1
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Gong N, Han X, Xue L, Billingsley MM, Huang X, El-Mayta R, Qin J, Sheppard NC, June CH, Mitchell MJ. Small-molecule-mediated control of the anti-tumour activity and off-tumour toxicity of a supramolecular bispecific T cell engager. Nat Biomed Eng 2024; 8:513-528. [PMID: 38378820 DOI: 10.1038/s41551-023-01147-6] [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] [Received: 01/22/2023] [Accepted: 10/24/2023] [Indexed: 02/22/2024]
Abstract
The broader clinical use of bispecific T cell engagers for inducing anti-tumour toxicity is hindered by their on-target off-tumour toxicity and the associated neurotoxicity and cytokine-release syndrome. Here we show that the off-tumour toxicity of a supramolecular bispecific T cell engager binding to the T cell co-receptor CD3 and to the human epidermal growth factor receptor 2 on breast tumour cells can be halted by disengaging the T cells from the tumour cells via the infusion of the small-molecule drug amantadine, which disassembles the supramolecular aggregate. In mice bearing human epidermal growth factor receptor 2-expressing tumours and with a human immune system, high intravenous doses of such a 'switchable T cell nanoengager' elicited strong tumour-specific adaptive immune responses that prevented tumour relapse, while the infusion of amantadine restricted off-tumour toxicity, cytokine-release syndrome and neurotoxicity. Supramolecular chemistry may be further leveraged to control the anti-tumour activity and off-tumour toxicity of bispecific antibodies.
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Affiliation(s)
- Ningqiang Gong
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Xuexiang Han
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Lulu Xue
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Xisha Huang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Rakan El-Mayta
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Jingya Qin
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Neil C Sheppard
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carl H June
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael J Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Precision Engineering for Health, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Structure-dependent recruitment and diffusion of guest proteins in liquid droplets of FUS. Sci Rep 2022; 12:7101. [PMID: 35501371 PMCID: PMC9061845 DOI: 10.1038/s41598-022-11177-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/19/2022] [Indexed: 12/26/2022] Open
Abstract
Liquid droplets of a host protein, formed by liquid–liquid phase separation, recruit guest proteins and provide functional fields. Recruitment into p53 droplets is similar between disordered and folded guest proteins, whereas the diffusion of guest proteins inside droplets depends on their structural types. In this study, to elucidate how the recruitment and diffusion properties of guest proteins are affected by a host protein, we characterized the properties of guest proteins in fused in sarcoma (FUS) droplets using single-molecule fluorescence microscopy in comparison with p53 droplets. Unlike p53 droplets, disordered guest proteins were recruited into FUS droplets more efficiently than folded guest proteins, suggesting physical exclusion of the folded proteins from the small voids of the droplet. The recruitment did not appear to depend on the physical parameters (electrostatic or cation–π) of guests, implying that molecular size exclusion limits intermolecular interaction-assisted uptake. The diffusion of disordered guest proteins was comparable to that of the host FUS, whereas that of folded proteins varied widely, similar to the results for host p53. The scaling exponent of diffusion highlights the molecular sieving of large folded proteins in droplets. Finally, we proposed a molecular recruitment and diffusion model for guest proteins in FUS droplets.
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3
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Tsuji K, Ishii T, Kobayakawa T, Ohashi N, Nomura W, Tamamura H. Fluorescence resonance energy transfer-based screening for protein kinase C ligands using 6-methoxynaphthalene-labeled 1,2-diacylglycerol-lactones. Org Biomol Chem 2021; 19:8264-8271. [PMID: 34338277 DOI: 10.1039/d1ob00814e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein kinase C (PKC) is associated with a central cellular signal transduction pathway and disorders such as cancer and Alzheimer-type dementia and is therefore a target for the treatment of these diseases. The development of simple methods suitable for high-throughput screening to find potent PKC ligands is desirable. We have developed an assay based on fluorescence-quenching screening with a solvatochromic fluorophore attached to a competitive probe and its alternative method based on Förster/fluorescence resonance energy transfer (FRET) phenomena. Here, an improved FRET-based PKC binding assay using a diacylglycerol (DAG) lactone labeled with a donor fluorescent dye, 6-methoxynaphthalene (6MN), was developed. The 6MN-labeled DAG-lactone has a higher binding affinity for the PKCδ C1b domain and the fluorescent PKCδ C1b domain labeled by fluorescein as an acceptor fluorescent dye (Fl-δC1b) than the diethylaminocoumarin (DEAC)-labeled DAG-lactone. The combination of the 6MN-labeled DAG-lactone and Fl-δC1b showed a change in fluorescence response larger than that of the DEAC-labeled DAG-lactone and Fl-δC1b. The IC50 values of known PKC ligands calculated by the present FRET-based method using 6MN-labeled DAG-lactone agree well with the Ki values obtained by the conventional radioisotope-based assays. Some false positive compounds, identified by the previous solvatochromic fluorophore-based method, were found to be negative by this method. The present FRET-based PKC binding assay is more sensitive and could be more useful.
