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Pino NW, Sizemore AR, Cleary L, Liu H, McSwiggen DT, Song D, Beck HP, Cheng K, Hardy M, Hsiung J, Tang Y, Anugula R, Lakshman S, Merneedi RK, Sinha P. Optimized Properties and Synthesis of Photoactivatable Diazoketorhodamines Facilitate and Enhance High-Throughput Single-Molecule Tracking. J Org Chem 2024. [PMID: 38836310 DOI: 10.1021/acs.joc.4c00718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Photoactivatable (PA) rhodamine dyes are widely used in single-molecule tracking (SMT) and a variety of other fluorescence-based imaging modalities. One of the most commonly employed scaffolds uses a diazoketone to lock the rhodamine in the nonfluorescent closed form, which can be activated with 405 nm light. However, poor properties of previously reported dyes require significant washing, which can be resource- and cost-intensive, especially when performing microscopy in a large scale and high-throughput fashion. Here, we report improved diazoketorhodamines that perform exceptionally well in single-molecule tracking microscopy. We also report on the optimization of an improved synthetic method for further iteration and tailoring of diazoketorhodamines to the requirements of a specific user.
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Affiliation(s)
- Nicholas W Pino
- Eikon Therapeutics Inc., Hayward, California 94545, United States
| | - Anne R Sizemore
- Eikon Therapeutics Inc., Hayward, California 94545, United States
| | - Leah Cleary
- Eikon Therapeutics Inc., Hayward, California 94545, United States
| | - Helen Liu
- Eikon Therapeutics Inc., Hayward, California 94545, United States
| | | | - Dan Song
- Eikon Therapeutics Inc., Hayward, California 94545, United States
| | - Hilary P Beck
- Eikon Therapeutics Inc., Hayward, California 94545, United States
| | - Kylie Cheng
- Eikon Therapeutics Inc., Hayward, California 94545, United States
| | - Miki Hardy
- Eikon Therapeutics Inc., Hayward, California 94545, United States
| | - Jessica Hsiung
- Eikon Therapeutics Inc., Hayward, California 94545, United States
| | - Yangzhong Tang
- Eikon Therapeutics Inc., Hayward, California 94545, United States
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2
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Shilleh AH, Viloria K, Broichhagen J, Campbell JE, Hodson DJ. GLP1R and GIPR expression and signaling in pancreatic alpha cells, beta cells and delta cells. Peptides 2024; 175:171179. [PMID: 38360354 DOI: 10.1016/j.peptides.2024.171179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/17/2024]
Abstract
Glucagon-like peptide-1 receptor (GLP1R) and glucose-dependent insulinotropic polypeptide receptor (GIPR) are transmembrane receptors involved in insulin, glucagon and somatostatin secretion from the pancreatic islet. Therapeutic targeting of GLP1R and GIPR restores blood glucose levels in part by influencing beta cell, alpha cell and delta cell function. Despite the importance of the incretin-mimetics for diabetes therapy, our understanding of GLP1R and GIPR expression patterns and signaling within the islet remain incomplete. Here, we present the evidence for GLP1R and GIPR expression in the major islet cell types, before addressing signaling pathway(s) engaged, as well as their influence on cell survival and function. While GLP1R is largely a beta cell-specific marker within the islet, GIPR is expressed in alpha cells, beta cells, and (possibly) delta cells. GLP1R and GIPR engage Gs-coupled pathways in most settings, although the exact outcome on hormone release depends on paracrine communication and promiscuous signaling. Biased agonism away from beta-arrestin is an emerging concept for improving therapeutic efficacy, and is also relevant for GLP1R/GIPR dual agonism. Lastly, dual agonists exert multiple effects on islet function through GIPR > GLP1R imbalance, increased GLP1R surface expression and cAMP signaling, as well as beneficial alpha cell-beta cell-delta cell crosstalk.
