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Cronan JE. Lipoic acid attachment to proteins: stimulating new developments. Microbiol Mol Biol Rev 2024; 88:e0000524. [PMID: 38624243 PMCID: PMC11332335 DOI: 10.1128/mmbr.00005-24] [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: 04/17/2024] Open
Abstract
SUMMARYLipoic acid-modified proteins are essential for central metabolism and pathogenesis. In recent years, the Escherichia coli and Bacillus subtilis lipoyl assembly pathways have been modified and extended to archaea and diverse eukaryotes including humans. These extensions include a new pathway to insert the key sulfur atoms of lipoate, several new pathways of lipoate salvage, and a novel use of lipoic acid in sulfur-oxidizing bacteria. Other advances are the modification of E. coli LplA for studies of protein localization and protein-protein interactions in cell biology and in enzymatic removal of lipoate from lipoyl proteins. Finally, scenarios have been put forth for the evolution of lipoate assembly in archaea.
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Affiliation(s)
- John E. Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
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2
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [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: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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3
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Gao Z, Li Y, Xing J, Lu Y, Shao Q, Hu J, Zhao S, He W, Sun B. Transition Metal Ru(II) Catalysts Immobilized Nanoreactors for Conditional Bioorthogonal Catalysis in Cells. ACS APPLIED MATERIALS & INTERFACES 2024; 16:15870-15878. [PMID: 38520329 DOI: 10.1021/acsami.3c19133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
Employing transition metal catalysts (TMCs) to perform bioorthogonal activation of prodrugs and pro-fluorophores in biological systems, particularly in a conditional fashion, remains a challenge. Here, we used a mesoporous organosilica nanoscaffold (RuMSN), which localizes Ru(II) conjugates on the pore wall, enabling the biorthogonal photoreduction reactions of azide groups. Due to easily adjustable surface charges and pore diameter, this efficiently engineering RuMSN catalyst, with abundant active sites on the inner pore well, could spontaneously repel or attract substrates with different molecular sizes and charges and thus ensure selective bioorthogonal catalysis. Depending on it, engineering RuMSN nanoreactors showed fascinating application scales from conditional bioorthogonal activation of prodrugs and pro-fluorophores in either intra- or extracellular localization to performing intracellular concurrent and tandem catalysis together with natural enzymes.
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Affiliation(s)
- Zhiguo Gao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 210009, China
| | - Yaojia Li
- School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, China
| | - Jiaqi Xing
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 210009, China
| | - Yougong Lu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 210009, China
| | - Quanlin Shao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 210009, China
| | - Jinzhong Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, China
| | - Shan Zhao
- School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, China
| | - Wei He
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 210009, China
| | - Baiwang Sun
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, China
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4
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Song Z, Zhang Q, Wu W, Pu Z, Yu H. Rational design of enzyme activity and enantioselectivity. Front Bioeng Biotechnol 2023; 11:1129149. [PMID: 36761300 PMCID: PMC9902596 DOI: 10.3389/fbioe.2023.1129149] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/16/2023] [Indexed: 01/25/2023] Open
Abstract
The strategy of rational design to engineer enzymes is to predict the potential mutants based on the understanding of the relationships between protein structure and function, and subsequently introduce the mutations using the site-directed mutagenesis. Rational design methods are universal, relatively fast and have the potential to be developed into algorithms that can quantitatively predict the performance of the designed sequences. Compared to the protein stability, it was more challenging to design an enzyme with improved activity or selectivity, due to the complexity of enzyme molecular structure and inadequate understanding of the relationships between enzyme structures and functions. However, with the development of computational force, advanced algorithm and a deeper understanding of enzyme catalytic mechanisms, rational design could significantly simplify the process of engineering enzyme functions and the number of studies applying rational design strategy has been increasing. Here, we reviewed the recent advances of applying the rational design strategy to engineer enzyme functions including activity and enantioselectivity. Five strategies including multiple sequence alignment, strategy based on steric hindrance, strategy based on remodeling interaction network, strategy based on dynamics modification and computational protein design are discussed and the successful cases using these strategies are introduced.
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Affiliation(s)
- Zhongdi Song
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, China
| | - Qunfeng Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wenhui Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang, China
| | - Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China,ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China,ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang, China,*Correspondence: Haoran Yu,
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5
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Effect of excited state inter- or intra-proton transfers on the fluorescence behaviors of firefly fluorescein analogues. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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6
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Yao Z, Caldwell DR, Love AC, Kolbaba-Kartchner B, Mills JH, Schnermann MJ, Prescher JA. Coumarin luciferins and mutant luciferases for robust multi-component bioluminescence imaging. Chem Sci 2021; 12:11684-11691. [PMID: 34659703 PMCID: PMC8442684 DOI: 10.1039/d1sc03114g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/20/2021] [Indexed: 12/21/2022] Open
Abstract
Multi-component bioluminescence imaging requires an expanded collection of luciferase-luciferin pairs that emit far-red or near-infrared light. Toward this end, we prepared a new class of luciferins based on a red-shifted coumarin scaffold. These probes (CouLuc-1s) were accessed in a two-step sequence via direct modification of commercial dyes. The bioluminescent properties of the CouLuc-1 analogs were also characterized, and complementary luciferase enzymes were identified using a two-pronged screening strategy. The optimized enzyme-substrate pairs displayed robust photon outputs and emitted a significant portion of near-infrared light. The CouLuc-1 scaffolds are also structurally distinct from existing probes, enabling rapid multi-component imaging. Collectively, this work provides novel bioluminescent tools along with a blueprint for crafting additional fluorophore-derived probes for multiplexed imaging.
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Affiliation(s)
- Zi Yao
- Department of Chemistry, University of California Irvine CA USA
| | - Donald R Caldwell
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - Anna C Love
- Department of Chemistry, University of California Irvine CA USA
| | - Bethany Kolbaba-Kartchner
- School of Molecular Sciences, Arizona State University Tempe AZ USA
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University Tempe AZ USA
| | - Jeremy H Mills
- School of Molecular Sciences, Arizona State University Tempe AZ USA
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University Tempe AZ USA
| | - Martin J Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California Irvine CA USA
- Department of Molecular Biology & Biochemistry, University of California Irvine CA USA
- Department of Pharmaceutical Sciences, University of California Irvine CA USA
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7
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Wolf P, Gavins G, Beck‐Sickinger AG, Seitz O. Strategies for Site-Specific Labeling of Receptor Proteins on the Surfaces of Living Cells by Using Genetically Encoded Peptide Tags. Chembiochem 2021; 22:1717-1732. [PMID: 33428317 PMCID: PMC8248378 DOI: 10.1002/cbic.202000797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Fluorescence microscopy imaging enables receptor proteins to be investigated within their biological context. A key challenge is to site-specifically incorporate reporter moieties into proteins without interfering with biological functions or cellular networks. Small peptide tags offer the opportunity to combine inducible labeling with small tag sizes that avoid receptor perturbation. Herein, we review the current state of live-cell labeling of peptide-tagged cell-surface proteins. Considering their importance as targets in medicinal chemistry, we focus on membrane receptors such as G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). We discuss peptide tags that i) are subject to enzyme-mediated modification reactions, ii) guide the complementation of reporter proteins, iii) form coiled-coil complexes, and iv) interact with metal complexes. Given our own contributions in the field, we place emphasis on peptide-templated labeling chemistry.