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Affiliation(s)
- Kohei Tsuji
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
| | - Takahiro Ishii
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
| | - Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
| | - Nami Ohashi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
| | - Wataru Nomura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
| | - Hirokazu Tamamura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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4
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Kamagata K, Iwaki N, Hazra MK, Kanbayashi S, Banerjee T, Chiba R, Sakomoto S, Gaudon V, Castaing B, Takahashi H, Kimura M, Oikawa H, Takahashi S, Levy Y. Molecular principles of recruitment and dynamics of guest proteins in liquid droplets. Sci Rep 2021; 11:19323. [PMID: 34588591 PMCID: PMC8481498 DOI: 10.1038/s41598-021-98955-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/16/2021] [Indexed: 11/10/2022] Open
Abstract
Despite the continuous discovery of host and guest proteins in membraneless organelles, complex host–guest interactions hinder the understanding of the molecular grammar governing liquid–liquid phase separation. In this study, we characterized the localization and dynamic properties of guest proteins in liquid droplets using single-molecule fluorescence microscopy. Eighteen guest proteins of different sizes, structures, and oligomeric states were examined in host p53 liquid droplets. Recruitment did not significantly depend on the structural properties of the guest proteins, but was moderately correlated with their length, total charge, and number of R and Y residues. In contrast, the diffusion of disordered guest proteins was comparable to that of host p53, whereas that of folded proteins varied widely. Molecular dynamics simulations suggest that folded proteins diffuse within the voids of the liquid droplet while interacting weakly with neighboring host proteins, whereas disordered proteins adapt their structures to form tight interactions with the host proteins. Our study provides insights into the key molecular principles of the localization and dynamics of guest proteins in liquid droplets.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan. .,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
| | - Nanako Iwaki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Milan Kumar Hazra
- Department of Structural Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Saori Kanbayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Trishit Banerjee
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Rika Chiba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Seiji Sakomoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Virginie Gaudon
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072, Orléans, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072, Orléans, France
| | - Hiroto Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Michiko Kimura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Hiroyuki Oikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan.,Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
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5
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de Vink PJ, van der Hek T, Brunsveld L. Light-driven release of cucurbit[8]uril from a bivalent cage. Chem Sci 2021; 12:6726-6731. [PMID: 34040748 PMCID: PMC8132991 DOI: 10.1039/d1sc01410b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/10/2021] [Indexed: 12/03/2022] Open
Abstract
Temporal control over supramolecular systems has great potential for the modulation of binding and assembly events, such as providing orthogonal control over protein activity. Especially light controlled triggering provides unique entries for supramolecular systems to interface in a controlled manner with enzymes. Here we report on the light-induced release of cucurbit[8]uril (CB[8]) from a bivalent cage molecule and its subsequent activation of a proteolytic enzyme, caspase-9, that itself is unresponsive to light. Central to the design is the bivalent binding of the cage with high affinity to CB[8], 100-fold stronger than the UV-inactivated products. The affinity switching occurs in the (sub-)micromolar concentration regime, matching the concentration characteristics required for dimerizing and activating caspase-9 by CB[8]. The light-responsive caged CB[8] concept presented offers a novel platform for tuning and application of switchable cucurbiturils and beyond.
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Affiliation(s)
- Pim J de Vink
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
| | - Tim van der Hek
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
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6
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Takahashi T. Generation of Active Protease Depending on Peptide-Protein Interactions Using Interaction-Dependent Native Chemical Ligation and Protein Trans-Splicing. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tsuyoshi Takahashi
- Chemistry and Chemical Biology, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjincho, Kiryu, Gunma 376-8515, Japan
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7
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Mo HM, Xu Y, Yu XW. Improved Soluble Expression and Catalytic Activity of a Thermostable Esterase Using a High-Throughput Screening System Based on a Split-GFP Assembly. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12756-12764. [PMID: 30411620 DOI: 10.1021/acs.jafc.8b04646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The thermostable esterase Aaeo1 displays a low expression level and forms a great amount of inclusion bodies in E. coli. Herein, a split-GFP system was established in which the fluorescence intensity exhibited a good linear correlation with the soluble protein expression level and the esterase activity. In the primary high-throughput screening, the mutant library was screened by flow cytometry via detection of a split-GFP reporter. Then, through a secondary screening against esterase activity, two mutants with improved soluble expression and catalytic activity were obtained. The soluble expression of the mutant enzymes in E. coli was improved by 2-fold. The kcat/ Km values of the mutant enzymes were 2-fold higher than that of the parent. We explored the relationship between the amino acid mutations in the two mutants and the enzyme activity. The enzyme activity of mutant I51V-E170D was 4.5 times higher than that of the parent.