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Affiliation(s)
- Ali H Shilleh
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Katrina Viloria
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Jonathan E Campbell
- Duke Molecular Physiology Institute, USA; Department of Medicine, Division of Endocrinology, Duke University, Durham, NC, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
| | - David J Hodson
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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3
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Lampkin BJ, Goldberg BJ, Kritzer JA. BenzoHTag, a fluorogenic self-labeling protein developed using molecular evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.29.564634. [PMID: 38617361 PMCID: PMC11014480 DOI: 10.1101/2023.10.29.564634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Self-labeling proteins are powerful tools in chemical biology as they enable the precise cellular localization of a synthetic molecule, often a fluorescent dye, with the genetic specificity of a protein fusion. HaloTag7 is the most popular self-labeling protein due to its fast labeling kinetics and the simplicity of its chloroalkane ligand. Reaction rates of HaloTag7 with different chloroalkane-containing substrates is highly variable and rates are only very fast for rhodamine-based dyes. This is a major limitation for the HaloTag system because fast labeling rates are critical for live-cell assays. Here, we report a molecular evolution system for HaloTag using yeast surface display that enables the screening of libraries up to 108 variants to improve reaction rates with any substrate of interest. We applied this method to produce a HaloTag variant, BenzoHTag, which has improved performance with a fluorogenic benzothiadiazole dye. The resulting system has improved brightness and conjugation kinetics, allowing for robust, no-wash fluorescent labeling in live cells. The new BenzoHTag-benzothiadiazole system has improved performance in live-cell assays compared to the existing HaloTag7-silicon rhodamine system, including saturation of intracellular enzyme in under 100 seconds and robust labeling at dye concentrations as low as 7 nM. It was also found to be orthogonal to the silicon HaloTag7-rhodamine system, enabling multiplexed no-wash labeling in live cells. The BenzoHTag system, and the ability to optimize HaloTag for a broader collection of substrates using molecular evolution, will be very useful for the development of cell-based assays for chemical biology and drug development.
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4
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Zhou Y, Wang Q, Chanmungkalakul S, Wu X, Xiao H, Miao R, Liu X, Fang Y. Fluorogenic Rhodamine Probes with Pyrrole Substitution Enables STED and Lifetime Imaging of Lysosomes in Live Cells. Chemistry 2024; 30:e202303707. [PMID: 38221317 DOI: 10.1002/chem.202303707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 01/16/2024]
Abstract
Fluorogenic dyes with high brightness, large turn-on ratios, excellent photostability, favorable specificity, low cytotoxicity, and high membrane permeability are essential for high-resolution fluorescence imaging in live cells. In this study, we endowed these desirable properties to a rhodamine derivative by simply replacing the N, N-diethyl group with a pyrrole substituent. The resulting dye, Rh-NH, exhibited doubled Stokes shifts (54 nm) and a red-shift of more than 50 nm in fluorescence spectra compared to Rhodamine B. Rh-NH preferentially exists in a non-emissive but highly permeable spirolactone form. Upon binding to lysosomes, the collective effects of low pH, low polarity, and high viscosity endow Rh-NH with significant fluorescence turn-on, making it a suitable candidate for wash-free, high-contrast lysosome tracking. Consequently, Rh-NH enabled us to successfully explore stimulated emission depletion (STED) super-resolution imaging of lysosome dynamics, as well as fluorescence lifetime imaging of lysosomes in live cells.
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Affiliation(s)
- Ying Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Qiuping Wang
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Supphachok Chanmungkalakul
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Xia Wu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Hui Xiao
- Colledge of Life Science, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Rong Miao
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Yu Fang
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
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5
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Nonaka H, Sakamoto S, Shiraiwa K, Ishikawa M, Tamura T, Okuno K, Kondo T, Kiyonaka S, Susaki EA, Shimizu C, Ueda HR, Kakegawa W, Arai I, Yuzaki M, Hamachi I. Bioorthogonal chemical labeling of endogenous neurotransmitter receptors in living mouse brains. Proc Natl Acad Sci U S A 2024; 121:e2313887121. [PMID: 38294939 PMCID: PMC10861872 DOI: 10.1073/pnas.2313887121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 12/16/2023] [Indexed: 02/02/2024] Open
Abstract
Neurotransmitter receptors are essential components of synapses for communication between neurons in the brain. Because the spatiotemporal expression profiles and dynamics of neurotransmitter receptors involved in many functions are delicately governed in the brain, in vivo research tools with high spatiotemporal resolution for receptors in intact brains are highly desirable. Covalent labeling by chemical reaction (chemical labeling) of proteins without genetic manipulation is now a powerful method for analyzing receptors in vitro. However, selective target receptor labeling in the brain has not yet been achieved. This study shows that ligand-directed alkoxyacylimidazole (LDAI) chemistry can be used to selectively tether synthetic probes to target endogenous receptors in living mouse brains. The reactive LDAI reagents with negative charges were found to diffuse well over the whole brain and could selectively label target endogenous receptors, including AMPAR, NMDAR, mGlu1, and GABAAR. This simple and robust labeling protocol was then used for various applications: three-dimensional spatial mapping of endogenous receptors in the brains of healthy and disease-model mice; multi-color receptor imaging; and pulse-chase analysis of the receptor dynamics in postnatal mouse brains. Here, results demonstrated that bioorthogonal receptor modification in living animal brains may provide innovative molecular tools that contribute to the in-depth understanding of complicated brain functions.
