexibility allows them to interact promiscuously and makes them capable of fulfilling unique and versatile regulatory roles in cellular processes. These functional benefits make IDPs widespread in nature, existing in every living organism from bacteria and fungi to plants and animals. Due to their open and exposed structural state, IDPs are much more prone to proteolytic degradation than their globular counterparts. Therefore, the purification of recombinant IDPs requires extra care and caution, such as maintaining low temperature throughout the purification, the use of protease inhibitor cocktails and fast workflow. Even so, in the case of long IDP targets, the appearance of truncated by-products often seems unavoidable. The separation of these unwanted proteins can be very challenging due to their similarity to the parent target protein. Here, we describe a tandem-tag purification method that offers a remedy to this problem. It contains only common affinity-chromatography steps (HisTrap and Heparin) to ensure low cost, easy access and scaling-up for possible industrial use. The effectiveness of the method is demonstrated with four examples, Tau-441 and two of its fragments and the transactivation domain (AF1) of androgen receptor.
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20
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Chen Z, Huang J, Li J. Protein purification, crystallization, and structure determination of human DEAD-box RNA helicase DDX21 in different unwinding states. STAR Protoc 2022; 3:101642. [PMID: 36042885 PMCID: PMC9420396 DOI: 10.1016/j.xpro.2022.101642] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA helicase DDX21 plays vital roles in ribosomal RNA processing and the regulation of host innate immunity during virus infection. Here, we describe the optimized protocols for nucleic acid-free protein purification and crystallization of DDX21 in its different unwinding states. Rational design of the flexible region within the helicase core, and biophysical approach to characterize interactions between DDX21 and RNA, leads to successful crystallization of DDX21. This protocol can be applied to the crystallography of other DExD/H-box RNA helicases. For complete details on the use and execution of this protocol, please refer to Chen et al. (2020). Optimized protocols for nucleic acid-free DDX21 protein purification Rational design of the flexible region within DDX21 helicase core Biophysical approach to characterize interactions between DDX21 and RNA Crystallization of ligand-free DDX21 or in complex with ATP analogs or RNA of interest
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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Affiliation(s)
- Zijun Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Engineering Research Center of Gene Technology of MOE, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Engineering Research Center of Gene Technology of MOE, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai 200438, China.
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21
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Birtles D, Oh AE, Lee J. Exploring the
pH
dependence of the
SARS‐CoV
‐2 complete fusion domain and the role of its unique structural features. Protein Sci 2022. [PMCID: PMC9538437 DOI: 10.1002/pro.4390] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
SARS‐CoV‐2 may enter target cells through the process of membrane fusion at either the plasma (~pH 7.4–7.0) or endosomal (~pH 6.5–5.0) membrane in order to deliver its genetic information. The fusion domain (FD) of the spike glycoprotein is responsible for initiating fusion and is thus integral to the viral life cycle. The FD of SARS‐CoV‐2 is unique in that it consists of two structurally distinctive regions referred to as the fusion peptide (FP) and the fusion loop (FL); yet the molecular mechanisms behind how this FD perturbs the membrane to initiate fusion remains unclear. In this study via solution NMR, we witnessed only a slight conformational change in the FD between pH 7.4 and pH 5.0, resulting in a minor elongation of helix 1. However, we found that the FD's ability to mediate membrane fusion has a large and significant pH dependence, with fusion events being more readily induced at low pH. Interestingly, a biphasic relationship between the environmental pH and fusogenicity was discovered, suggesting a preference for the FD to initiate fusion at the late endosomal membrane. Furthermore, the conserved disulfide bond and hydrophobic motif “LLF” were found to be critical for the function of the complete FD, with minimal activity witnessed when either was perturbed. In conclusion, these findings indicate that the SARS‐CoV‐2 FD preferably initiates fusion at a pH similar to the late endosome through a mechanism that heavily relies on the internal disulfide bond of the FL and hydrophobic LLF motif within the FP.
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Affiliation(s)
- Daniel Birtles
- Department of Chemistry and Biochemistry University of Maryland College Park Maryland USA
| | - Anna E. Oh
- Department of Chemistry and Biochemistry University of Maryland College Park Maryland USA
| | - Jinwoo Lee
- Department of Chemistry and Biochemistry University of Maryland College Park Maryland USA
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22
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Abstract
All known triterpenes are generated by triterpene synthases (TrTSs) from squalene or oxidosqualene1. This approach is fundamentally different from the biosynthesis of short-chain (C10–C25) terpenes that are formed from polyisoprenyl diphosphates2–4. In this study, two fungal chimeric class I TrTSs, Talaromyces verruculosus talaropentaene synthase (TvTS) and Macrophomina phaseolina macrophomene synthase (MpMS), were characterized. Both enzymes use dimethylallyl diphosphate and isopentenyl diphosphate or hexaprenyl diphosphate as substrates, representing the first examples, to our knowledge, of non-squalene-dependent triterpene biosynthesis. The cyclization mechanisms of TvTS and MpMS and the absolute configurations of their products were investigated in isotopic labelling experiments. Structural analyses of the terpene cyclase domain of TvTS and full-length MpMS provide detailed insights into their catalytic mechanisms. An AlphaFold2-based screening platform was developed to mine a third TrTS, Colletotrichum gloeosporioides colleterpenol synthase (CgCS). Our findings identify a new enzymatic mechanism for the biosynthesis of triterpenes and enhance understanding of terpene biosynthesis in nature. Chimeric triterpene synthases are identified that catalyse non-squalene-dependent triterpene biosynthesis.