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Affiliation(s)
- Hong-Mei Mo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , PR China
- Suqian Industrial Technology Research Institute of Jiangnan University , Suqian 223814 , PR China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , PR China
- Suqian Industrial Technology Research Institute of Jiangnan University , Suqian 223814 , PR China
| | - Xiao-Wei Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , PR China
- Suqian Industrial Technology Research Institute of Jiangnan University , Suqian 223814 , PR China
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8
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Finbloom JA, Francis MB. Supramolecular strategies for protein immobilization and modification. Curr Opin Chem Biol 2018; 46:91-98. [DOI: 10.1016/j.cbpa.2018.05.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/19/2018] [Accepted: 05/29/2018] [Indexed: 02/03/2023]
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9
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Bertucci A, Porchetta A, Ricci F. Antibody-Templated Assembly of an RNA Mimic of Green Fluorescent Protein. Anal Chem 2017; 90:1049-1053. [PMID: 29131585 DOI: 10.1021/acs.analchem.7b02102] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
One of the most intriguing ways through which nature achieves regulation of biological pathways encompasses the coordination of noncovalent interactions that bring biomolecules to be colocalized in a designated restricted space. Inspired by this mechanism, we have explored the possibility of using antibodies as bivalent biomolecular substrates for the templated assembly of a functional RNA structure. We have developed a biosupramolecular complementation assay by assembling a fluorescent Spinach aptamer, which is a synthetic RNA mimic of the Green Fluorescent Protein, from its split segments. We have employed two antigen-tagged RNA strands that, upon binding to the target antibody, are colocalized in a confined space and can reassemble into the native Spinach conformation, yielding a measurable fluorescence emission as a function of the templating antibody concentration. We have demonstrated the generality of our approach using two different antigen/antibody systems and found that both platforms show high binding affinity, specificity for the target antibody, and enough selectivity to work in crude cellular extracts. This study highlights the potential of biosupramolecular RNA engineering for the development of innovative biomimetic tools for nanobiotechnology and bioanalytical assays.
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Affiliation(s)
- Alessandro Bertucci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133, Rome, Italy
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10
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de Vink PJ, Briels JM, Schrader T, Milroy L, Brunsveld L, Ottmann C. A Binary Bivalent Supramolecular Assembly Platform Based on Cucurbit[8]uril and Dimeric Adapter Protein 14-3-3. Angew Chem Int Ed Engl 2017; 56:8998-9002. [PMID: 28510303 PMCID: PMC5575475 DOI: 10.1002/anie.201701807] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Indexed: 01/16/2023]
Abstract
Interactions between proteins frequently involve recognition sequences based on multivalent binding events. Dimeric 14-3-3 adapter proteins are a prominent example and typically bind partner proteins in a phosphorylation-dependent mono- or bivalent manner. Herein we describe the development of a cucurbit[8]uril (Q8)-based supramolecular system, which in conjunction with the 14-3-3 protein dimer acts as a binary and bivalent protein assembly platform. We fused the phenylalanine-glycine-glycine (FGG) tripeptide motif to the N-terminus of the 14-3-3-binding epitope of the estrogen receptor α (ERα) for selective binding to Q8. Q8-induced dimerization of the ERα epitope augmented its affinity towards 14-3-3 through a binary bivalent binding mode. The crystal structure of the Q8-induced ternary complex revealed molecular insight into the multiple supramolecular interactions between the protein, the peptide, and Q8.