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Affiliation(s)
- Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Kazuki Shiraiwa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Mamoru Ishikawa
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Kyohei Okuno
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Takumi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya464-8603, Japan
| | - Shigeki Kiyonaka
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya464-8603, Japan
| | - Etsuo A. Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo113-8421, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
| | - Chika Shimizu
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| | - Wataru Kakegawa
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
- Department of Neurophysiology, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Itaru Arai
- Department of Neurophysiology, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Michisuke Yuzaki
- Department of Neurophysiology, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
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6
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Kubota R, Hamachi I. Cell-Like Synthetic Supramolecular Soft Materials Realized in Multicomponent, Non-/Out-of-Equilibrium Dynamic Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306830. [PMID: 38018341 PMCID: PMC10885657 DOI: 10.1002/advs.202306830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/30/2023] [Indexed: 11/30/2023]
Abstract
Living cells are complex, nonequilibrium supramolecular systems capable of independently and/or cooperatively integrating multiple bio-supramolecules to execute intricate physiological functions that cannot be accomplished by individual biomolecules. These biological design strategies offer valuable insights for the development of synthetic supramolecular systems with spatially controlled hierarchical structures, which, importantly, exhibit cell-like responses and functions. The next grand challenge in supramolecular chemistry is to control the organization of multiple types of supramolecules in a single system, thus integrating the functions of these supramolecules in an orthogonal and/or cooperative manner. In this perspective, the recent progress in constructing multicomponent supramolecular soft materials through the hybridization of supramolecules, such as self-assembled nanofibers/gels and coacervates, with other functional molecules, including polymer gels and enzymes is highlighted. Moreover, results show that these materials exhibit bioinspired responses to stimuli, such as bidirectional rheological responses of supramolecular double-network hydrogels, temporal stimulus pattern-dependent responses of synthetic coacervates, and 3D hydrogel patterning in response to reaction-diffusion processes are presented. Autonomous active soft materials with cell-like responses and spatially controlled structures hold promise for diverse applications, including soft robotics with directional motion, point-of-care disease diagnosis, and tissue regeneration.
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Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological ChemistryGraduate School of EngineeringKyoto UniversityKatsuraNishikyo‐kuKyoto615‐8510Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological ChemistryGraduate School of EngineeringKyoto UniversityKatsuraNishikyo‐kuKyoto615‐8510Japan
- JST‐ERATOHamachi Innovative Molecular Technology for NeuroscienceKyoto UniversityNishikyo‐kuKatsura615‐8530Japan
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7
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Waly SMA, Benniston AC, Harriman A. Deducing the conformational space for an octa-proline helix. Chem Sci 2024; 15:1657-1671. [PMID: 38303943 PMCID: PMC10829019 DOI: 10.1039/d3sc05287g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024] Open
Abstract
A molecular dyad, PY-P8-PER, comprising a proline octamer sandwiched between pyrene and perylene terminals has been synthesized in order to address the dynamics of electronic energy transfer (EET) along the oligo-proline chain. A simple pyrene-based control compound equipped with a bis-proline attachment serves as a reference for spectroscopic studies. The N-H NMR signal at the terminal pyrene allows distinction between cis and trans amides and, although the crystal structure for the control has the trans conformation, temperature-dependent NMR studies provide clear evidence for trans/cis isomerisation in D6-DMSO. Polar solvents tend to stabilise the trans structure for the pyrene amide group, even for longer oligo-proline units. Circular dichroism shows that the proline spacer for PY-P8-PER exists mainly in the all-trans geometry in methanol. Preferential excitation of the pyrene chromophore is possible at wavelengths in the 320-350 nm range and, for the dyad, is followed by efficacious EET to the perylene emitter. The probability for intramolecular EET, obtained from analysis of steady-state spectroscopic data, is ca. 80-90% in solvents of disparate polarity. Comparison with the Förster critical distance suggests the terminals are ca. 18 Å apart. Time-resolved fluorescence spectroscopy, in conjunction with DFT calculations, indicates the dyad exists as a handful of conformers displaying a narrow range of EET rates. Optimisation of a distributive model allows accurate simulation of the EET dynamics in terms of reasonable structures based on isomerisation of certain amide groups.