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23
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Heikkinen HA, Aranko AS, Iwaï H. The NMR structure of the engineered halophilic DnaE intein for segmental isotopic labeling using conditional protein splicing. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 338:107195. [PMID: 35398651 DOI: 10.1016/j.jmr.2022.107195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/02/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
Protein trans-splicing catalyzed by split inteins has been used for segmental isotopic labeling of proteins for alleviating the complexity of NMR signals. Whereas inteins spontaneously trigger protein splicing upon protein folding, inteins from extremely halophilic organisms require a high salinity condition to induce protein splicing. We designed and created a salt-inducible intein from the widely used DnaE intein from Nostoc punctiforme by introducing 29 mutations, which required a lower salt concentration than naturally occurring halo-obligate inteins. We determined the NMR solution structure of the engineered salt-inducible DnaE intein in 2 M NaCl, showing the essentially identical three-dimensional structure to the original one, albeit it unfolds without salts. The NMR structure of a halo-obligate intein under high salinity suggests that the stabilization of the active folded conformation is not a mere result of various intramolecular interactions but the subtle energy balance from the complex interactions, including the solvation energy, which involve waters, ions, co-solutes, and protein polypeptide chains.
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Affiliation(s)
- Harri A Heikkinen
- Institute of Biotechnology, University of Helsinki, PO Box 65, Helsinki, FIN-00014, Finland
| | - A Sesilja Aranko
- Institute of Biotechnology, University of Helsinki, PO Box 65, Helsinki, FIN-00014, Finland.
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, PO Box 65, Helsinki, FIN-00014, Finland.
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24
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Beyer HM, Iwaï H. Structural Basis for the Propagation of Homing Endonuclease-Associated Inteins. Front Mol Biosci 2022; 9:855511. [PMID: 35372505 PMCID: PMC8966425 DOI: 10.3389/fmolb.2022.855511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Inteins catalyze their removal from a host protein through protein splicing. Inteins that contain an additional site-specific endonuclease domain display genetic mobility via a process termed “homing” and thereby act as selfish DNA elements. We elucidated the crystal structures of two archaeal inteins associated with an active or inactive homing endonuclease domain. This analysis illustrated structural diversity in the accessory domains (ACDs) associated with the homing endonuclease domain. To augment homing endonucleases with highly specific DNA cleaving activity using the intein scaffold, we engineered the ACDs and characterized their homing site recognition. Protein engineering of the ACDs in the inteins illuminated a possible strategy for how inteins could avoid their extinction but spread via the acquisition of a diverse accessory domain.
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Affiliation(s)
- Hannes M. Beyer
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- *Correspondence: Hideo Iwaï, or,
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25
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Ortega C, Oppezzo P, Correa A. Overcoming the Solubility Problem in E. coli: Available Approaches for Recombinant Protein Production. Methods Mol Biol 2022; 2406:35-64. [PMID: 35089549 DOI: 10.1007/978-1-0716-1859-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Despite the importance of recombinant protein production in the academy and industrial fields, many issues concerning the expression of soluble and homogeneous products are still unsolved. Several strategies were developed to overcome these obstacles; however, at present, there is no magic bullet that can be applied for all cases. Indeed, several key expression parameters need to be evaluated for each protein. Among the different hosts for protein expression, Escherichia coli is by far the most widely used. In this chapter, we review many of the different tools employed to circumvent protein insolubility problems.
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Affiliation(s)
- Claudia Ortega
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Oppezzo
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
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26
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Cáceres JC, Bailey CA, Yokoyama K, Greene BL. Selenocysteine substitutions in thiyl radical enzymes. Methods Enzymol 2022; 662:119-141. [DOI: 10.1016/bs.mie.2021.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Imaging of anthrax intoxication in mice reveals shared and individual functions of surface receptors CMG-2 and TEM-8 in cellular toxin entry. J Biol Chem 2021; 298:101467. [PMID: 34871548 PMCID: PMC8716333 DOI: 10.1016/j.jbc.2021.101467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/12/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022] Open
Abstract
Bacillus anthracis lethal toxin and edema toxin are binary toxins that consist of a common cell-binding moiety, protective antigen (PA), and the enzymatic moieties, lethal factor (LF) and edema factor (EF). PA binds to either of two receptors, capillary morphogenesis protein-2 (CMG-2) or tumor endothelial marker-8 (TEM-8), which triggers the binding and cytoplasmic translocation of LF and EF. However, the distribution of functional TEM-8 and CMG-2 receptors during anthrax toxin intoxication in animals has not been fully elucidated. Herein, we describe an assay to image anthrax toxin intoxication in animals, and we use it to visualize TEM-8- and CMG-2-dependent intoxication in mice. Specifically, we generated a chimeric protein consisting of the N-terminal domain of LF fused to a nuclear localization signal-tagged Cre recombinase (LFn-NLS-Cre). When PA and LFn-NLS-Cre were coadministered to transgenic mice expressing a red fluorescent protein in the absence of Cre and a green fluorescent protein in the presence of Cre, intoxication could be visualized at single-cell resolution by confocal microscopy or flow cytometry. Using this assay, we found that: (a) CMG-2 is critical for intoxication in the liver and heart, (b) TEM-8 is required for intoxication in the kidney and spleen, (c) CMG-2 and TEM-8 are redundant for intoxication of some organs, (d) combined loss of CMG-2 and TEM-8 completely abolishes intoxication, and (e) CMG-2 is the dominant receptor on leukocytes. The novel assay will be useful for basic and clinical/translational studies of Bacillus anthracis infection and for clinical development of reengineered toxin variants for cancer treatment.
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28
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Birtles D, Lee J. Identifying Distinct Structural Features of the SARS-CoV-2 Spike Protein Fusion Domain Essential for Membrane Interaction. Biochemistry 2021; 60:2978-2986. [PMID: 34570469 PMCID: PMC8491435 DOI: 10.1021/acs.biochem.1c00543] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/20/2021] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 spike protein is the primary antigenic determinant of the virus and has been studied extensively, yet the process of membrane fusion remains poorly understood. The fusion domain (FD) of viral glycoproteins is well established as facilitating the initiation of membrane fusion. An improved understanding of the structural plasticity associated with these highly conserved regions aids in our knowledge of the molecular mechanisms that drive viral fusion. Within the spike protein, the FD of SARS-CoV-2 exists immediately following S2' cleavage at the N-terminus of the S2 domain. Here we have shown that following the introduction of a membrane at pH 7.4, the FD undergoes a transition from a random coil to a more structurally well-defined postfusion state. Furthermore, we have classified the domain into two distinct regions, a fusion peptide (FP, S816-G838) and a fusion loop (FL, D839-F855). The FP forms a helix-turn-helix motif upon association with a membrane, and the favorable entropy gained during this transition from a random coil is likely the driving force behind membrane insertion. Membrane depth experiments then revealed the FP is found inserted within the membrane below the lipid headgroups, while the interaction of the FL with the membrane is shallower in nature. Thus, we propose a structural model relevant to fusion at the plasma membrane in which the FP inserts itself just below the phospholipid headgroups and the FL lays upon the lipid membrane surface.