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Affiliation(s)
- Pim J. de Vink
- Laboratory of Chemical Biology and Institute of Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyDen Dolech 25612 AZEindhovenThe Netherlands
| | - Jeroen M. Briels
- Laboratory of Chemical Biology and Institute of Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyDen Dolech 25612 AZEindhovenThe Netherlands
- Department of ChemistryUniversity of Duisburg-EssenUniversitätsstrasse 745117EssenGermany
| | - Thomas Schrader
- Department of ChemistryUniversity of Duisburg-EssenUniversitätsstrasse 745117EssenGermany
| | - Lech‐Gustav Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyDen Dolech 25612 AZEindhovenThe Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute of Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyDen Dolech 25612 AZEindhovenThe Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology and Institute of Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyDen Dolech 25612 AZEindhovenThe Netherlands
- Department of ChemistryUniversity of Duisburg-EssenUniversitätsstrasse 745117EssenGermany
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11
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de Vink PJ, Briels JM, Schrader T, Milroy LG, Brunsveld L, Ottmann C. A Binary Bivalent Supramolecular Assembly Platform Based on Cucurbit[8]uril and Dimeric Adapter Protein 14-3-3. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701807] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Pim J. de Vink
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Jeroen M. Briels
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
- Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45117 Essen Germany
| | - Thomas Schrader
- Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45117 Essen Germany
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
- Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45117 Essen Germany
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12
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Koch G, Wermser C, Acosta IC, Kricks L, Stengel ST, Yepes A, Lopez D. Attenuating Staphylococcus aureus Virulence by Targeting Flotillin Protein Scaffold Activity. Cell Chem Biol 2017; 24:845-857.e6. [PMID: 28669526 DOI: 10.1016/j.chembiol.2017.05.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/11/2017] [Accepted: 05/30/2017] [Indexed: 01/13/2023]
Abstract
Scaffold proteins are ubiquitous chaperones that bind proteins and facilitate physical interaction of multi-enzyme complexes. Here we used a biochemical approach to dissect the scaffold activity of the flotillin-homolog protein FloA of the multi-drug-resistant human pathogen Staphylococcus aureus. We show that FloA promotes oligomerization of membrane protein complexes, such as the membrane-associated RNase Rny, which forms part of the RNA-degradation machinery called the degradosome. Cells lacking FloA had reduced Rny function and a consequent increase in the targeted sRNA transcripts that negatively regulate S. aureus toxin expression. Small molecules that altered FloA oligomerization also reduced Rny function and decreased the virulence potential of S. aureus in vitro, as well as in vivo, using invertebrate and murine infection models. Our results suggest that flotillin assists in the assembly of protein complexes involved in S. aureus virulence, and could thus be an attractive target for the development of new antimicrobial therapies.
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Affiliation(s)
- Gudrun Koch
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Charlotte Wermser
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Ivan C Acosta
- National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain
| | - Lara Kricks
- National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain
| | - Stephanie T Stengel
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Ana Yepes
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Daniel Lopez
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany; National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain.
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13
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Yin C, Wang M, Lei C, Wang Z, Li P, Li Y, Li W, Huang Y, Nie Z, Yao S. Phosphorylation-Mediated Assembly of a Semisynthetic Fluorescent Protein for Label-Free Detection of Protein Kinase Activity. Anal Chem 2015; 87:6311-8. [DOI: 10.1021/acs.analchem.5b01160] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Chao Yin
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Ming Wang
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Zhen Wang
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Pei Li
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Yong Li
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Wang Li
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
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14
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Dang DT, Bosmans RPG, Moitzi C, Voets IK, Brunsveld L. Solution structure of a cucurbit[8]uril induced compact supramolecular protein dimer. Org Biomol Chem 2014; 12:9341-4. [PMID: 25337659 DOI: 10.1039/c4ob01729c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Supramolecular assembly of a beta-barrel protein via cucurbit[8]uril results in compact z-shaped protein dimers. SAXS data reveal the formation of a well ordered protein dimer, notwithstanding being connected by a reversible and flexible peptide linker, and highlight the supramolecular induced interplay of the proteins, analogous to covalently linked proteins.
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Affiliation(s)
- Dung T Dang
- Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ, Eindhoven, The Netherlands.
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15
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Milroy LG, Grossmann TN, Hennig S, Brunsveld L, Ottmann C. Modulators of Protein–Protein Interactions. Chem Rev 2014; 114:4695-748. [DOI: 10.1021/cr400698c] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lech-Gustav Milroy
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
| | - Luc Brunsveld
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
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16
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Maity B, Chatterjee A, Seth D. The photophysics of 7-(diethylamino)coumarin-3-carboxylic acid N-succinimidyl ester in reverse micelle: excitation wavelength dependent dynamics. RSC Adv 2014. [DOI: 10.1039/c3ra44240c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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17
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Suzuki M, Ishimaru Y, Saito A, Nishigaki K. Simple preparation of green fluorescent protein conjugated with β-cyclodextrin in a site specific manner. ANAL SCI 2013; 29:811-4. [PMID: 23934562 DOI: 10.2116/analsci.29.811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have site-directedly linked a green fluorescent protein (GFP) variant and a β-cyclodextrin (β-CD) with a simple method to develop a basic complex for sophisticated supramolecules. We have confirmed β-CD grafting on GFP with several methods including matrix-assisted laser desorption/ionization linear time-of-flight mass spectrometry (MALDI-TOF MS) without protease digestion and characterized the complex as well. In consideration of the resulting properties, the product we plainly and efficiently obtained could have applications related to sensing devices and drug delivery systems.