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Affiliation(s)
- Philipp Wolf
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Georgina Gavins
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| | - Annette G. Beck‐Sickinger
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Oliver Seitz
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
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8
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Development of a versatile and efficient C–N lyase platform for asymmetric hydroamination via computational enzyme redesign. Nat Catal 2021. [DOI: 10.1038/s41929-021-00604-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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9
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Mineev KS, Goncharuk SA, Goncharuk MV, Povarova NV, Sokolov AI, Baleeva NS, Smirnov AY, Myasnyanko IN, Ruchkin DA, Bukhdruker S, Remeeva A, Mishin A, Borshchevskiy V, Gordeliy V, Arseniev AS, Gorbachev DA, Gavrikov AS, Mishin AS, Baranov MS. NanoFAST: structure-based design of a small fluorogen-activating protein with only 98 amino acids. Chem Sci 2021; 12:6719-6725. [PMID: 34040747 PMCID: PMC8132994 DOI: 10.1039/d1sc01454d] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/08/2021] [Indexed: 12/31/2022] Open
Abstract
One of the essential characteristics of any tag used in bioscience and medical applications is its size. The larger the label, the more it may affect the studied object, and the more it may distort its behavior. In this paper, using NMR spectroscopy and X-ray crystallography, we have studied the structure of fluorogen-activating protein FAST both in the apo form and in complex with the fluorogen. We showed that significant change in the protein occurs upon interaction with the ligand. While the protein is completely ordered in the complex, its apo form is characterized by higher mobility and disordering of its N-terminus. We used structural information to design the shortened FAST (which we named nanoFAST) by truncating 26 N-terminal residues. Thus, we created the shortest genetically encoded tag among all known fluorescent and fluorogen-activating proteins, which is composed of only 98 amino acids.
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Affiliation(s)
- Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Natalia V Povarova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Anatolii I Sokolov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Dmitry A Ruchkin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Sergey Bukhdruker
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
- ESRF - The European Synchrotron Grenoble 38000 France
| | - Alina Remeeva
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Alexey Mishin
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Valentin Borshchevskiy
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes, CEA, CNRS Grenoble France
| | - Alexander S Arseniev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Dmitriy A Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Research Medical University Ostrovitianov 1 Moscow 117997 Russia
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10
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Kudriaeva AA, Livneh I, Baranov MS, Ziganshin RH, Tupikin AE, Zaitseva SO, Kabilov MR, Ciechanover A, Belogurov AA. In-depth characterization of ubiquitin turnover in mammalian cells by fluorescence tracking. Cell Chem Biol 2021; 28:1192-1205.e9. [PMID: 33675681 DOI: 10.1016/j.chembiol.2021.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/29/2020] [Accepted: 02/11/2021] [Indexed: 01/01/2023]
Abstract
Despite almost 40 years having passed from the initial discovery of ubiquitin (Ub), fundamental questions related to its intracellular metabolism are still enigmatic. Here we utilized fluorescent tracking for monitoring ubiquitin turnover in mammalian cells, resulting in obtaining qualitatively new data. In the present study we report (1) short Ub half-life estimated as 4 h; (2) for a median of six Ub molecules per substrate as a dynamic equilibrium between Ub ligases and deubiquitinated enzymes (DUBs); (3) loss on average of one Ub molecule per four acts of engagement of polyubiquitinated substrate by the proteasome; (4) direct correlation between incorporation of Ub into the distinct type of chains and Ub half-life; and (5) critical influence of the single lysine residue K27 on the stability of the whole Ub molecule. Concluding, our data provide a comprehensive understanding of ubiquitin-proteasome system dynamics on the previously unreachable state of the art.
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Affiliation(s)
- Anna A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Ido Livneh
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, 3109602 Haifa, Israel
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation; Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russian Federation
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentieva 8, 630090 Novosibirsk, Russian Federation
| | - Snizhana O Zaitseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentieva 8, 630090 Novosibirsk, Russian Federation
| | - Aaron Ciechanover
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, 3109602 Haifa, Israel
| | - Alexey A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation; Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russian Federation.
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11
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Tian L, Feng H, Dai Z, Zhang R. Resorufin-based responsive probes for fluorescence and colorimetric analysis. J Mater Chem B 2020; 9:53-79. [PMID: 33226060 DOI: 10.1039/d0tb01628d] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The fluorescence imaging technique has attracted increasing attention in the detection of various biological molecules in situ and in real-time owing to its inherent advantages including high selectivity and sensitivity, outstanding spatiotemporal resolution and fast feedback. In the past few decades, a number of fluorescent probes have been developed for bioassays and imaging by exploiting different fluorophores. Among various fluorophores, resorufin exhibits a high fluorescence quantum yield, long excitation/emission wavelength and pronounced ability in both fluorescence and colorimetric analysis. This fluorophore has been widely utilized in the design of responsive probes specific for various bioactive species. In this review, we summarize the advances in the development of resorufin-based fluorescent probes for detecting various analytes, such as cations, anions, reactive (redox-active) sulfur species, small molecules and biological macromolecules. The chemical structures of probes, response mechanisms, detection limits and practical applications are investigated, which is followed by the discussion of recent challenges and future research perspectives. This review article is expected to promote the further development of resorufin-based responsive fluorescent probes and their biological applications.
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Affiliation(s)
- Lu Tian
- Key Laboratory of Functional Nanomaterials and Technology in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China.
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12
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Macias‐Contreras M, Zhu L. The Collective Power of Genetically Encoded Protein/Peptide Tags and Bioorthogonal Chemistry in Biological Fluorescence Imaging. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Macias‐Contreras
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
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13
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Plaks JG, Brewer JA, Jacobsen NK, McKenna M, Uzarski JR, Lawton TJ, Filocamo SF, Kaar JL. Rosetta-Enabled Structural Prediction of Permissive Loop Insertion Sites in Proteins. Biochemistry 2020; 59:3993-4002. [PMID: 32970423 DOI: 10.1021/acs.biochem.0c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While loop motifs frequently play a major role in protein function, our understanding of how to rationally engineer proteins with novel loop domains remains limited. In the absence of rational approaches, the incorporation of loop domains often destabilizes proteins, thereby requiring massive screening and selection to identify sites that can accommodate loop insertion. We developed a computational strategy for rapidly scanning the entire structure of a scaffold protein to determine the impact of loop insertion at all possible amino acid positions. This approach is based on the Rosetta kinematic loop modeling protocol and was demonstrated by identifying sites in lipase that were permissive to insertion of the LAP peptide. Interestingly, the identification of permissive sites was dependent on the contribution of the residues in the near-loop environment on the Rosetta score and did not correlate with conventional structural features (e.g., B-factors). As evidence of this, several insertion sites (e.g., following residues 17, 47-49, and 108), which were predicted and confirmed to be permissive, interrupted helices, while others (e.g., following residues 43, 67, 116, 119, and 121), which are situated in loop regions, were nonpermissive. This approach was further shown to be predictive for β-glucosidase and human phosphatase and tensin homologue (PTEN), and to facilitate the engineering of insertion sites through in silico mutagenesis. By enabling the design of loop-containing protein libraries with high probabilities of soluble expression, this approach has broad implications in many areas of protein engineering, including antibody design, improving enzyme activity, and protein modification.
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Affiliation(s)
- Joseph G Plaks
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Jeff A Brewer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Nicole K Jacobsen
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Michael McKenna
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Joshua R Uzarski
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Timothy J Lawton
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Shaun F Filocamo
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
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14
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Yao Z, Zhang BS, Steinhardt RC, Mills JH, Prescher JA. Multicomponent Bioluminescence Imaging with a π-Extended Luciferin. J Am Chem Soc 2020; 142:14080-14089. [PMID: 32787261 PMCID: PMC7867379 DOI: 10.1021/jacs.0c01064] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Bioluminescence imaging with luciferase-luciferin pairs is commonly used for monitoring biological processes in cells and whole organisms. Traditional bioluminescent probes are limited in scope, though, as they cannot be easily distinguished in biological environments, precluding efforts to visualize multicellular processes. Additionally, many luciferase-luciferin pairs emit light that is poorly tissue penetrant, hindering efforts to visualize targets in deep tissues. To address these issues, we synthesized a set of π-extended luciferins that were predicted to be red-shifted luminophores. The scaffolds were designed to be rotationally labile such that they produced light only when paired with luciferases capable of enforcing planarity. A luciferin comprising an intramolecular "lock" was identified as a viable light-emitting probe. Native luciferases were unable to efficiently process the analog, but a complementary luciferase was identified via Rosetta-guided enzyme design. The unique enzyme-substrate pair is red-shifted compared to well-known bioluminescent tools. The probe set is also orthogonal to other luciferase-luciferin probes and can be used for multicomponent imaging. Four substrate-resolved luciferases were imaged in a single session. Collectively, this work provides the first example of Rosetta-guided design in engineering bioluminescent tools and expands the scope of orthogonal imaging probes.