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Affiliation(s)
- Sara M A Waly
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Andrew C Benniston
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Anthony Harriman
- Molecular Photonics Laboratory, Bedson Building, School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
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8
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Mir MH, Parmar S, Singh C, Kalia D. Location-agnostic site-specific protein bioconjugation via Baylis Hillman adducts. Nat Commun 2024; 15:859. [PMID: 38286847 PMCID: PMC10825175 DOI: 10.1038/s41467-024-45124-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
Proteins labelled site-specifically with small molecules are valuable assets for chemical biology and drug development. The unique reactivity profile of the 1,2-aminothiol moiety of N-terminal cysteines (N-Cys) of proteins renders it highly attractive for regioselective protein labelling. Herein, we report an ultrafast Z-selective reaction between isatin-derived Baylis Hillman adducts and 1,2-aminothiols to form a bis-heterocyclic scaffold, and employ it for stable protein bioconjugation under both in vitro and live-cell conditions. We refer to our protein bioconjugation technology as Baylis Hillman orchestrated protein aminothiol labelling (BHoPAL). Furthermore, we report a lipoic acid ligase-based technology for introducing the 1,2-aminothiol moiety at any desired site within proteins, rendering BHoPAL location-agnostic (not limited to N-Cys). By using this approach in tandem with BHoPAL, we generate dually labelled protein bioconjugates appended with different labels at two distinct specific sites on a single protein molecule. Taken together, the protein bioconjugation toolkit that we disclose herein will contribute towards the generation of both mono and multi-labelled protein-small molecule bioconjugates for applications as diverse as biophysical assays, cellular imaging, and the production of therapeutic protein-drug conjugates. In addition to protein bioconjugation, the bis-heterocyclic scaffold we report herein will find applications in synthetic and medicinal chemistry.
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Affiliation(s)
- Mudassir H Mir
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Sangeeta Parmar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Chhaya Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Dimpy Kalia
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India.
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9
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Rimbault C, Breillat C, Compans B, Toulmé E, Vicente FN, Fernandez-Monreal M, Mascalchi P, Genuer C, Puente-Muñoz V, Gauthereau I, Hosy E, Claverol S, Giannone G, Chamma I, Mackereth CD, Poujol C, Choquet D, Sainlos M. Engineering paralog-specific PSD-95 recombinant binders as minimally interfering multimodal probes for advanced imaging techniques. eLife 2024; 13:e69620. [PMID: 38167295 PMCID: PMC10803022 DOI: 10.7554/elife.69620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Despite the constant advances in fluorescence imaging techniques, monitoring endogenous proteins still constitutes a major challenge in particular when considering dynamics studies or super-resolution imaging. We have recently evolved specific protein-based binders for PSD-95, the main postsynaptic scaffold proteins at excitatory synapses. Since the synthetic recombinant binders recognize epitopes not directly involved in the target protein activity, we consider them here as tools to develop endogenous PSD-95 imaging probes. After confirming their lack of impact on PSD-95 function, we validated their use as intrabody fluorescent probes. We further engineered the probes and demonstrated their usefulness in different super-resolution imaging modalities (STED, PALM, and DNA-PAINT) in both live and fixed neurons. Finally, we exploited the binders to enrich at the synapse genetically encoded calcium reporters. Overall, we demonstrate that these evolved binders constitute a robust and efficient platform to selectively target and monitor endogenous PSD-95 using various fluorescence imaging techniques.