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Affiliation(s)
- Miho Suzuki
- Department of Functional Materials and Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura, Saitama 338-8570, Japan.
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18
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Sakamoto S, Terauchi M, Araki Y, Wada T. Design and semisynthesis of photoactivable split-GFP by incorporation of photocleavable functionality. Biopolymers 2013; 100:773-9. [PMID: 23893715 DOI: 10.1002/bip.22304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/13/2013] [Accepted: 05/30/2013] [Indexed: 11/07/2022]
Abstract
The design of proteins whose structure and function can be manipulated by the external stimuli has been of great interest in the field of protein engineering. In particular, caged proteins which can be activated by photo-irradiation become powerful tools for investigating a variety of biological events. Although protein caging is straightforward to render light-responsive protein functions, this approach mostly have difficulties based on the preparation of caged proteins in which amino acid residues required for biological activities must be specifically modified with synthetic photolabile groups. The synthetic peptide-based strategy for photoactivation of protein function may expand the versatility of protein caging approaches since the photolabile protecting group can be easily introduced into the peptide by means of standard solid-phase methods in a site-specific manner. In this study, we designed a new photoactivable green fluorescent protein (GFP), in which a relatively short C-terminal fragment (residues 214-230) of a dissected protein was modified with 7-diethylamino-4-hydroxymethylcoumarin (DECM) as a photoresponsive-protecting group. The introduced DECM unit completely inhibited the reconstitution with the GFP N-terminal fragment (residues 2-214). However, irradiation of visible light (>400 nm) resulted in efficient cleavage of DECM group, leading to acceleration of protein reassembly and concomitant GFP fluorescence recovery. These results demonstrated direct control of protein structure and function by application of the synthetic photocleavable functionality to a fragmented protein. The combined system of fragmented proteins and synthetic photocleavable elements will provide the useful and potentially wide applicable strategy for the regulation of protein structure and function by the light in a temporal and spacial manner.
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Affiliation(s)
- Seiji Sakamoto
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
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19
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Guo-jian W, Qi Z, Hong-ping D, Da-li W, Xin-yuan Z, De-yue Y. FLUORESCENCE ENHANCEMENT OF GFP CHROMOPHORE THROUGH POLYMERIC SELF-ASSEMBLY. ACTA POLYM SIN 2013. [DOI: 10.3724/sp.j.1105.2013.12418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Lee JW, Heo SW, Lee SJC, Ko JY, Kim H, Kim HI. Probing conformational changes of ubiquitin by host-guest chemistry using electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:21-29. [PMID: 23247966 DOI: 10.1007/s13361-012-0496-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 09/04/2012] [Accepted: 09/08/2012] [Indexed: 06/01/2023]
Abstract
We report mechanistic studies of structural changes of ubiquitin (Ub) by host-guest chemistry with cucurbit[6]uril (CB[6]) using electrospray ionization mass spectrometry (ESI-MS) combined with circular dichroism spectroscopy and molecular dynamics (MD) simulation. CB[6] binds selectively to lysine (Lys) residues of proteins. Low energy collision-induced dissociation (CID) of the protein-CB[6] complex reveals CB[6] binding sites. We previously reported (Anal. Chem. 2011, 83, 7916-7923) shifts in major charge states along with Ub-CB[6] complexes in the ESI-MS spectrum with addition of CB[6] to Ub from water. We also reported that CB[6] is present only at Lys(6) or Lys(11) in high charge state (+13) complex. In this study, we provide additional information to explain unique conformational change mechanisms of Ub by host-guest chemistry with CB[6] compared with solvent-driven conformational change of Ub. Additional CID study reveals that CB[6] is bound only to Lys(48) and Lys(63) in low charge state (+7) complex. MD simulation studies reveal that the high charge state complexes are attributed to the CB[6] bound to Lys(11). The complexation prohibits salt bridge formation between Lys(11) and Glu(34) and induces conformational change of Ub. This results in formation of high charge state complexes in the gas phase. Then, by utilizing stronger host-guest chemistry of CB[6] with pentamethylenediamine, refolding of Ub via detaching CB[6] from the protein is performed. Overall, this study gives an insight into the mechanism of denatured Ub ion formation via host-guest interactions with CB[6]. Furthermore, this provides a direction for designing function-controllable supramolecular system comprising proteins and synthetic host molecules.