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Affiliation(s)
- Zi Yao
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Brendan S. Zhang
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Rachel C. Steinhardt
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Jeremy H. Mills
- Department of Chemistry and Biochemistry, Arizona State University, Tempe AZ, USA
- The Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ, USA
- The Biodesign Institute, Arizona State University, Tempe AZ, USA
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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15
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Luo F, Qin G, Xia T, Fang X. Single-Molecule Imaging of Protein Interactions and Dynamics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:337-361. [PMID: 32228033 DOI: 10.1146/annurev-anchem-091619-094308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Live-cell single-molecule fluorescence imaging has become a powerful analytical tool to investigate cellular processes that are not accessible to conventional biochemical approaches. This has greatly enriched our understanding of the behaviors of single biomolecules in their native environments and their roles in cellular events. Here, we review recent advances in fluorescence-based single-molecule bioimaging of proteins in living cells. We begin with practical considerations of the design of single-molecule fluorescence imaging experiments such as the choice of imaging modalities, fluorescent probes, and labeling methods. We then describe analytical observables from single-molecule data and the associated molecular parameters along with examples of live-cell single-molecule studies. Lastly, we discuss computational algorithms developed for single-molecule data analysis.
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Affiliation(s)
- Fang Luo
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gege Qin
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tie Xia
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohong Fang
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
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16
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Safaei M, Mobini GR, Abiri A, Shojaeian A. Synthetic biology in various cellular and molecular fields: applications, limitations, and perspective. Mol Biol Rep 2020; 47:6207-6216. [PMID: 32507922 DOI: 10.1007/s11033-020-05565-6] [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: 05/03/2020] [Accepted: 05/28/2020] [Indexed: 01/10/2023]
Abstract
Synthetic biology breakthroughs have facilitated genetic circuit engineering to program cells through novel biological functions, dynamic gene expressions, as well as logic controls. SynBio can also participate in the rapid development of new treatments required for the human lifestyle. Moreover, these technologies are applied in the development of innovative therapeutic, diagnostic, as well as discovery-related methods within a wide range of cellular and molecular applications. In the present review study, SynBio applications in various cellular and molecular fields such as novel strategies for cancer therapy, biosensing, metabolic engineering, protein engineering, and tissue engineering were highlighted and summarized. The major safety and regulatory concerns about synthetic biology will be the environmental release, legal concerns, and risks of the engineered organisms. The final sections focused on limitations to SynBio.
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Affiliation(s)
- Mohsen Safaei
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Gholam-Reza Mobini
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Shojaeian
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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17
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Cortés I, di Liberto MG, Kaufman TS, Derita MG, Bracca ABJ. Synthesis and evaluation of aromatic methoxime derivatives against five postharvest phytopathogenic fungi of fruits. Main structure-activity relationships. Food Chem 2020; 321:126701. [PMID: 32283502 DOI: 10.1016/j.foodchem.2020.126701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/16/2023]
Abstract
The antifungal activity of a library of twenty-four aromatic methoximes was examined against five representative postharvest phytopathogenic fungi. The panel included Penicillium digitatum, Penicillium italicum, Rhizopus stolonifer, Botrytis cinerea and Monilinia fructicola, all of which cause relevant economic losses worldwide as a result of affecting harvested fruits. The minimum inhibitory concentrations and minimum fungicidal concentrations of each compound were defined and the main structure-activity relationships were determined. Although other congeners were more potent, drug likeliness considerations pointed to the methoxime derived from 2,4-dihydroxypropiophenone as the compound with the most suitable profile. The morphology of the colonies of the fungal strains treated with the methoxime was examined microscopically and the compound was also tested in freshly harvested peaches and oranges, exhibiting promising control profiles in both fruits, similar to those of the commercial agents Imazalil and Carbendazim.
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Affiliation(s)
- Iván Cortés
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (2000) Rosario, Argentina
| | - Melina G di Liberto
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
| | - Teodoro S Kaufman
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (2000) Rosario, Argentina.
| | - Marcos G Derita
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina; Instituto de Ciencias Agropecuarias del Litoral (ICiAgro Litoral, Universidad Nacional del Litoral-CONICET), Kreder 2805, (3080) Esperanza, Argentina.
| | - Andrea B J Bracca
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (2000) Rosario, Argentina.
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18
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Santos EM, Berbasova T, Wang W, Salmani RE, Sheng W, Vasileiou C, Geiger JH, Borhan B. Engineering of a Red Fluorogenic Protein/Merocyanine Complex for Live-Cell Imaging. Chembiochem 2020; 21:723-729. [PMID: 31482666 PMCID: PMC7379159 DOI: 10.1002/cbic.201900428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Indexed: 12/25/2022]
Abstract
A reengineered human cellular retinol binding protein II (hCRBPII), a 15-kDa protein belonging to the intracellular lipid binding protein (iLBP) family, generates a highly fluorescent red pigment through the covalent linkage of a merocyanine aldehyde to an active site lysine residue. The complex exhibits "turn-on" fluorescence, due to a weakly fluorescent aldehyde that "lights up" with subsequent formation of a strongly fluorescent merocyanine dye within the binding pocket of the protein. Cellular penetration of merocyanine is rapid, and fluorophore maturation is nearly instantaneous. The hCRBPII/merocyanine complex displays high quantum yield, low cytotoxicity, specificity in labeling organelles, and compatibility in both cancer cell lines and yeast cells. The hCRBPII/merocyanine tag is brighter than most common red fluorescent proteins.
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Affiliation(s)
- Elizabeth M. Santos
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Tetyana Berbasova
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Wenjing Wang
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | | | - Wei Sheng
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - James H. Geiger
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Babak Borhan
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
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19
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Chen Y, Wu KL, Tang J, Loredo A, Clements J, Pei J, Peng Z, Gupta R, Fang X, Xiao H. Addition of Isocyanide-Containing Amino Acids to the Genetic Code for Protein Labeling and Activation. ACS Chem Biol 2019; 14:2793-2799. [PMID: 31682403 DOI: 10.1021/acschembio.9b00678] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Site-specific introduction of bioorthogonal handles into biomolecules provides powerful tools for studying and manipulating the structures and functions of proteins. Recent advances in bioorthogonal chemistry demonstrate that tetrazine-based bioorthogonal cycloaddition is a particularly useful methodology due to its high reactivity, biological selectivity, and turn-on property for fluorescence imaging. Despite its broad applications in protein labeling and imaging, utilization of tetrazine-based bioorthogonal cycloaddition has been limited to date by the requirement of a hydrophobic strained alkene reactive moiety. Circumventing this structural requirement, we report the site-specific incorporation of noncanonical amino acids (ncAAs) with a small isocyanide (or isonitrile) group into proteins in both bacterial and mammalian cells. We showed that under physiological conditions and in the absence of a catalyst these isocyanide-containing ncAAs could react selectively with tetrazine molecules via [4 + 1]-cycloaddition, thus providing a versatile bioorthogonal handle for site-specific protein labeling and protein decaging. Significantly, these bioorthogonal reactions between isocyanides and tetrazines also provide a unique mechanism for the activation of tetrazine-quenched fluorophores. The addition of these isocyanide-containing ncAAs to the list of 20 commonly used, naturally occurring amino acids expands our repertoire of reagents for bioorthogonal chemistry, therefore enabling new biological applications ranging from protein labeling and imaging studies to the chemical activation of proteins.