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Affiliation(s)
- Daniel Birtles
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Jinwoo Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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29
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The Inducible Intein-Mediated Self-Cleaving Tag (IIST) System: A Novel Purification and Amidation System for Peptides and Proteins. Molecules 2021; 26:molecules26195948. [PMID: 34641492 PMCID: PMC8512742 DOI: 10.3390/molecules26195948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022] Open
Abstract
An efficient self-cleavable purification tag could be a powerful tool for purifying recombinant proteins and peptides without additional proteolytic processes using specific proteases. Thus, the intein-mediated self-cleavage tag was developed and has been commercially available as the IMPACT™ system. However, uncontrolled cleavages of the purification tag by the inteins in the IMPACT™ system have been reported, thereby reducing final yields. Therefore, controlling the protein-splicing activity of inteins has become critical. Here we utilized conditional protein splicing by salt conditions. We developed the inducible intein-mediated self-cleaving tag (IIST) system based on salt-inducible protein splicing of the MCM2 intein from the extremely halophilic archaeon, Halorhabdus utahensis and applied it to small peptides. Moreover, we described a method for the amidation using the same IIST system and demonstrated 15N-labeling of the C-terminal amide group of a single domain antibody (VHH).
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30
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Use of tandem affinity-buffer exchange chromatography online with native mass spectrometry for optimizing overexpression and purification of recombinant proteins. Methods Enzymol 2021; 659:37-70. [PMID: 34752295 DOI: 10.1016/bs.mie.2021.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Purification of recombinant proteins typically entails overexpression in heterologous systems and subsequent chromatography-based isolation. While denaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis is routinely used to screen a variety of overexpression conditions (e.g., host, medium, inducer concentration, post-induction temperature and/or incubation time) and to assess the purity of the final product, its limitations, including aberrant protein migration due to compositional eccentricities or incomplete denaturation, often preclude firm conclusions regarding the extent of overexpression and/or purification. Therefore, we recently reported an automated liquid chromatography-mass spectrometry-based strategy that couples immobilized metal affinity chromatography (IMAC) with size exclusion-based online buffer exchange (OBE) and native mass spectrometry (nMS) to directly analyze cell lysates for the presence of target proteins. IMAC-OBE-nMS can be used to assess whether target proteins (1) are overexpressed in soluble form, (2) bind and elute from an IMAC resin, (3) oligomerize, and (4) have the expected mass. Here, we use four poly-His-tagged proteins to demonstrate the potential of IMAC-OBE-nMS for expedient optimization of overexpression and purification conditions for recombinant protein production.
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31
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Hsu STD, Lee YTC, Mikula KM, Backlund SM, Tascón I, Goldman A, Iwaï H. Tying up the Loose Ends: A Mathematically Knotted Protein. Front Chem 2021; 9:663241. [PMID: 34109153 PMCID: PMC8182377 DOI: 10.3389/fchem.2021.663241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
Knots have attracted scientists in mathematics, physics, biology, and engineering. Long flexible thin strings easily knot and tangle as experienced in our daily life. Similarly, long polymer chains inevitably tend to get trapped into knots. Little is known about their formation or function in proteins despite >1,000 knotted proteins identified in nature. However, these protein knots are not mathematical knots with their backbone polypeptide chains because of their open termini, and the presence of a “knot” depends on the algorithm used to create path closure. Furthermore, it is generally not possible to control the topology of the unfolded states of proteins, therefore making it challenging to characterize functional and physicochemical properties of knotting in any polymer. Covalently linking the amino and carboxyl termini of the deeply trefoil-knotted YibK from Pseudomonas aeruginosa allowed us to create the truly backbone knotted protein by enzymatic peptide ligation. Moreover, we produced and investigated backbone cyclized YibK without any knotted structure. Thus, we could directly probe the effect of the backbone knot and the decrease in conformational entropy on protein folding. The backbone cyclization did not perturb the native structure and its cofactor binding affinity, but it substantially increased the thermal stability and reduced the aggregation propensity. The enhanced stability of a backbone knotted YibK could be mainly originated from an increased ruggedness of its free energy landscape and the destabilization of the denatured state by backbone cyclization with little contribution from a knot structure. Despite the heterogeneity in the side-chain compositions, the chemically unfolded cyclized YibK exhibited several macroscopic physico-chemical attributes that agree with theoretical predictions derived from polymer physics.
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Affiliation(s)
- Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Yun-Tzai Cloud Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Kornelia M Mikula
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sofia M Backlund
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Igor Tascón
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Adrian Goldman
- Division of Biochemistry, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, West Yorkshire, United Kingdom
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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32
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Fatima K, Naqvi F, Younas H. A Review: Molecular Chaperone-mediated Folding, Unfolding and Disaggregation of Expressed Recombinant Proteins. Cell Biochem Biophys 2021; 79:153-174. [PMID: 33634426 DOI: 10.1007/s12013-021-00970-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/01/2021] [Indexed: 12/26/2022]
Abstract
The advancements in biotechnology over time have led to an increase in the demand of pure, soluble and functionally active proteins. Recombinant protein production has thus been employed to obtain high expression of purified proteins in bulk. E. coli is considered as the most desirable host for recombinant protein production due to its inexpensive and fast cultivation, simple nutritional requirements and known genetics. Despite all these benefits, recombinant protein production often comes with drawbacks, such as, the most common being the formation of inclusion bodies due to improper protein folding. Consequently, this can lead to the loss of the structure-function relationship of a protein. Apart from various strategies, one major strategy to resolve this issue is the use of molecular chaperones that act as folding modulators for proteins. Molecular chaperones assist newly synthesized, aggregated or misfolded proteins to fold into their native conformations. Chaperones have been widely used to improve the expression of various proteins which are otherwise difficult to produce in E. coli. Here, we discuss the structure, function, and role of major E. coli molecular chaperones in recombinant technology such as trigger factor, GroEL, DnaK and ClpB.