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Affiliation(s)
- Jong Wha Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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21
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Keem JO, Lee IH, Kim SY, Jung Y, Chung BH. Splitting and self-assembling of far-red fluorescent protein with an engineered beta strand peptide: application for alpha-synuclein imaging in mammalian cells. Biomaterials 2011; 32:9051-8. [PMID: 21880361 DOI: 10.1016/j.biomaterials.2011.08.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 08/10/2011] [Indexed: 12/30/2022]
Abstract
We introduce the strategic development of self-assembling peptide/protein fragments based on the far-red fluorescent protein mPlum. The first beta strand (mPlum 1, 18 amino acids) of mPlum was engineered to spontaneously bind with the rest of the protein (mPlum 2-11, next 10 beta strands) and to form a native chromophore. The target beta strand mPlum 1 was separated from mPlum 2-11 and linked via a flexible peptide linker, resulting in fluorescently inactive circularly permuted mPlum protein (CpmPlum). In vitro evolution of this CpmPlum to a fluorescently active form and the subsequent splitting of the engineered mPlum 1 peptide afforded self-assembling mPlum fragments. Recombinantly expressed and synthetically prepared beta strand peptides were successfully assembled with the remaining mPlum protein in vitro and in cells. This developed pair of peptide/protein fragments was effectively used for peptide tag detection of alpha-synuclein in mammalian cells. Sequential expression of self-assembling mPlum fragments offered an entirely genetically encoded sensing system of naturally unfolded alpha-synuclein.
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Affiliation(s)
- Joo Oak Keem
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon, Republic of Korea
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22
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Shekhawat SS, Ghosh I. Split-protein systems: beyond binary protein-protein interactions. Curr Opin Chem Biol 2011; 15:789-97. [PMID: 22070901 DOI: 10.1016/j.cbpa.2011.10.014] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 10/07/2011] [Accepted: 10/17/2011] [Indexed: 11/29/2022]
Abstract
It has been estimated that 650,000 protein-protein interactions exist in the human interactome (Stumpf et al., 2008), a subset of all possible macromolecular partnerships that dictate life. Thus there is a continued need for the development of sensitive and user-friendly methods for cataloguing biomacromolecules in complex environments and for detecting their interactions, modifications, and cellular location. Such methods also allow for establishing differences in the interactome between a normal and diseased cellular state and for quantifying the outcome of therapeutic intervention. A promising approach for deconvoluting the role of macromolecular partnerships is split-protein reassembly, also called protein fragment complementation. This approach relies on the appropriate fragmentation of protein reporters, such as the green fluorescent protein or firefly luciferase, which when attached to possible interacting partners can reassemble and regain function, thereby confirming the partnership. Split-protein methods have been effectively utilized for detecting protein-protein interactions in cell-free systems, Escherichia coli, yeast, mammalian cells, plants, and live animals. Herein, we present recent advances in engineering split-protein systems that allow for the rapid detection of ternary protein complexes, small molecule inhibitors, as well as a variety of macromolecules including nucleic acids, poly(ADP) ribose, and iron sulfur clusters. We also present advances that combine split-protein systems with chemical inducers of dimerization strategies that allow for regulating the activity of orthogonal split-proteases as well as aid in identifying enzyme inhibitors. Finally, we discuss autoinhibition strategies leading to turn-on sensors as well as future directions in split-protein methodology including possible therapeutic approaches.
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Affiliation(s)
- Sujan S Shekhawat
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Blvd, Tucson, AZ 85721, USA
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23
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Xiao W, Chen WH, Zhang J, Li C, Zhuo RX, Zhang XZ. Design of a Photoswitchable Hollow Microcapsular Drug Delivery System by Using a Supramolecular Drug-Loading Approach. J Phys Chem B 2011; 115:13796-802. [DOI: 10.1021/jp208692c] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Wang Xiao
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China
| | - Wei-Hai Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China
| | - Jing Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China
| | - Cao Li
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China
| | - Ren-Xi Zhuo
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China
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24
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Xiao W, Chen WH, Li C, Chen JX, Zhang XZ, Zhuo RX. A plug and play polymeric template driven by supramolecular interactions. J Biomed Mater Res A 2011; 100:149-54. [PMID: 21997960 DOI: 10.1002/jbm.a.33254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 08/25/2011] [Accepted: 08/30/2011] [Indexed: 11/08/2022]
Abstract
A new "plug and play" polymeric template with the driving force of host-guest interaction between β-CD and naphthalene-modified functional groups was designed and studied. Multiple functional groups can be loaded into the template directly and conveniently. Importantly, the "plug and play" effect of the polymeric template is reversible and the functional groups could be removed from the polymeric template conveniently by adding AD-HCl. The studies on the cell viability and phagocytosis proved that the loading and unloading process of this template could be realized in vitro.