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Affiliation(s)
- Yuda Chen
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Kuan-Lin Wu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Juan Tang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Axel Loredo
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jordan Clements
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jingqi Pei
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Zane Peng
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ruchi Gupta
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Xinlei Fang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Han Xiao
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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20
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Doh JK, Enns CA, Beatty KE. Implementing VIPER for Imaging Cellular Proteins by Fluorescence Microscopy. Bio Protoc 2019; 9:e3413. [PMID: 32665966 PMCID: PMC7360171 DOI: 10.21769/bioprotoc.3413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022] Open
Abstract
Genetically-encoded tags are useful tools for multicolor and multi-scale cellular imaging. Versatile Interacting Peptide (VIP) tags, such as VIPER, are new genetically-encoded tags that can be used in various imaging applications. VIP tags consist of a coiled-coil heterodimer, with one peptide serving as the genetic tag and the other ("probe peptide") delivering a reporter compatible with imaging. Heterodimer formation is rapid and specific, allowing proteins to be selectively labeled for live-cell and fixed-cell imaging. In this Bio-Protocol, we include a detailed guide for implementing the VIPER technology for imaging receptors on live cells and intracellular targets in fixed cells. This protocol is complemented by two other Bio-Protocols outlining the use of VIPER (Doh et al., 2019a and 2019b).
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Affiliation(s)
- Julia K. Doh
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Caroline A. Enns
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Kimberly E. Beatty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
- OHSU Center for Spatial Systems Biomedicine, Oregon Health & Science University, Portland, Oregon 97239, USA
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21
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Thornlow DN, Cox EC, Walker JA, Sorkin M, Plesset JB, DeLisa MP, Alabi CA. Dual Site-Specific Antibody Conjugates for Sequential and Orthogonal Cargo Release. Bioconjug Chem 2019; 30:1702-1710. [PMID: 31083974 DOI: 10.1021/acs.bioconjchem.9b00244] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibody-drug conjugates utilize the antigen specificity of antibodies and the potency of chemotherapeutic and antibiotic drugs for targeted therapy. However, as cancers and bacteria evolve to resist the action of drugs, innovative controlled release methods must be engineered to deliver multidrug cocktails. In this work, we engineer lipoate-acid ligase A (LplA) acceptor peptide (LAP) tags into the constant heavy and light chain of a humanized Her2 targeted antibody, trastuzumab. These engineered LAP tags, along with the glutamine 295 (Q295) residue in the heavy chain, were used to generate orthogonally cleavable site-specific antibody conjugates via a one-pot chemoenzymatic ligation with microbial transglutaminase (mTG) and LplA. We demonstrate orthogonal cargo release from these dual-labeled antibody bioconjugates via matrix metalloproteinase-2 and cathepsin-B-mediated bond cleavage. To the best of our knowledge, this is the first demonstration of temporal control on dual-labeled antibody conjugates, and we believe this platform will allow for sequential release and cooperative drug combinations on a single antibody bioconjugate.
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Affiliation(s)
- Dana N Thornlow
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall, Ithaca , New York 14853 , United States
| | - Emily C Cox
- Biological and Biomedical Sciences , Cornell University College of Veterinary Medicine , Ithaca , New York 14853 , United States
| | - Joshua A Walker
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall, Ithaca , New York 14853 , United States
| | - Michelle Sorkin
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall, Ithaca , New York 14853 , United States
| | - Jacqueline B Plesset
- Meinig School of Biomedical Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall, Ithaca , New York 14853 , United States
| | - Christopher A Alabi
- Robert F. Smith School of Chemical and Biomolecular Engineering , Cornell University , 120 Olin Hall, Ithaca , New York 14853 , United States
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22
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Baumann T, Hauf M, Richter F, Albers S, Möglich A, Ignatova Z, Budisa N. Computational Aminoacyl-tRNA Synthetase Library Design for Photocaged Tyrosine. Int J Mol Sci 2019; 20:ijms20092343. [PMID: 31083552 PMCID: PMC6539999 DOI: 10.3390/ijms20092343] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 01/20/2023] Open
Abstract
Engineering aminoacyl-tRNA synthetases (aaRSs) provides access to the ribosomal incorporation of noncanonical amino acids via genetic code expansion. Conventional targeted mutagenesis libraries with 5–7 positions randomized cover only marginal fractions of the vast sequence space formed by up to 30 active site residues. This frequently results in selection of weakly active enzymes. To overcome this limitation, we use computational enzyme design to generate a focused library of aaRS variants. For aaRS enzyme redesign, photocaged ortho-nitrobenzyl tyrosine (ONBY) was chosen as substrate due to commercial availability and its diverse applications. Diversifying 17 first- and second-shell sites and performing conventional aaRS positive and negative selection resulted in a high-activity aaRS. This MjTyrRS variant carries ten mutations and outperforms previously reported ONBY-specific aaRS variants isolated from traditional libraries. In response to a single in-frame amber stop codon, it mediates the in vivo incorporation of ONBY with an efficiency matching that of the wild type MjTyrRS enzyme acylating cognate tyrosine. These results exemplify an improved general strategy for aaRS library design and engineering.
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Affiliation(s)
- Tobias Baumann
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Matthias Hauf
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Florian Richter
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
| | - Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.
| | - Andreas Möglich
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
- Lehrstuhl für Biochemie, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.
| | - Nediljko Budisa
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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23
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Baalmann M, Ziegler MJ, Werther P, Wilhelm J, Wombacher R. Enzymatic and Site-Specific Ligation of Minimal-Size Tetrazines and Triazines to Proteins for Bioconjugation and Live-Cell Imaging. Bioconjug Chem 2019; 30:1405-1414. [PMID: 30883100 DOI: 10.1021/acs.bioconjchem.9b00157] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Diels-Alder reactions with inverse electron demand (DAinv) have emerged as an indispensable tool for bioorthogonal labeling and the manipulation of biomolecules. In this context, reactions between tetrazines and strained dienophiles have received attention because of high reaction rates. Current methods for the DAinv-mediated functionalization of proteins suffer from slow reactivity, impaired stability, isomerization, or elimination of the incorporated strained dienophiles. We report here a versatile platform for the posttranslational, highly selective, and quantitative modification of proteins with stable dienes. New synthetic access to minimal size tetrazine and triazine derivatives enabled us to synthesize tailored diene substrates for the lipoic acid protein ligase A (LplA) from Escherichia coli, which we employ for the rapid, mild, and quantitative bioconjugation of proteins by DAinv. The presented method benefits from the minimal tag size for LplA recognition and can be applied to proteins from any source organism. We demonstrate its broad suitability by site-specific in vitro protein labeling and live cell labeling for fluorescence microscopy. With this work we expand the scope of DAinv bioorthogonal chemistry for site-specific protein labeling, providing additional experimental flexibility for preparing well-defined bioconjugates and addressing biological questions in complex biological environments.
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Affiliation(s)
- Mathis Baalmann
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Michael J Ziegler
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Philipp Werther
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Jonas Wilhelm
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany
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24
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Das R, Landis RF, Tonga GY, Cao-Milán R, Luther DC, Rotello VM. Control of Intra- versus Extracellular Bioorthogonal Catalysis Using Surface-Engineered Nanozymes. ACS NANO 2019; 13:229-235. [PMID: 30516966 PMCID: PMC6779054 DOI: 10.1021/acsnano.8b05370] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Bioorthogonal transformation of prodrugs and profluorophores using transition metal catalysts (TMCs) offers a promising strategy for therapeutic and imaging applications. Here, we report the surface engineering of nanoparticles to specifically localize gold nanoparticles (AuNPs) with encapsulated TMCs (nanozymes) to either the inside or outside of cells. The ability to control nanozyme localization and hence activity was demonstrated by the activation of pro-fluorophores and prodrugs intra- and extracellularly, establishing the potential of engineered nanozyme platforms for both diagnostic and therapeutic purposes.