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Affiliation(s)
- Komal Fatima
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan
| | - Fatima Naqvi
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan
| | - Hooria Younas
- Department of Biochemistry, Kinnaird College for Women, Lahore, Punjab, Pakistan.
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33
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Fiore KE, Phan HAT, Robkis DM, Walters CR, Petersson EJ. Incorporating thioamides into proteins by native chemical ligation. Methods Enzymol 2021; 656:295-339. [PMID: 34325791 PMCID: PMC8617429 DOI: 10.1016/bs.mie.2021.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The thioamide is a versatile replacement of the peptide backbone with altered hydrogen bonding and conformational preferences, as well the ability participate in energy and electron transfer processes. Semi-synthetic incorporation of a thioamide into a protein can be used to study protein folding or protein/protein interactions using these properties. Semi-synthesis also provides the opportunity to study the role of thioamides in natural proteins. Here we outline the semi-synthesis of a model protein, the B1 domain of protein G (GB1) with a thioamide at the N-terminus or the C-terminus. The thioamide is synthetically incorporated into a fragment by solid-phase peptide synthesis, whereas the remainder of the protein is recombinantly expressed. Then, the two fragments are joined by native chemical ligation. The explicit protocol for GB1 synthesis is accompanied by examples of applications with GB1 and other proteins in structural biology and protein misfolding studies.
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Affiliation(s)
- Kristen E Fiore
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Hoang Anh T Phan
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - D Miklos Robkis
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, United States
| | - Christopher R Walters
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States.
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34
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Raducanu V, Raducanu D, Ouyang Y, Tehseen M, Takahashi M, Hamdan SM. TSGIT: An N- and C-terminal tandem tag system for purification of native and intein-mediated ligation-ready proteins. Protein Sci 2021; 30:497-512. [PMID: 33150985 PMCID: PMC7784762 DOI: 10.1002/pro.3989] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 11/26/2022]
Abstract
A large variety of fusion tags have been developed to improve protein expression, solubilization, and purification. Nevertheless, these tags have been combined in a rather limited number of composite tags and usually these composite tags have been dictated by traditional commercially-available expression vectors. Moreover, most commercially-available expression vectors include either N- or C-terminal fusion tags but not both. Here, we introduce TSGIT, a fusion-tag system composed of both N- and a C-terminal composite fusion tags. The system includes two affinity tags, two solubilization tags and two cleavable tags distributed at both termini of the protein of interest. Therefore, the N- and the C-terminal composite fusion tags in TSGIT are fully orthogonal in terms of both affinity selection and cleavage. For using TSGIT, we streamlined the cloning, expression, and purification procedures. Each component tag is selected to maximize its benefits toward the final construct. By expressing and partially purifying the protein of interest between the components of the TSGIT fusion, the full-length protein is selected over truncated forms, which has been a long-standing problem in protein purification. Moreover, due to the nature of the cleavable tags in TSGIT, the protein of interest is obtained in its native form without any additional undesired N- or C-terminal amino acids. Finally, the resulting purified protein is ready for efficient ligation with other proteins or peptides for downstream applications. We demonstrate the use of this system by purifying a large amount of native fluorescent mRuby3 protein and bacteriophage T7 gp2.5 ssDNA-binding protein.
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Affiliation(s)
- Vlad‐Stefan Raducanu
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Daniela‐Violeta Raducanu
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Yujing Ouyang
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Muhammad Tehseen
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Masateru Takahashi
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Samir M. Hamdan
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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35
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NMR Structure Determinations of Small Proteins Using only One Fractionally 20% 13C- and Uniformly 100% 15N-Labeled Sample. Molecules 2021; 26:molecules26030747. [PMID: 33535444 PMCID: PMC7867066 DOI: 10.3390/molecules26030747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/17/2022] Open
Abstract
Uniformly 13C- and 15N-labeled samples ensure fast and reliable nuclear magnetic resonance (NMR) assignments of proteins and are commonly used for structure elucidation by NMR. However, the preparation of uniformly labeled samples is a labor-intensive and expensive step. Reducing the portion of 13C-labeled glucose by a factor of five using a fractional 20% 13C- and 100% 15N-labeling scheme could lower the total chemical costs, yet retaining sufficient structural information of uniformly [13C, 15N]-labeled sample as a result of the improved sensitivity of NMR instruments. Moreover, fractional 13C-labeling can facilitate reliable resonance assignments of sidechains because of the biosynthetic pathways of each amino-acid. Preparation of only one [20% 13C, 100% 15N]-labeled sample for small proteins (<15 kDa) could also eliminate redundant sample preparations of 100% 15N-labeled and uniformly 100% [13C, 15N]-labeled samples of proteins. We determined the NMR structures of a small alpha-helical protein, the C domain of IgG-binding protein A from Staphylococcus aureus (SpaC), and a small beta-sheet protein, CBM64 module using [20% 13C, 100% 15N]-labeled sample and compared with the crystal structures and the NMR structures derived from the 100% [13C, 15N]-labeled sample. Our results suggest that one [20% 13C, 100% 15N]-labeled sample of small proteins could be routinely used as an alternative to conventional 100% [13C, 15N]-labeling for backbone resonance assignments, NMR structure determination, 15N-relaxation analysis, and ligand–protein interaction.