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Affiliation(s)
- Charlotte Rimbault
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Christelle Breillat
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Benjamin Compans
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Estelle Toulmé
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Filipe Nunes Vicente
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Monica Fernandez-Monreal
- University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4BordeauxFrance
| | - Patrice Mascalchi
- University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4BordeauxFrance
| | - Camille Genuer
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Virginia Puente-Muñoz
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Isabel Gauthereau
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Eric Hosy
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | | | - Gregory Giannone
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Ingrid Chamma
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | | | - Christel Poujol
- University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4BordeauxFrance
| | - Daniel Choquet
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Matthieu Sainlos
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
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10
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Fujimura A, Ishida H, Nozaki T, Terada S, Azumaya Y, Ishiguro T, Kamimura YR, Kujirai T, Kurumizaka H, Kono H, Yamatsugu K, Kawashima SA, Kanai M. Designer Adaptor Proteins for Functional Conversion of Peptides to Small-Molecule Ligands toward In-Cell Catalytic Protein Modification. ACS CENTRAL SCIENCE 2023; 9:2115-2128. [PMID: 38033808 PMCID: PMC10683481 DOI: 10.1021/acscentsci.3c00930] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/19/2023] [Accepted: 10/12/2023] [Indexed: 12/02/2023]
Abstract
Peptides are privileged ligands for diverse biomacromolecules, including proteins; however, their utility is often limited due to low membrane permeability and in-cell instability. Here, we report peptide ligand-inserted eDHFR (PLIED) fusion protein as a universal adaptor for targeting proteins of interest (POI) with cell-permeable and stable synthetic functional small molecules (SFSM). PLIED binds to POI through the peptide moiety, properly orienting its eDHFR moiety, which then recruits trimethoprim (TMP)-conjugated SFSM to POI. Using a lysine-acylating BAHA catalyst as SFSM, we demonstrate that POI (MDM2 and chromatin histone) are post-translationally and synthetically acetylated at specific lysine residues. The residue-selectivity is predictable in an atomic resolution from molecular dynamics simulations of the POI/PLIED/TMP-BAHA (MTX was used as a TMP model) ternary complex. This designer adaptor approach universally enables functional conversion of impermeable peptide ligands to permeable small-molecule ligands, thus expanding the in-cell toolbox of chemical biology.
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Affiliation(s)
- Akiko Fujimura
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Hisashi Ishida
- Institute
for Quantum Life Science, National Institutes
for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Tamiko Nozaki
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Shuhei Terada
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Yuto Azumaya
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Tadashi Ishiguro
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Yugo R. Kamimura
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Tomoya Kujirai
- Institute
for Quantitative Biosciences, The University
of Tokyo, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Institute
for Quantitative Biosciences, The University
of Tokyo, Tokyo 113-0032, Japan
| | - Hidetoshi Kono
- Institute
for Quantum Life Science, National Institutes
for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Kenzo Yamatsugu
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Shigehiro A. Kawashima
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
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11
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Grimm J, Tkachuk AN, Patel R, Hennigan ST, Gutu A, Dong P, Gandin V, Osowski AM, Holland KL, Liu ZJ, Brown TA, Lavis LD. Optimized Red-Absorbing Dyes for Imaging and Sensing. J Am Chem Soc 2023; 145:23000-23013. [PMID: 37842926 PMCID: PMC10603817 DOI: 10.1021/jacs.3c05273] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Indexed: 10/17/2023]
Abstract
Rhodamine dyes are excellent scaffolds for developing a broad range of fluorescent probes. A key property of rhodamines is their equilibrium between a colorless lactone and fluorescent zwitterion. Tuning the lactone-zwitterion equilibrium constant (KL-Z) can optimize dye properties for specific biological applications. Here, we use known and novel organic chemistry to prepare a comprehensive collection of rhodamine dyes to elucidate the structure-activity relationships that govern KL-Z. We discovered that the auxochrome substituent strongly affects the lactone-zwitterion equilibrium, providing a roadmap for the rational design of improved rhodamine dyes. Electron-donating auxochromes, such as julolidine, work in tandem with fluorinated pendant phenyl rings to yield bright, red-shifted fluorophores for live-cell single-particle tracking (SPT) and multicolor imaging. The N-aryl auxochrome combined with fluorination yields red-shifted Förster resonance energy transfer (FRET) quencher dyes useful for creating a new semisynthetic indicator to sense cAMP using fluorescence lifetime imaging microscopy (FLIM). Together, this work expands the synthetic methods available for rhodamine synthesis, generates new reagents for advanced fluorescence imaging experiments, and describes structure-activity relationships that will guide the design of future probes.