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Affiliation(s)
- Riddha Das
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | | | | | - Roberto Cao-Milán
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - David C. Luther
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
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25
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Plaks JG, Kaar JL. Lipoic Acid Ligase-Promoted Bioorthogonal Protein Modification and Immobilization. Methods Mol Biol 2019; 2012:279-297. [PMID: 31161513 DOI: 10.1007/978-1-4939-9546-2_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein bioconjugation benefits from precise regional and temporal control. One notable way of achieving this control is through the enzymatic attachment of bioorthogonal reactive handles to peptide recognition sequences that are genetically fused to target proteins of interest. The lipoic acid ligase variant, LplAW37V, functionalizes proteins by covalently attaching an azide-bearing lipoic acid derivative to a 13-amino acid recognition sequence known as the lipoic acid ligase acceptor peptide (LAP). Once attached, the azide group can be modified with diverse chemical entities through azide-alkyne click chemistry, enabling conjugation of chemical probes such as fluorophores and facilitating polymer attachment, glycosylation, and protein immobilization in addition to many other possible chemical modifications. The versatility of the attached azide group is complemented by the modular nature of the LAP sequence, which can be introduced within a protein at internal and/or terminal sites as well as at multiple sites simultaneously. In this chapter we describe the in vitro LplAW37V-mediated ligation of 10-azidodecanoic acid to a LAP-containing target protein (i.e., green fluorescent protein (GFP)) and the characterization of the ligation reaction products. Additionally, methods for the modification and immobilization of azide-functionalized LAP-GFP are discussed.
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Affiliation(s)
- Joseph G Plaks
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA.
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26
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Lechner H, Ferruz N, Höcker B. Strategies for designing non-natural enzymes and binders. Curr Opin Chem Biol 2018; 47:67-76. [PMID: 30248579 DOI: 10.1016/j.cbpa.2018.07.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/20/2022]
Abstract
The design of tailor-made enzymes is a major goal in biochemical research that can result in wide-range applications and will lead to a better understanding of how proteins fold and function. In this review we highlight recent advances in enzyme and small molecule binder design. A focus is placed on novel strategies for the design of scaffolds, developments in computational methods, and recent applications of these techniques on receptors, sensors, and enzymes. Further, the integration of computational and experimental methodologies is discussed. The outlined examples of designed enzymes and binders for various purposes highlight the importance of this topic and underline the need for tailor-made proteins.
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Affiliation(s)
- Horst Lechner
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.
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27
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Gainza-Cirauqui P, Correia BE. Computational protein design-the next generation tool to expand synthetic biology applications. Curr Opin Biotechnol 2018; 52:145-152. [PMID: 29729544 DOI: 10.1016/j.copbio.2018.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 11/25/2022]
Abstract
One powerful approach to engineer synthetic biology pathways is the assembly of proteins sourced from one or more natural organisms. However, synthetic pathways often require custom functions or biophysical properties not displayed by natural proteins, limitations that could be overcome through modern protein engineering techniques. Structure-based computational protein design is a powerful tool to engineer new functional capabilities in proteins, and it is beginning to have a profound impact in synthetic biology. Here, we review efforts to increase the capabilities of synthetic biology using computational protein design. We focus primarily on computationally designed proteins not only validated in vitro, but also shown to modulate different activities in living cells. Efforts made to validate computational designs in cells can illustrate both the challenges and opportunities in the intersection of protein design and synthetic biology. We also highlight protein design approaches, which although not validated as conveyors of new cellular function in situ, may have rapid and innovative applications in synthetic biology. We foresee that in the near-future, computational protein design will vastly expand the functional capabilities of synthetic cells.
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Affiliation(s)
- Pablo Gainza-Cirauqui
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Bruno Emanuel Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland.
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28
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Oesterle S, Roberts TM, Widmer LA, Mustafa H, Panke S, Billerbeck S. Sequence-based prediction of permissive stretches for internal protein tagging and knockdown. BMC Biol 2017; 15:100. [PMID: 29084520 PMCID: PMC5661948 DOI: 10.1186/s12915-017-0440-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Internal tagging of proteins by inserting small functional peptides into surface accessible permissive sites has proven to be an indispensable tool for basic and applied science. Permissive sites are typically identified by transposon mutagenesis on a case-by-case basis, limiting scalability and their exploitation as a system-wide protein engineering tool. METHODS We developed an apporach for predicting permissive stretches (PSs) in proteins based on the identification of length-variable regions (regions containing indels) in homologous proteins. RESULTS We verify that a protein's primary structure information alone is sufficient to identify PSs. Identified PSs are predicted to be predominantly surface accessible; hence, the position of inserted peptides is likely suitable for diverse applications. We demonstrate the viability of this approach by inserting a Tobacco etch virus protease recognition site (TEV-tag) into several PSs in a wide range of proteins, from small monomeric enzymes (adenylate kinase) to large multi-subunit molecular machines (ATP synthase) and verify their functionality after insertion. We apply this method to engineer conditional protein knockdowns directly in the Escherichia coli chromosome and generate a cell-free platform with enhanced nucleotide stability. CONCLUSIONS Functional internally tagged proteins can be rationally designed and directly chromosomally implemented. Critical for the successful design of protein knockdowns was the incorporation of surface accessibility and secondary structure predictions, as well as the design of an improved TEV-tag that enables efficient hydrolysis when inserted into the middle of a protein. This versatile and portable approach can likely be adapted for other applications, and broadly adopted. We provide guidelines for the design of internally tagged proteins in order to empower scientists with little or no protein engineering expertise to internally tag their target proteins.
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Affiliation(s)
- Sabine Oesterle
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Tania Michelle Roberts
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Lukas Andreas Widmer
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
- Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland
- Life Science Zürich Graduate School in Systems Biology, Zürich, Switzerland
| | - Harun Mustafa
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sonja Billerbeck
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
- Present address: Chemistry Department, Columbia University, 550 West 120th Street, New York, NY, 10027, USA.
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29
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Abstract
Chemistry, once king of fluorescence microscopy, was usurped by the field of fluorescent proteins. The increased demands of modern microscopy techniques on the "photon budget" require better and brighter fluorophores, causing a renewed interest in synthetic dyes. Here, we review the recent advances in biochemistry, protein engineering, and organic synthesis that have allowed a triumphant return of chemical fluorophores to modern biological imaging.
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Affiliation(s)
- Luke D Lavis
- Howard Hughes Medical Institute , Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, United States
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30
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Bozhanova NG, Baranov MS, Klementieva NV, Sarkisyan KS, Gavrikov AS, Yampolsky IV, Zagaynova EV, Lukyanov SA, Lukyanov KA, Mishin AS. Protein labeling for live cell fluorescence microscopy with a highly photostable renewable signal. Chem Sci 2017; 8:7138-7142. [PMID: 29147545 PMCID: PMC5676496 DOI: 10.1039/c7sc01628j] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/01/2017] [Indexed: 11/21/2022] Open
Abstract
A novel method of protein labeling uses the highly dynamic reversible association of a cell-permeable fluorogenic dye and lipocalin Blc mutants.
We present protein-PAINT – the implementation of the general principles of PAINT (Point Accumulation for Imaging in Nanoscale Topography) for live-cell protein labeling. Our method employs the specific binding of cell-permeable fluorogenic dyes to genetically encoded protein tags. We engineered three mutants of the bacterial lipocalin Blc that possess different affinities to a fluorogenic dye and exhibit a strong increase in fluorescence intensity upon binding. This allows for rapid labeling and washout of intracellular targets on a time scale from seconds to a few minutes. We demonstrate an order of magnitude higher photostability of the fluorescence signal in comparison with spectrally similar fluorescent proteins. Protein-PAINT ensures prolonged super-resolution fluorescence microscopy of living cells in both single molecule detection and stimulated emission depletion regimes.
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Affiliation(s)
- Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia .
| | | | - Karen S Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Centre for Genomic Regulation (CRG) , The Barcelona Institute for Science and Technology , Dr Aiguader 88 , 08003 Barcelona , Spain
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia .
| | - Ilia V Yampolsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Pirogov Russian National Research Medical University , Moscow , Russia
| | | | - Sergey A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia.,Pirogov Russian National Research Medical University , Moscow , Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
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31
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Li N, Zhao R, Sun Y, Ye Z, He K, Fang X. Single-molecule imaging and tracking of molecular dynamics in living cells. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nww055] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Unlike the ensemble-averaging measurements, the single-molecule imaging and tracking (SMIT) in living cells provides the real-time quantitative information about the locations, kinetics, dynamics and interactions of individual molecules in their native environments with high spatiotemporal resolution and minimal perturbation. The past decade has witnessed a transforming development in the methods of SMIT with living cells, including fluorescent probes, labeling strategies, fluorescence microscopy, and detection and tracking algorithms. In this review, we will discuss these aspects with a particular focus on their recent advancements. We will then describe representative single-molecule studies to illustrate how the single-molecule approaches can be applied to monitor biomolecular interaction/reaction dynamics, and extract the molecular mechanistic information for different cellular systems.