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36
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Liu J, Xue Z, Vann KR, Shi X, Kutateladze TG. Protocol for Biochemical Analysis and Structure Determination of the ZZ Domain of the E3 Ubiquitin Ligase HERC2. STAR Protoc 2020; 1:100155. [PMID: 33377049 PMCID: PMC7757301 DOI: 10.1016/j.xpro.2020.100155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Since its discovery, several ligands of the ZZ domain have been identified; however, molecular and structural information underlying binding of these ligands remains limited. Here, we describe a protocol for biochemical and structural analysis of the ZZ domain of human E3 ubiquitin ligase HERC2 (HERC2ZZ) and its interaction with its ligands: the N-terminal tails of histone H3 and SUMO1. This methodology could be applied for characterization of binding activities of other histone readers. For complete details on the use and execution of this protocol, please refer to Liu et al. (2020). Optimized protocol to purify HERC2ZZ from bacteria and mammalian cells Strategy to characterize binding of HERC2ZZ to histone tails in vitro and in cells Biochemical analysis and structure determination of histone reader
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Affiliation(s)
- Jiuyang Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Zhaoyu Xue
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Kendra R Vann
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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37
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Beyer HM, Virtanen SI, Aranko AS, Mikula KM, Lountos GT, Wlodawer A, Ollila OHS, Iwaï H. The Convergence of the Hedgehog/Intein Fold in Different Protein Splicing Mechanisms. Int J Mol Sci 2020; 21:ijms21218367. [PMID: 33171880 PMCID: PMC7664689 DOI: 10.3390/ijms21218367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/01/2020] [Accepted: 11/05/2020] [Indexed: 11/16/2022] Open
Abstract
Protein splicing catalyzed by inteins utilizes many different combinations of amino-acid types at active sites. Inteins have been classified into three classes based on their characteristic sequences. We investigated the structural basis of the protein splicing mechanism of class 3 inteins by determining crystal structures of variants of a class 3 intein from Mycobacterium chimaera and molecular dynamics simulations, which suggested that the class 3 intein utilizes a different splicing mechanism from that of class 1 and 2 inteins. The class 3 intein uses a bond cleavage strategy reminiscent of proteases but share the same Hedgehog/INTein (HINT) fold of other intein classes. Engineering of class 3 inteins from a class 1 intein indicated that a class 3 intein would unlikely evolve directly from a class 1 or 2 intein. The HINT fold appears as structural and functional solution for trans-peptidyl and trans-esterification reactions commonly exploited by diverse mechanisms using different combinations of amino-acid types for the active-site residues.
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Affiliation(s)
- Hannes M. Beyer
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
| | - Salla I. Virtanen
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
| | - A. Sesilja Aranko
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
| | - Kornelia M. Mikula
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
| | - George T. Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA;
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA;
| | - O. H. Samuli Ollila
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland; (H.M.B.); (S.I.V.); (A.S.A.); (K.M.M.); (O.H.S.O.)
- Correspondence: ; Tel.: +358-2941-59752
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38
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Kuan WC, Lai JW, Lee WC. Covalent binding of glutathione on magnetic nanoparticles: Application for immobilizing small fragment ubiquitin-like-specific protease 1. Enzyme Microb Technol 2020; 143:109697. [PMID: 33375983 DOI: 10.1016/j.enzmictec.2020.109697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/17/2020] [Accepted: 10/17/2020] [Indexed: 10/23/2022]
Abstract
Magnetic nanoparticles bound with glutathione (GSH) are useful for diagnostics, enzyme immobilization, and affinity precipitation by using the strong and specific interaction of GSH with glutathione S-transferase (GST)-fused proteins. Our studies revealed that GSH-bound magnetic nanoparticles could be obtained using the covalent bond linkage of GSH and nanoparticles to promote the stability of bound GSH. To yield this conjugate, superparamagnetic iron oxide nanoparticles (SPIONs) were prepared and modified using tetraethoxysilane (TEOS) and 3-aminopropyltriethoxysilane (APTES), which introduced amino groups that were then activated with maleic anhydride (MA) for covalent binding of GSH. After MA was used to activate the amino-grafted SPION for 24 h, the yield of GSH conjugation increased over 4 days from 37 % to 74 % of the original amine density on the surface as the incubation of GSH with MA-activated SPION. These GSH-bound magnetic nanoparticles, designated as SPION@silica-GSH with approximately 103 nmol GSH/mg particles, were ready for coupling with GST-fused protein through the GSH-GST affinity interaction. A GST-tagged small fragment of ubiquitin-like-specific protease 1 (sfULP1) was used as the model protein for immobilization on SPION@silica-GSH. ULP1 is a small ubiquitin-like modifier (SUMO) protease. Results indicated that this immobilized GST-sfULP1 could retain 87 % ± 5 % enzyme activity of free protease before immobilization and could catalyze the cleavage of the SUMO-fused peptide (SUMO-GLP-1) to obtain glucagon-like peptide-1, a peptide hormone for type 2 diabetes therapy.
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Affiliation(s)
- Wei-Chih Kuan
- Department of Chemical Engineering, Systems Biology and Tissue Engineering Research Center, National Chung Cheng University, Chiayi 621, Taiwan
| | - Jian-Wen Lai
- Department of Chemical Engineering, Systems Biology and Tissue Engineering Research Center, National Chung Cheng University, Chiayi 621, Taiwan
| | - Wen-Chien Lee
- Department of Chemical Engineering, Systems Biology and Tissue Engineering Research Center, National Chung Cheng University, Chiayi 621, Taiwan.