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Affiliation(s)
- Jonathan
B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Ariana N. Tkachuk
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Ronak Patel
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - S. Thomas Hennigan
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Alina Gutu
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Valentina Gandin
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Anastasia M. Osowski
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Katie L. Holland
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Zhe J. Liu
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Timothy A. Brown
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
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12
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Phanumartwiwath A, Kesornpun C, Chokchaichamnankit D, Khongmanee A, Diskul-Na-Ayudthaya P, Ruangjaroon T, Srisomsap C, Kittakoop P, Svasti J, Ruchirawat S. Protein Modification via Nitrile Oxide-Dehydroalanine Cycloaddition: Formation of Isoxazoline Ring on the Protein Backbone. Chembiochem 2023; 24:e202300268. [PMID: 37199473 DOI: 10.1002/cbic.202300268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/26/2023] [Accepted: 05/18/2023] [Indexed: 05/19/2023]
Abstract
Here we describe a novel catalyst-free 1,3-dipolar cycloaddition bioconjugation approach for chemical modification of proteins. The dehydroalanine (Dha)-containing protein reacts with nitrile oxides generated in situ through 1,3-dipolar cycloaddition in fully aqueous-buffered systems. This leads to the formation of a new isoxazoline ring at a pre-defined site (Dha) of the protein. Furthermore, the 1-pyrene isoxazoline-installed annexin V acts as a fluorescent probe, which successfully labels the outer cellular membranes of human cholangiocarcinoma (HuCCA-1) cells for detection of apoptosis.
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Affiliation(s)
- Anuchit Phanumartwiwath
- College of Public Health Sciences, Chulalongkorn University, Phyathai Road, Bangkok, 10330, Thailand
- Chemical Biology Program, Chulabhorn Graduate Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
- Centre of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, 10400, Thailand
| | - Chatchai Kesornpun
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
| | | | - Amnart Khongmanee
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
| | | | - Theetat Ruangjaroon
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
| | - Chantragan Srisomsap
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
| | - Prasat Kittakoop
- Chemical Biology Program, Chulabhorn Graduate Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
- Centre of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, 10400, Thailand
| | - Jisnuson Svasti
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
| | - Somsak Ruchirawat
- Chemical Biology Program, Chulabhorn Graduate Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
- Centre of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, 10400, Thailand
- Chulabhorn Research Institute, Kamphaeng Phet6 Road, Lak Si, Bangkok, 10210, Thailand
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13
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Hellweg L, Edenhofer A, Barck L, Huppertz MC, Frei MS, Tarnawski M, Bergner A, Koch B, Johnsson K, Hiblot J. A general method for the development of multicolor biosensors with large dynamic ranges. Nat Chem Biol 2023; 19:1147-1157. [PMID: 37291200 PMCID: PMC10449634 DOI: 10.1038/s41589-023-01350-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/25/2023] [Indexed: 06/10/2023]
Abstract
Fluorescent biosensors enable the study of cell physiology with spatiotemporal resolution; yet, most biosensors suffer from relatively low dynamic ranges. Here, we introduce a family of designed Förster resonance energy transfer (FRET) pairs with near-quantitative FRET efficiencies based on the reversible interaction of fluorescent proteins with a fluorescently labeled HaloTag. These FRET pairs enabled the straightforward design of biosensors for calcium, ATP and NAD+ with unprecedented dynamic ranges. The color of each of these biosensors can be readily tuned by changing either the fluorescent protein or the synthetic fluorophore, which enables simultaneous monitoring of free NAD+ in different subcellular compartments following genotoxic stress. Minimal modifications of these biosensors furthermore allow their readout to be switched to fluorescence intensity, fluorescence lifetime or bioluminescence. These FRET pairs thus establish a new concept for the development of highly sensitive and tunable biosensors.