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Affiliation(s)
- Nan Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Zhao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yahong Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi Ye
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kangmin He
- Department of Cell Biology, Harvard Medical School, and Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Xiaohong Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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32
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Gallo E, Jarvik JW. Breaking the color barrier - a multi-selective antibody reporter offers innovative strategies of fluorescence detection. J Cell Sci 2017; 130:2644-2653. [PMID: 28615413 DOI: 10.1242/jcs.202952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/08/2017] [Indexed: 01/14/2023] Open
Abstract
A novel bi-partite fluorescence platform exploits the high affinity and selectivity of antibody scaffolds to capture and activate small-molecule fluorogens. In this report, we investigated the property of multi-selectivity activation by a single antibody against diverse cyanine family fluorogens. Our fluorescence screen identified three cell-impermeant fluorogens, each with unique emission spectra (blue, green and red) and nanomolar affinities. Most importantly, as a protein fusion tag to G-protein-coupled receptors, the antibody biosensor retained full activity - displaying bright fluorogen signals with minimal background on live cells. Because fluorogen-activating antibodies interact with their target ligands via non-covalent interactions, we were able to perform advanced multi-color detection strategies on live cells, previously difficult or impossible with conventional reporters. We found that by fine-tuning the concentrations of the different color fluorogen molecules in solution, a user may interchange the fluorescence signal (onset versus offset), execute real-time signal exchange via fluorogen competition, measure multi-channel fluorescence via co-labeling, and assess real-time cell surface receptor traffic via pulse-chase experiments. Thus, here we inform of an innovative reporter technology based on tri-color signal that allows user-defined fluorescence tuning in live-cell applications.
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Affiliation(s)
- Eugenio Gallo
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jonathan W Jarvik
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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33
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Guerra AJ, Afanador GA, Prigge ST. Crystal structure of lipoate-bound lipoate ligase 1, LipL1, from Plasmodium falciparum. Proteins 2017; 85:1777-1783. [PMID: 28543853 DOI: 10.1002/prot.25324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/04/2017] [Accepted: 05/17/2017] [Indexed: 11/08/2022]
Abstract
Plasmodium falciparum lipoate protein ligase 1 (PfLipL1) is an ATP-dependent ligase that belongs to the biotin/lipoate A/B protein ligase family (PFAM PF03099). PfLipL1 is the only known canonical lipoate ligase in Pf and functions as a redox switch between two lipoylation routes in the parasite mitochondrion. Here, we report the crystal structure of a deletion construct of PfLipL1 (PfLipL1Δ243-279 ) bound to lipoate, and validate the lipoylation activity of this construct in both an in vitro lipoylation assay and a cell-based lipoylation assay. This characterization represents the first step in understanding the redox dependence of the lipoylation mechanism in malaria parasites. Proteins 2017; 85:1777-1783. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Alfredo J Guerra
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Gustavo A Afanador
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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34
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Kang MG, Park J, Balboni G, Lim MH, Lee C, Rhee HW. Genetically Encodable Bacterial Flavin Transferase for Fluorogenic Protein Modification in Mammalian Cells. ACS Synth Biol 2017; 6:667-677. [PMID: 28035820 DOI: 10.1021/acssynbio.6b00284] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A bacterial flavin transferase (ApbE) was recently employed for flavin mononucleotide (FMN) modification on the Na+-translocating NADH:quinone oxidoreductase C (NqrC) protein in the pathogenic Gram-negative bacterium Vibrio cholerae. We employed this unique post-translational modification in mammalian cells and found that the FMN transfer reaction robustly occurred when NqrC and ApbE were genetically targeted in the cytosol of live mammalian cells. Moreover, NqrC expression in the endoplasmic reticulum (NqrC-ER) induced the retro-translocation of NqrC to the cytosol, leading to the proteasome-mediated ER-associated degradation of NqrC, which is considered to be an innate immunological response toward the bacterial protein. This unexpected cellular process of NqrC-ER could be exploited for the construction of an in cellulo proteasome inhibitor screening system, and our proposed approach yielded substantially improved results compared to a previous method. In addition, a truncated version of RnfG (half-RnfG) was found to be potentially useful as a genetically encoded tag for monitoring protein-protein interactions in a specific compartment, even in the ER, in a live cell according to its fluorogenic post-translational modification via ApbE. This new genetically encoded system in mammalian cells should serve as a valuable tool for anticancer drug screening and other applications in molecular and synthetic biology.
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Affiliation(s)
| | | | - Gianfranco Balboni
- Department
of Life and Environmental Sciences, Pharmaceutical, Pharmacological
and Nutraceutical Sciences Unit, University of Cagliari, I-09124 Cagliari, Italy
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35
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Schneider AFL, Hackenberger CPR. Fluorescent labelling in living cells. Curr Opin Biotechnol 2017; 48:61-68. [PMID: 28395178 DOI: 10.1016/j.copbio.2017.03.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/10/2017] [Indexed: 11/15/2022]
Abstract
The labelling of proteins with green fluorescent protein enabled the visualization of proteins in living cells for the first time. Since then, much progress has been made in the field. Modern strategies allow the labelling of proteins in live cells through a range of specialized methods with sophisticated chemical probes that show enhanced photophysical properties compared to fluorescent proteins. This review briefly summarizes recent advances in the field of fluorescent chemical protein labelling inside living cells and illustrates key aspects on the requirements and advantages of each given method.
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Affiliation(s)
- Anselm Fabian Lowell Schneider
- Leibniz-Institut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP), Campus Berlin-Buch, Robert-Roessle-Str. 10, D-13125 Berlin, Germany
| | - Christian Peter Richard Hackenberger
- Leibniz-Institut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP), Campus Berlin-Buch, Robert-Roessle-Str. 10, D-13125 Berlin, Germany; Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, D-12489 Berlin, Germany.
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36
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Schumacher D, Lemke O, Helma J, Gerszonowicz L, Waller V, Stoschek T, Durkin PM, Budisa N, Leonhardt H, Keller BG, Hackenberger CPR. Broad substrate tolerance of tubulin tyrosine ligase enables one-step site-specific enzymatic protein labeling. Chem Sci 2017; 8:3471-3478. [PMID: 28507719 PMCID: PMC5418632 DOI: 10.1039/c7sc00574a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/18/2017] [Indexed: 12/31/2022] Open
Abstract
The broad substrate tolerance of tubulin tyrosine ligase enables its wide applicability for protein functionalization.
The broad substrate tolerance of tubulin tyrosine ligase is the basic rationale behind its wide applicability for chemoenzymatic protein functionalization. In this context, we report that the wild-type enzyme enables ligation of various unnatural amino acids that are substantially bigger than and structurally unrelated to the natural substrate, tyrosine, without the need for extensive protein engineering. This unusual substrate flexibility is due to the fact that the enzyme's catalytic pocket forms an extended cavity during ligation, as confirmed by docking experiments and all-atom molecular dynamics simulations. This feature enabled one-step C-terminal biotinylation and fluorescent coumarin labeling of various functional proteins as demonstrated with ubiquitin, an antigen binding nanobody, and the apoptosis marker Annexin V. Its broad substrate tolerance establishes tubulin tyrosine ligase as a powerful tool for in vitro enzyme-mediated protein modification with single functional amino acids in a specific structural context.