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Zhang JZ, Lu TW, Stolerman LM, Tenner B, Yang JR, Zhang JF, Falcke M, Rangamani P, Taylor SS, Mehta S, Zhang J. Phase Separation of a PKA Regulatory Subunit Controls cAMP Compartmentation and Oncogenic Signaling. Cell 2020; 182:1531-1544.e15. [PMID: 32846158 PMCID: PMC7502557 DOI: 10.1016/j.cell.2020.07.043] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/30/2020] [Accepted: 07/30/2020] [Indexed: 12/25/2022]
Abstract
The fidelity of intracellular signaling hinges on the organization of dynamic activity architectures. Spatial compartmentation was first proposed over 30 years ago to explain how diverse G protein-coupled receptors achieve specificity despite converging on a ubiquitous messenger, cyclic adenosine monophosphate (cAMP). However, the mechanisms responsible for spatially constraining this diffusible messenger remain elusive. Here, we reveal that the type I regulatory subunit of cAMP-dependent protein kinase (PKA), RIα, undergoes liquid-liquid phase separation (LLPS) as a function of cAMP signaling to form biomolecular condensates enriched in cAMP and PKA activity, critical for effective cAMP compartmentation. We further show that a PKA fusion oncoprotein associated with an atypical liver cancer potently blocks RIα LLPS and induces aberrant cAMP signaling. Loss of RIα LLPS in normal cells increases cell proliferation and induces cell transformation. Our work reveals LLPS as a principal organizer of signaling compartments and highlights the pathological consequences of dysregulating this activity architecture.
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Affiliation(s)
- Jason Z Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tsan-Wen Lu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lucas M Stolerman
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brian Tenner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica R Yang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jin-Fan Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Department of Physics, Humboldt University, 12489 Berlin, Germany
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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40
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Jaakkonen A, Volkmann G, Iwaï H. An off-the-Shelf Approach for the Production of Fc Fusion Proteins by Protein Trans-Splicing towards Generating a Lectibody In Vitro. Int J Mol Sci 2020; 21:ijms21114011. [PMID: 32503354 PMCID: PMC7313076 DOI: 10.3390/ijms21114011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/19/2022] Open
Abstract
Monoclonal antibodies, engineered antibodies, and antibody fragments have become important biological therapeutic platforms. The IgG format with bivalent binding sites has a modular structure with different biological roles, i.e., effector and binding functions, in different domains. We demonstrated the reconstruction of an IgG-like domain structure in vitro by protein ligation using protein trans-splicing. We produced various binding domains to replace the binding domain of IgG from Escherichia coli and the Fc domain of human IgG from Brevibacillus choshinensis as split-intein fusions. We showed that in vitro protein ligation could produce various Fc-fusions at the N-terminus in vitro from the independently produced domains from different organisms. We thus propose an off-the-shelf approach for the combinatorial production of Fc fusions in vitro with several distinct binding domains, particularly from naturally occurring binding domains. Antiviral lectins from algae are known to inhibit virus entry of HIV and SARS coronavirus. We demonstrated that a lectin could be fused with the Fc-domain in vitro by protein ligation, producing an IgG-like molecule as a “lectibody”. Such an Fc-fusion could be produced in vitro by this approach, which could be an attractive method for developing potential therapeutic agents against rapidly emerging infectious diseases like SARS coronavirus without any genetic fusion and expression optimization.
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Affiliation(s)
- Anniina Jaakkonen
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; (A.J.); (G.V.)
- Present Address: Microbiology Unit, Finnish Food Authority, FI-00790 Helsinki, Finland
| | - Gerrit Volkmann
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; (A.J.); (G.V.)
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland; (A.J.); (G.V.)
- Correspondence: ; Tel.: +358-2941-59752
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41
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Semisynthesis of an evasin from tick saliva reveals a critical role of tyrosine sulfation for chemokine binding and inhibition. Proc Natl Acad Sci U S A 2020; 117:12657-12664. [PMID: 32461364 DOI: 10.1073/pnas.2000605117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Blood-feeding arthropods produce antiinflammatory salivary proteins called evasins that function through inhibition of chemokine-receptor signaling in the host. Herein, we show that the evasin ACA-01 from the Amblyomma cajennense tick can be posttranslationally sulfated at two tyrosine residues, albeit as a mixture of sulfated variants. Homogenously sulfated variants of the proteins were efficiently assembled via a semisynthetic native chemical ligation strategy. Sulfation significantly improved the binding affinity of ACA-01 for a range of proinflammatory chemokines and enhanced the ability of ACA-01 to inhibit chemokine signaling through cognate receptors. Comparisons of evasin sequences and structural data suggest that tyrosine sulfation serves as a receptor mimetic strategy for recognizing and suppressing the proinflammatory activity of a wide variety of mammalian chemokines. As such, the incorporation of this posttranslational modification (PTM) or mimics thereof into evasins may provide a strategy to optimize tick salivary proteins for antiinflammatory applications.
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42
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Beyer HM, Mikula KM, Li M, Wlodawer A, Iwaï H. The crystal structure of the naturally split gp41-1 intein guides the engineering of orthogonal split inteins from cis-splicing inteins. FEBS J 2020; 287:1886-1898. [PMID: 31665813 PMCID: PMC7190452 DOI: 10.1111/febs.15113] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/01/2019] [Accepted: 10/29/2019] [Indexed: 01/09/2023]
Abstract
Protein trans-splicing catalyzed by split inteins has increasingly become useful as a protein engineering tool. We solved the 1.0 Å-resolution crystal structure of a fused variant from the naturally split gp41-1 intein, previously identified from environmental metagenomic sequence data. The structure of the 125-residue gp41-1 intein revealed a compact pseudo-C2-symmetry commonly found in the Hedgehog/Intein superfamily with extensive charge-charge interactions between the split N- and C-terminal intein fragments that are common among naturally occurring split inteins. We successfully created orthogonal split inteins by engineering a similar charge network into the same region of a cis-splicing intein. This strategy could be applicable for creating novel natural-like split inteins from other, more prevalent cis-splicing inteins. DATABASE: Structural data are available in the RCSB Protein Data Bank under the accession number 6QAZ.