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Affiliation(s)
- Wang Xiao
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China
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25
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Targeting and imaging single biomolecules in living cells by complementation-activated light microscopy with split-fluorescent proteins. Proc Natl Acad Sci U S A 2011; 108:E201-10. [PMID: 21606345 DOI: 10.1073/pnas.1101929108] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-molecule (SM) microscopy allows outstanding insight into biomolecular mechanisms in cells. However, selective detection of single biomolecules in their native environment remains particularly challenging. Here, we introduce an easy methodology that combines specific targeting and nanometer accuracy imaging of individual biomolecules in living cells. In this method, named complementation-activated light microscopy (CALM), proteins are fused to dark split-fluorescent proteins (split-FPs), which are activated into bright FPs by complementation with synthetic peptides. Using CALM, the diffusion dynamics of a controlled subset of extracellular and intracellular proteins are imaged with nanometer precision, and SM tracking can additionally be performed with fluorophores and quantum dots. In cells, site-specific labeling of these probes is verified by coincidence SM detection with the complemented split-FP fusion proteins or intramolecular single-pair Förster resonance energy transfer. CALM is simple and combines advantages from genetically encoded and synthetic fluorescent probes to allow high-accuracy imaging of single biomolecules in living cells, independently of their expression level and at very high probe concentrations.
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26
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Nomura W, Ohashi N, Okuda Y, Narumi T, Ikura T, Ito N, Tamamura H. Fluorescence-quenching screening of protein kinase C ligands with an environmentally sensitive fluorophore. Bioconjug Chem 2011; 22:923-30. [PMID: 21434694 DOI: 10.1021/bc100567k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel fluorescence-quenching screening method for protein kinase C (PKC) ligands was developed utilizing solvatochromic fluorophores. Solvatochromic dyes, highly sensitive to the presence or the absence of competitive ligands in their binding to the C1b domain of PKCδ (δC1b), were combined with a known pharmacophoric moiety of 1,2-diacylglycerol (DAG) lactones, PKC ligands. Addition of δC1b to the fluorescent compounds caused a gradual increase in the fluorescent intensity in proportion to the increase of δC1b. As a competitive ligand was added to the complex of δC1b domain and fluorescent compounds, a gradual decrease in the fluorescent intensity was observed. The relative binding affinities of known ligands were successfully determined by this fluorescent method and corresponded well to the K(i) values measured by a radioisotope method. These results indicate that washing, which is a laborious step in binding evaluations, is not required for this environmentally sensitive fluorophore based system. Screening with the system was performed for 2560 preselected library compounds with possible pharmacophores, and some lead compounds were found. This fluorescence-based method could be applied widely to known ligand-receptor combinations.
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Affiliation(s)
- Wataru Nomura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, Japan
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27
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Abstract
Truncated green fluorescent protein (GFP) with the 11th β-strand removed is potentially interesting for bioconjugation, imaging, and the preparation of semisynthetic proteins with novel spectroscopic or functional properties. Surprisingly, the truncated GFP generated by removing the 11th strand, once refolded, does not reassemble with a synthetic peptide corresponding to strand 11 but does reassemble following light activation. The mechanism of this process has been studied in detail by absorption, fluorescence, and Raman spectroscopy. The chromophore in this refolded truncated GFP is found to be in the trans configuration. Upon exposure to light a photostationary state is formed between the trans and cis conformations of the chromophore, and only truncated GFP with the cis configuration of the chromophore binds the peptide. A kinetic model describing the light-activated reassembly of this split GFP is discussed. This unique light-driven reassembly is potentially useful for controlling protein-protein interactions.
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Affiliation(s)
- Kevin P Kent
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
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28
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Isogai M, Kawamoto Y, Inahata K, Fukada H, Sugimoto K, Tada T. Structure and characteristics of reassembled fluorescent protein, a new insight into the reassembly mechanisms. Bioorg Med Chem Lett 2011; 21:3021-4. [PMID: 21463942 DOI: 10.1016/j.bmcl.2011.03.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 03/08/2011] [Accepted: 03/10/2011] [Indexed: 11/15/2022]
Abstract
Bimolecular fluorescence complementation (BiFC) assay has been used widely to visualize protein-protein interactions in cells. However, there is a problem that fluorescent protein fragments have an ability to associate with each other independent of an interaction between proteins fused to the fragments. To facilitate the BiFC assay, we have attempted to determine the structure and characteristics of reassembled fluorescent protein, Venus. The anion-exchange chromatography showed an oligomer and a monomer of reassembled Venus. Our results suggested that the oligomer was formed by β-strands swapping without any serious steric clashes and was converted to the monomer. Crystal structure of reassembled Venus had an 11-stranded β-barrel fold, typical of GFP-derived fluorescent proteins. Based on the structural features, we have mutated to β-strand 7 and measured T(m) values. The results have revealed that the mutation influences the thermal stability of reassembled fluorescent complex.