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Affiliation(s)
- Dominik Schumacher
- Department of Chemical-Biology , Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , 13125 Berlin , Germany . .,Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| | - Oliver Lemke
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustr. 3 , 14195 Berlin , Germany .
| | - Jonas Helma
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Lena Gerszonowicz
- Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| | - Verena Waller
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Tina Stoschek
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Patrick M Durkin
- Department of Chemistry , TU Berlin , Müller-Breslau-Str. 10 , 10623 Berlin , Germany
| | - Nediljko Budisa
- Department of Chemistry , TU Berlin , Müller-Breslau-Str. 10 , 10623 Berlin , Germany
| | - Heinrich Leonhardt
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustr. 3 , 14195 Berlin , Germany .
| | - Christian P R Hackenberger
- Department of Chemical-Biology , Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , 13125 Berlin , Germany . .,Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
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37
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Zane HK, Doh JK, Enns CA, Beatty KE. Versatile Interacting Peptide (VIP) Tags for Labeling Proteins with Bright Chemical Reporters. Chembiochem 2017; 18:470-474. [PMID: 28052473 PMCID: PMC5785092 DOI: 10.1002/cbic.201600627] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Indexed: 11/06/2022]
Abstract
Fluorescence microscopy is an essential tool for the biosciences, enabling the direct observation of proteins in their cellular environment. New methods that facilitate attachment of photostable synthetic fluorophores with genetic specificity are needed to advance the frontiers of biological imaging. Here, we describe a new set of small, selective, genetically encoded tags for proteins based on a heterodimeric coiled-coil interaction between two peptides: CoilY and CoilZ. Proteins expressed as a fusion to CoilZ were selectively labeled with the complementary CoilY fluorescent probe peptide. Fluorophore-labeled target proteins were readily detected in cell lysates with high specificity and sensitivity. We found that these versatile interacting peptide (VIP) tags allowed rapid and specific delivery of bright organic dyes or quantum dots to proteins displayed on living cells. Additionally, we validated that either CoilY or CoilZ could serve as the VIP tag, which enabled us to observe two distinct cell-surface protein targets with this one heterodimeric pair.
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Affiliation(s)
- Hannah K Zane
- Department of Biomedical Engineering, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
| | - Julia K Doh
- Department of Biomedical Engineering, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
| | - Caroline A Enns
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
| | - Kimberly E Beatty
- Department of Biomedical Engineering, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
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38
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Mei M, Zhou Y, Peng W, Yu C, Ma L, Zhang G, Yi L. Application of modified yeast surface display technologies for non-Antibody protein engineering. Microbiol Res 2017; 196:118-128. [DOI: 10.1016/j.micres.2016.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 10/21/2016] [Accepted: 12/09/2016] [Indexed: 02/07/2023]
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39
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Kipper K, Lundius EG, Ćurić V, Nikić I, Wiessler M, Lemke EA, Elf J. Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli. ACS Synth Biol 2017; 6:233-255. [PMID: 27775882 DOI: 10.1021/acssynbio.6b00138] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small synthetic fluorophores are in many ways superior to fluorescent proteins as labels for imaging. A major challenge is to use them for a protein-specific labeling in living cells. Here, we report on our use of noncanonical amino acids that are genetically encoded via the pyrrolysyl-tRNA/pyrrolysyl-RNA synthetase pair at artificially introduced TAG codons in a recoded E. coli strain. The strain is lacking endogenous TAG codons and the TAG-specific release factor RF1. The amino acids contain bioorthogonal groups that can be clicked to externally supplied dyes, thus enabling protein-specific labeling in live cells. We find that the noncanonical amino acid incorporation into the target protein is robust for diverse amino acids and that the usefulness of the recoded E. coli strain mainly derives from the absence of release factor RF1. However, the membrane permeable dyes display high nonspecific binding in intracellular environment and the electroporation of hydrophilic nonmembrane permeable dyes severely impairs growth of the recoded strain. In contrast, proteins exposed on the outer membrane of E. coli can be labeled with hydrophilic dyes with a high specificity as demonstrated by labeling of the osmoporin OmpC. Here, labeling can be made sufficiently specific to enable single molecule studies as exemplified by OmpC single particle tracking.
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Affiliation(s)
- Kalle Kipper
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
| | - Ebba G. Lundius
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
| | - Vladimir Ćurić
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
| | - Ivana Nikić
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Manfred Wiessler
- Biological
Chemistry, Deutsche Krebsforschungszentrum, Heidelberg, 69120, Germany
| | - Edward A. Lemke
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Johan Elf
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
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40
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Paeth M, Stapleton J, Dougherty ML, Fischesser H, Shepherd J, McCauley M, Falatach R, Page RC, Berberich JA, Konkolewicz D. Approaches for Conjugating Tailor-Made Polymers to Proteins. Methods Enzymol 2017; 590:193-224. [DOI: 10.1016/bs.mie.2016.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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41
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Kries H. Biosynthetic engineering of nonribosomal peptide synthetases. J Pept Sci 2016; 22:564-70. [DOI: 10.1002/psc.2907] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 06/16/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Hajo Kries
- Laboratory of Organic Chemistry; ETH Zurich; CH-8093 Zurich Switzerland
- Department of Biological Chemistry; The John Innes Centre; Norwich Research Park Norwich NR4 7UH UK
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42
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DIVERSE System: De Novo Creation of Peptide Tags for Non-enzymatic Covalent Labeling by In Vitro Evolution for Protein Imaging Inside Living Cells. ACTA ACUST UNITED AC 2016; 22:1671-9. [PMID: 26687484 DOI: 10.1016/j.chembiol.2015.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/10/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Polypeptide-tag/small-molecule pairs for specific cellular protein labeling are useful for visualizing cellular proteins and controlling their activity. Here, we report the development of an in vitro evolution-based (poly)peptide tag identification system named the DIVERSE (Directed In Vitro Evolution of Reactive peptide tags via Sequential Enrichment) system. In this system, an extremely diverse (10(14)) library of peptide tags, displayed by covalent attachment to their encoding cDNAs, is continuously prepared from the DNA library in a one-pot approach. Using this system, we demonstrated de novo creation of non-enzymatically covalent-labeling peptide tags for a synthetic small-molecule target from a random peptide library. Protein labeling with these tags was applicable to N- and C-terminal fusions, multiple different proteins and fluorophores, and intracellular labeling. The DIVERSE system can be used not only for the de novo creation of polypeptide tags but also sequence optimization of existing polypeptide tags from extremely diverse libraries.
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43
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Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
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44
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Haidekker MA, Theodorakis EA. Ratiometric mechanosensitive fluorescent dyes: Design and applications. JOURNAL OF MATERIALS CHEMISTRY. C 2016; 4:2707-2718. [PMID: 27127631 PMCID: PMC4844075 DOI: 10.1039/c5tc03504j] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Fluorescent molecules, with their almost instantaneous response to external influences and relatively low-cost measurement instrumentation, have been attractive analytical tools and biosensors for centuries. More recently, advanced chemical synthesis and targeted design have accelerated the development of fluorescent probes. This article focuses on dyes with segmental mobility (known as fluorescent molecular rotors) that act as mechanosensors, which are known for their relationship of emission quantum yield with microviscosity. Fluorescence lifetime is directly related to quantum yield, but steady-state emission intensity is not. To remove confounding factors with steady-state instrumentation, dual-band emission dyes can be used, and molecular rotors have been developed that either have intrinsic dual emission or that have a non-sensitive reference unit to provide a calibration emission band. We report on theory, chemical structure, applications and targeted design of several classes of dual-emission molecular rotors.