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Affiliation(s)
- Hannes Michael Beyer
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Kornelia Malgorzata Mikula
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Mi Li
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
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43
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Ciragan A, Backlund SM, Mikula KM, Beyer HM, Samuli Ollila OH, Iwaï H. NMR Structure and Dynamics of TonB Investigated by Scar-Less Segmental Isotopic Labeling Using a Salt-Inducible Split Intein. Front Chem 2020; 8:136. [PMID: 32266203 PMCID: PMC7098700 DOI: 10.3389/fchem.2020.00136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/13/2020] [Indexed: 11/22/2022] Open
Abstract
The growing understanding of partially unfolded proteins increasingly points to their biological relevance in allosteric regulation, complex formation, and protein design. However, the structural characterization of disordered proteins remains challenging. NMR methods can access both the dynamics and structures of such proteins, yet suffering from a high degeneracy of NMR signals. Here, we overcame this bottleneck utilizing a salt-inducible split intein to produce segmentally isotope-labeled samples with the native sequence, including the ligation junction. With this technique, we investigated the NMR structure and conformational dynamics of TonB from Helicobacter pylori in the presence of a proline-rich low complexity region. Spin relaxation experiments suggest that the several nano-second time scale dynamics of the C-terminal domain (CTD) is almost independent of the faster pico-to-nanosecond dynamics of the low complexity central region (LCCR). Our results demonstrate the utility of segmental isotopic labeling for proteins with heterogenous dynamics such as TonB and could advance NMR studies of other partially unfolded proteins.
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Affiliation(s)
- Annika Ciragan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sofia M Backlund
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kornelia M Mikula
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hannes M Beyer
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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44
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A novel approach for production of an active N-terminally truncated Ulp1 (SUMO protease 1) catalytic domain from Escherichia coli inclusion bodies. Protein Expr Purif 2020; 166:105507. [DOI: 10.1016/j.pep.2019.105507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/23/2019] [Accepted: 10/02/2019] [Indexed: 01/21/2023]
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45
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Molugu TR, Oita RC, Chawla U, Camp SM, Brown MF, Garcia JGN. Nicotinamide phosphoribosyltransferase purification using SUMO expression system. Anal Biochem 2020; 598:113597. [PMID: 31982408 DOI: 10.1016/j.ab.2020.113597] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 02/08/2023]
Abstract
Nicotinamide phosphoribosyltransferase (NAMPT) is a rate-limiting enzyme in the salvage pathway required for nicotinamide adenine dinucleotide synthesis. The secreted NAMPT protein serves as a master regulatory cytokine involved in activation of evolutionarily conserved inflammatory networks. Appreciation of the role of NAMPT as a damage-associated molecular pattern protein (DAMP) has linked its activities to several disorders via Toll-like receptor 4 (TLR4) binding and inflammatory cascade activation. Information is currently lacking concerning the precise mode of the NAMPT protein functionality due to limited availability of purified protein for use in in vitro and in vivo studies. Here we report successful NAMPT expression using the pET-SUMO expression vector in E. coli strain SHuffle containing a hexa-His tag for purification. The Ulp1 protease was used to cleave the SUMO and hexa-His tags, and the protein was purified by immobilized-metal affinity chromatography. The protein yield was ~4 mg/L and initial biophysical characterization of the protein using circular dichroism revealed the secondary structural elements, while dynamic light scattering demonstrated the presence of oligomeric units. The NAMPT-SUMO showed a predominantly dimeric protein with functional enzymatic activity. Finally, we report NAMPT solubilization in n-dodecyl-β-d-maltopyranoside (DDM) detergent in monomeric form, thus enhancing the opportunity for further structural and functional investigations.
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Affiliation(s)
- Trivikram R Molugu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Radu C Oita
- Department of Medicine, University of Arizona Health Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Udeep Chawla
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Sara M Camp
- Department of Medicine, University of Arizona Health Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA; Department of Physics, University of Arizona, Tucson, AZ, 85721, USA.
| | - Joe G N Garcia
- Department of Medicine, University of Arizona Health Sciences, University of Arizona, Tucson, AZ, 85721, USA.
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46
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Yoganand KN, Muralidharan M, Nimkar S, Anand B. Fidelity of prespacer capture and processing is governed by the PAM-mediated interactions of Cas1-2 adaptation complex in CRISPR-Cas type I-E system. J Biol Chem 2019; 294:20039-20053. [PMID: 31748409 PMCID: PMC6937570 DOI: 10.1074/jbc.ra119.009438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 11/18/2019] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes deploy CRISPR-Cas-based RNA-guided adaptive immunity to fend off mobile genetic elements such as phages and plasmids. During CRISPR adaptation, which is the first stage of CRISPR immunity, the Cas1-2 integrase complex captures invader-derived prespacer DNA and specifically integrates it at the leader-repeat junction as spacers. For this integration, several variants of CRISPR-Cas systems use Cas4 as an indispensable nuclease for selectively processing the protospacer adjacent motif (PAM) containing prespacers to a defined length. Surprisingly, however, a few CRISPR-Cas systems, such as type I-E, are bereft of Cas4. Despite the absence of Cas4, how the prespacers show impeccable conservation for length and PAM selection in type I-E remains intriguing. Here, using in vivo and in vitro integration assays, deep sequencing, and exonuclease footprinting, we show that Cas1-2/I-E-via the type I-E-specific extended C-terminal tail of Cas1-displays intrinsic affinity for PAM containing prespacers of variable length in Escherichia coli Although Cas1-2/I-E does not prune the prespacers, its binding protects the prespacer boundaries from exonuclease action. This ensures the pruning of exposed ends by exonucleases to aptly sized substrates for integration into the CRISPR locus. In summary, our work reveals that in a few CRISPR-Cas variants, such as type I-E, the specificity of PAM selection resides with Cas1-2, whereas the prespacer processing is co-opted by cellular non-Cas exonucleases, thereby offsetting the need for Cas4.