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Affiliation(s)
- Masami Isogai
- Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan
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29
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Oltra NS, Bos J, Roelfes G. Control over enzymatic activity by DNA-directed split enzyme reassembly. Chembiochem 2011; 11:2255-8. [PMID: 20941727 DOI: 10.1002/cbic.201000517] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Núria Sancho Oltra
- Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
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30
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Uhlenheuer DA, Milroy LG, Neirynck P, Brunsveld L. Strong supramolecular control over protein self-assembly using a polyamine decorated β-cyclodextrin as synthetic recognition element. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm12736e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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31
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Vidal Pinheiro A, Conde J, Parola A, Lima J, Baptista P. Use of cyclodextrins as scavengers of inhibitory photo-products in light controlled in vitro synthesis of RNA. J Photochem Photobiol A Chem 2010. [DOI: 10.1016/j.jphotochem.2010.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Uhlenheuer DA, Petkau K, Brunsveld L. Combining supramolecular chemistry with biology. Chem Soc Rev 2010; 39:2817-26. [PMID: 20461247 DOI: 10.1039/b820283b] [Citation(s) in RCA: 290] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Supramolecular chemistry has primarily found its inspiration in biological molecules, such as proteins and lipids, and their interactions. Currently the supramolecular assembly of designed compounds can be controlled to great extent. This provides the opportunity to combine these synthetic supramolecular elements with biomolecules for the study of biological phenomena. This tutorial review focuses on the possibilities of the marriage of synthetic supramolecular architectures and biological systems. It highlights that synthetic supramolecular elements are for example ideal platforms for the recognition and modulation of proteins and cells. The unique features of synthetic supramolecular systems with control over size, shape, valency, and interaction strength allow the generation of structures fitting the demands to approach the biological problems at hand. Supramolecular chemistry has come full circle, studying the biology and its molecules which initially inspired its conception.
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Affiliation(s)
- Dana A Uhlenheuer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612AZ Eindhoven, The Netherlands
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33
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Nguyen HD, Dang DT, van Dongen JLJ, Brunsveld L. Protein Dimerization Induced by Supramolecular Interactions with Cucurbit[8]uril. Angew Chem Int Ed Engl 2010; 49:895-8. [PMID: 20039237 DOI: 10.1002/anie.200904413] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hoang D Nguyen
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany
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34
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Nguyen H, Dang D, van Dongen J, Brunsveld L. Protein Dimerization Induced by Supramolecular Interactions with Cucurbit[8]uril. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904413] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Kent KP, Oltrogge LM, Boxer SG. Synthetic control of green fluorescent protein. J Am Chem Soc 2010; 131:15988-9. [PMID: 19839621 DOI: 10.1021/ja906303f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Semisynthetic green fluorescent proteins (GFPs) can be prepared by producing truncated GFPs recombinantly and assembling them with synthetic beta-strands of GFP. The yield from expressing the truncated GFPs is low, and the chromophore is either partially formed or not formed. An alternative method is presented in which full-length proteins are produced recombinantly with a protease site inserted between the structural element to be removed and the rest of the protein. The native peptide can then be replaced by cutting the protease site with trypsin, denaturing in guanidine hydrochloride to disrupt the complex, separating the native peptide from the rest of the protein by size exclusion, and refolding the protein in the presence of a synthetic peptide. We show that this method allows for removal and replacement of the interior chromophore containing helix and that the GFP barrel is capable of inducing chromophore formation in a synthetic interior helix.
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Affiliation(s)
- Kevin P Kent
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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36
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Young JF, Nguyen HD, Yang L, Huskens J, Jonkheijm P, Brunsveld L. Strong and Reversible Monovalent Supramolecular Protein Immobilization. Chembiochem 2009; 11:180-3. [DOI: 10.1002/cbic.200900599] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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37
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Uhlenheuer D, Wasserberg D, Nguyen H, Zhang L, Blum C, Subramaniam V, Brunsveld L. Modulation of Protein Dimerization by a Supramolecular Host-Guest System. Chemistry 2009; 15:8779-90. [DOI: 10.1002/chem.200900462] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Gómez-Biagi RF, Jagt RBC, Nitz M. Remarkably stable inclusion complexes with heptakis-[6-deoxy-6-(2-aminoethylsulfanyl)]-β-cyclodextrin. Org Biomol Chem 2008; 6:4622-6. [DOI: 10.1039/b813999g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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