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Affiliation(s)
- Mark A. Haidekker
- College of Engineering, University of Georgia, 597 D. W. Brooks Drive, Athens, GA 30602, USA
| | - Emmanuel A. Theodorakis
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive MC: 0358, La Jolla, CA 92093-0358, USA. Fax: 1-858-822-0386; Tel: 1-858-822-0456
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Assembly of Lipoic Acid on Its Cognate Enzymes: an Extraordinary and Essential Biosynthetic Pathway. Microbiol Mol Biol Rev 2016; 80:429-50. [PMID: 27074917 DOI: 10.1128/mmbr.00073-15] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although the structure of lipoic acid and its role in bacterial metabolism were clear over 50 years ago, it is only in the past decade that the pathways of biosynthesis of this universally conserved cofactor have become understood. Unlike most cofactors, lipoic acid must be covalently bound to its cognate enzyme proteins (the 2-oxoacid dehydrogenases and the glycine cleavage system) in order to function in central metabolism. Indeed, the cofactor is assembled on its cognate proteins rather than being assembled and subsequently attached as in the typical pathway, like that of biotin attachment. The first lipoate biosynthetic pathway determined was that of Escherichia coli, which utilizes two enzymes to form the active lipoylated protein from a fatty acid biosynthetic intermediate. Recently, a more complex pathway requiring four proteins was discovered in Bacillus subtilis, which is probably an evolutionary relic. This pathway requires the H protein of the glycine cleavage system of single-carbon metabolism to form active (lipoyl) 2-oxoacid dehydrogenases. The bacterial pathways inform the lipoate pathways of eukaryotic organisms. Plants use the E. coli pathway, whereas mammals and fungi probably use the B. subtilis pathway. The lipoate metabolism enzymes (except those of sulfur insertion) are members of PFAM family PF03099 (the cofactor transferase family). Although these enzymes share some sequence similarity, they catalyze three markedly distinct enzyme reactions, making the usual assignment of function based on alignments prone to frequent mistaken annotations. This state of affairs has possibly clouded the interpretation of one of the disorders of human lipoate metabolism.
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Self-labelling enzymes as universal tags for fluorescence microscopy, super-resolution microscopy and electron microscopy. Sci Rep 2015; 5:17740. [PMID: 26643905 PMCID: PMC4672345 DOI: 10.1038/srep17740] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/04/2015] [Indexed: 11/17/2022] Open
Abstract
Research in cell biology demands advanced microscopy techniques such as confocal fluorescence microscopy (FM), super-resolution microscopy (SRM) and transmission electron microscopy (TEM). Correlative light and electron microscopy (CLEM) is an approach to combine data on the dynamics of proteins or protein complexes in living cells with the ultrastructural details in the low nanometre scale. To correlate both data sets, markers functional in FM, SRM and TEM are required. Genetically encoded markers such as fluorescent proteins or self-labelling enzyme tags allow observations in living cells. Various genetically encoded tags are available for FM and SRM, but only few tags are suitable for CLEM. Here, we describe the red fluorescent dye tetramethylrhodamine (TMR) as a multimodal marker for CLEM. TMR is used as fluorochrome coupled to ligands of genetically encoded self-labelling enzyme tags HaloTag, SNAP-tag and CLIP-tag in FM and SRM. We demonstrate that TMR can additionally photooxidize diaminobenzidine (DAB) to an osmiophilic polymer visible on TEM sections, thus being a marker suitable for FM, SRM and TEM. We evaluated various organelle markers with enzymatic tags in mammalian cells labelled with TMR-coupled ligands and demonstrate the use as efficient and versatile DAB photooxidizer for CLEM approaches.
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Siraj N, El-Zahab B, Hamdan S, Karam TE, Haber LH, Li M, Fakayode SO, Das S, Valle B, Strongin RM, Patonay G, Sintim HO, Baker GA, Powe A, Lowry M, Karolin JO, Geddes CD, Warner IM. Fluorescence, Phosphorescence, and Chemiluminescence. Anal Chem 2015; 88:170-202. [PMID: 26575092 DOI: 10.1021/acs.analchem.5b04109] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Noureen Siraj
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Bilal El-Zahab
- Department of Mechanical and Materials Engineering, Florida International University , Miami, Florida 33174, United States
| | - Suzana Hamdan
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Tony E Karam
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Louis H Haber
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Min Li
- Process Development Center, Albemarle Corporation , Baton Rouge, Louisiana 70805, United States
| | - Sayo O Fakayode
- Department of Chemistry, Winston-Salem State University , Winston-Salem, North Carolina 27110, United States
| | - Susmita Das
- Department of Civil Engineering, Adamas Institute of Technology , Barasat, Kolkata 700126, West Bengal India
| | - Bertha Valle
- Department of Chemistry, Texas Southern University , Houston, Texas 77004, United States
| | - Robert M Strongin
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Gabor Patonay
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-4098, United States
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Gary A Baker
- Department of Chemistry, University of Missouri Columbia , Columbia, Missouri 65211-7600, United States
| | - Aleeta Powe
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40208, United States
| | - Mark Lowry
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Jan O Karolin
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Chris D Geddes
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Isiah M Warner
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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Ariotti N, Hall TE, Rae J, Ferguson C, McMahon KA, Martel N, Webb RE, Webb RI, Teasdale RD, Parton RG. Modular Detection of GFP-Labeled Proteins for Rapid Screening by Electron Microscopy in Cells and Organisms. Dev Cell 2015; 35:513-25. [PMID: 26585296 DOI: 10.1016/j.devcel.2015.10.016] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 09/16/2015] [Accepted: 10/19/2015] [Indexed: 10/22/2022]
Abstract
Reliable and quantifiable high-resolution protein localization is critical for understanding protein function. However, the time required to clone and characterize any protein of interest is a significant bottleneck, especially for electron microscopy (EM). We present a modular system for enzyme-based protein tagging that allows for improved speed and sampling for analysis of subcellular protein distributions using existing clone libraries to EM-resolution. We demonstrate that we can target a modified soybean ascorbate peroxidase (APEX) to any GFP-tagged protein of interest by engineering a GFP-binding peptide (GBP) directly to the APEX-tag. We demonstrate that APEX-GBP (1) significantly reduces the time required to characterize subcellular protein distributions of whole libraries to less than 3 days, (2) provides remarkable high-resolution localization of proteins to organelle subdomains, and (3) allows EM localization of GFP-tagged proteins, including proteins expressed at endogenous levels, in vivo by crossing existing GFP-tagged transgenic zebrafish lines with APEX-GBP transgenic lines.
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Affiliation(s)
- Nicholas Ariotti
- Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia
| | - Thomas E Hall
- Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia
| | - James Rae
- Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia
| | - Charles Ferguson
- Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia
| | - Kerrie-Ann McMahon
- Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia
| | - Nick Martel
- Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia
| | - Robyn E Webb
- Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard I Webb
- Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, QLD 4072, Australia
| | - Rohan D Teasdale
- Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia; Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, QLD 4072, Australia.
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González-Vera JA, Morris MC. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases. Proteomes 2015; 3:369-410. [PMID: 28248276 PMCID: PMC5217393 DOI: 10.3390/proteomes3040369] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/30/2015] [Accepted: 10/23/2015] [Indexed: 12/20/2022] Open
Abstract
Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.
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Affiliation(s)
- Juan A González-Vera
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
| | - May C Morris
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
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Sunbul M, Nacheva L, Jäschke A. Proximity-Induced Covalent Labeling of Proteins with a Reactive Fluorophore-Binding Peptide Tag. Bioconjug Chem 2015; 26:1466-9. [PMID: 26086394 DOI: 10.1021/acs.bioconjchem.5b00304] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Labeling of proteins with fluorescent dyes in live cells enables the investigation of their roles in biological systems by fluorescence microscopy. Because the labeling procedure should not disturb the native function of the protein of interest, it is of high importance to find the optimum labeling method for the problem to be studied. Here, we developed a rapid one-step method to covalently and site-specifically label proteins with a TexasRed fluorophore in vitro and in live bacteria. To this end, a genetically encodable TexasRed fluorophore-binding peptide (TR512) was converted into a reactive tag (ReacTR) by adjoining a cysteine residue which rapidly reacts with N-α-chloroacetamide-conjugated TexasRed fluorophore owing to the proximity effect; ReacTR tag first binds to the TexasRed fluorophore and this interaction brings the nucleophilic cysteine and the electrophilic N-α-chloroacetamide groups in close proximity. Our method has several advantages over existing methods: (i) it utilizes a peptide tag much smaller than fluorescent proteins, the SNAP, CLIP, or HaLo tags; (ii) it allows for labeling of proteins with a small, photostable, red-emitting TexasRed fluorophore; (iii) the probe used is very easy to synthesize; (iv) no enzyme is required to transfer the fluorophore to the peptide tag; and (v) labeling yields a stable covalent product in a very fast reaction.
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Affiliation(s)
- Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
| | - Lora Nacheva
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
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