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Affiliation(s)
- Kakimani Nagarajan Yoganand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Manasasri Muralidharan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Siddharth Nimkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Baskaran Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
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47
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Mahmoodi S, Pourhassan-Moghaddam M, Wood DW, Majdi H, Zarghami N. Current affinity approaches for purification of recombinant proteins. ACTA ACUST UNITED AC 2019. [DOI: 10.1080/23312025.2019.1665406] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Sahar Mahmoodi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Pourhassan-Moghaddam
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - David W. Wood
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Hasan Majdi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nosratollah Zarghami
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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48
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Crystal structures of CDC21-1 inteins from hyperthermophilic archaea reveal the selection mechanism for the highly conserved homing endonuclease insertion site. Extremophiles 2019; 23:669-679. [PMID: 31363851 PMCID: PMC6801210 DOI: 10.1007/s00792-019-01117-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/09/2019] [Indexed: 11/27/2022]
Abstract
Self-splicing inteins are mobile genetic elements invading host genes via nested homing endonuclease (HEN) domains. All HEN domains residing within inteins are inserted at a highly conserved insertion site. A purifying selection mechanism directing the location of the HEN insertion site has not yet been identified. In this work, we solved the three-dimensional crystal structures of two inteins inserted in the cell division control protein 21 of the hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii. A comparison between the structures provides the structural basis for the thermo-stabilization mechanism of inteins that have lost the HEN domain during evolution. The presence of an entire extein domain in the intein structure from Pyrococcus horikoshii suggests the selection mechanism for the highly conserved HEN insertion point.
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49
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Correddu D, Montaño López JDJ, Vadakkedath PG, Lai A, Pernes JI, Watson PR, Leung IKH. An improved method for the heterologous production of soluble human ribosomal proteins in Escherichia coli. Sci Rep 2019; 9:8884. [PMID: 31222068 PMCID: PMC6586885 DOI: 10.1038/s41598-019-45323-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 05/31/2019] [Indexed: 11/11/2022] Open
Abstract
Human ribosomal proteins play important structural and functional roles in the ribosome and in protein synthesis. An efficient method to recombinantly produce and purify these proteins would enable their full characterisation. However, the production of human ribosomal proteins can be challenging. The only published method about the recombinant production of human ribosomal proteins involved the recovery of proteins from inclusion bodies, a process that is tedious and may lead to significant loss of yield. Herein, we explored the use of different Escherichia coli competent cells and fusion protein tags for the recombinant production of human ribosomal proteins. We found that, by using thioredoxin as a fusion protein, soluble ribosomal protein could be obtained directly from cell lysates, thus leading to an improved method to recombinantly produce these proteins.
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Affiliation(s)
- Danilo Correddu
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - José de Jesús Montaño López
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,Facultad de Ingeniería, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad Universitaria, Coyoacán, Cd. Mx., CP 04510, Mexico
| | - Praveen G Vadakkedath
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Amy Lai
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Jane I Pernes
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Paris R Watson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.
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de Araujo ED, Erdogan F, Neubauer HA, Meneksedag-Erol D, Manaswiyoungkul P, Eram MS, Seo HS, Qadree AK, Israelian J, Orlova A, Suske T, Pham HTT, Boersma A, Tangermann S, Kenner L, Rülicke T, Dong A, Ravichandran M, Brown PJ, Audette GF, Rauscher S, Dhe-Paganon S, Moriggl R, Gunning PT. Structural and functional consequences of the STAT5B N642H driver mutation. Nat Commun 2019; 10:2517. [PMID: 31175292 PMCID: PMC6555848 DOI: 10.1038/s41467-019-10422-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 05/10/2019] [Indexed: 11/30/2022] Open
Abstract
Hyper-activated STAT5B variants are high value oncology targets for pharmacologic intervention. STAT5BN642H, a frequently-occurring oncogenic driver mutation, promotes aggressive T-cell leukemia/lymphoma in patient carriers, although the molecular origins remain unclear. Herein, we emphasize the aggressive nature of STAT5BN642H in driving T-cell neoplasia upon hematopoietic expression in transgenic mice, revealing evidence of multiple T-cell subset organ infiltration. Notably, we demonstrate STAT5BN642H-driven transformation of γδ T-cells in in vivo syngeneic transplant models, comparable to STAT5BN642H patient γδ T-cell entities. Importantly, we present human STAT5B and STAT5BN642H crystal structures, which propose alternative mutation-mediated SH2 domain conformations. Our biophysical data suggests STAT5BN642H can adopt a hyper-activated and hyper-inactivated state with resistance to dephosphorylation. MD simulations support sustained interchain cross-domain interactions in STAT5BN642H, conferring kinetic stability to the mutant anti-parallel dimer. This study provides a molecular explanation for the STAT5BN642H activating potential, and insights into pre-clinical models for targeted intervention of hyper-activated STAT5B.
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Affiliation(s)
- Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON, L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Fettah Erdogan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON, L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Heidi A Neubauer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Ludwig Boltzmann Institute for Cancer Research, 1090, Vienna, Austria
| | - Deniz Meneksedag-Erol
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON, L5L 1C6, Canada
- Department of Physics, University of Toronto, 60 St. George Street, Toronto, ON, M5S 1A7, Canada
| | - Pimyupa Manaswiyoungkul
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON, L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Mohammad S Eram
- Dalriada Drug Discovery, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON, L5L 1C6, Canada
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Abdul K Qadree
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON, L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Johan Israelian
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON, L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Anna Orlova
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Ludwig Boltzmann Institute for Cancer Research, 1090, Vienna, Austria
| | - Tobias Suske
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Ha T T Pham
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Ludwig Boltzmann Institute for Cancer Research, 1090, Vienna, Austria
| | - Auke Boersma
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Simone Tangermann
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Lukas Kenner
- Ludwig Boltzmann Institute for Cancer Research, 1090, Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Clinical Institute of Pathology, Department for Experimental and Laboratory Animal Pathology, Medical University of Vienna, 1090, Vienna, Austria
| | - Thomas Rülicke
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, ON, M5G 1L7, Canada
| | - Manimekalai Ravichandran
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, ON, M5G 1L7, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, ON, M5G 1L7, Canada
| | - Gerald F Audette
- Department of Chemistry, York University, 327C Life Sciences Building, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Sarah Rauscher
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON, L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
- Department of Physics, University of Toronto, 60 St. George Street, Toronto, ON, M5S 1A7, Canada
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 450 Brookline Avenue, Boston, MA, 02215, USA.
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
- Ludwig Boltzmann Institute for Cancer Research, 1090, Vienna, Austria.
- Medical University of Vienna, 1090, Vienna, Austria.
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, ON, L5L 1C6, Canada.
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.
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