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Affiliation(s)
- Lars Hellweg
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Anna Edenhofer
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Lucas Barck
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Magnus-Carsten Huppertz
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Michelle S Frei
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Andrea Bergner
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
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14
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Molla R, Joshi PN, Reddy NC, Biswas D, Rai V. Protein-Protein Interaction in Multicomponent Reaction Enables Chemoselective, Site-Selective, and Modular Labeling of Native Proteins. Org Lett 2023; 25:6385-6390. [PMID: 37603545 DOI: 10.1021/acs.orglett.3c02405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
A protein's pool of functionalities presents a formidable challenge for its single-site modification. Here, we report a method to harness protein-protein interaction (PPI) to drive selective modification. It involves the chemoselective reversible generation of reactive intermediates and utilizes PPI-specificity to drive the subsequent site-selective irreversible step. The disintegrate (DIN) theory-driven multicomponent aza-Morita-Baylis-Hillman (aza-MBH) reaction offers homogeneous and modular single-site protein modification capable of late-stage mono- and dual-probe installation.
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Affiliation(s)
- Rajib Molla
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066, M.P., India
| | - Pralhad N Joshi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066, M.P., India
| | - Neelesh C Reddy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066, M.P., India
| | - Dwaipayan Biswas
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066, M.P., India
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066, M.P., India
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15
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Zhang P, Wang X, Wang X, Huang C, James TD, Sun X, Qian X. Chemoselective Fluorogenic Bioconjugation of Vicinal Dithiol-Containing Proteins for Live Cellular Imaging via Small Molecular Conjugate Acceptors. Anal Chem 2023; 95:11953-11959. [PMID: 37490273 DOI: 10.1021/acs.analchem.3c01518] [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: 07/26/2023]
Abstract
To develop small molecular fluorogenic tools for the chemoselective labeling of vicinal dithiol-containing proteins (VDPs) in live cells is important for studying intracellular redox homeostasis. With this research, we developed small molecule-based fluorescent probes, achieving selective labeling of VDPs through thiol-thiol substitutions on bisvinylogous thioester conjugated acceptors (IDAs). Initially, IDAs demonstrated its ability to bridge vicinal cysteine-sulfhydryls on a peptide as a mimic. Then, the peptide complex could be decoupled to recover the original peptide-SH in the presence of dithiothreitol. Furthermore, fluorometric signal amplification of the fluorescent probes occurred with high sensitivity, low limit of detection, and selectivity toward vicinal dithiols on reduced bovine serum albumin, as an example of real world VDPs. More importantly, the probes were utilized successfully for labeling of endogenous VDPs at different redox states in live cells. Thus, the bisvinylogous thioester-based receptor as a functional probe represents a new platform for uncovering the function of VDPs in live cells.
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Affiliation(s)
- Peng Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, No. 28, West Xianning Road, Xi'an 710049, People's Republic of China
| | - Xuechuan Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
| | - Xiao Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
| | - Chusen Huang
- The Education Ministry Key Laboratory of Resource Chemistry, Shanghai Normal University, No. 100 Guilin Road, Shanghai 200234, People's Republic of China
| | - Tony D James
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Xiaolong Sun
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, No. 28, West Xianning Road, Xi'an 710049, People's Republic of China
| | - Xuhong Qian
- State Key Laboratory of Bioreactor Engineering; Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, No. 130 Meilong Road, Shanghai 200237, People's Republic of China
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16
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Zhang D, Chen Z, Du Z, Bao B, Su N, Chen X, Ge Y, Lin Q, Yang L, Hua Y, Wang S, Hua X, Zuo F, Li N, Liu R, Jiang L, Bao C, Zhao Y, Loscalzo J, Yang Y, Zhu L. Design of a palette of SNAP-tag mimics of fluorescent proteins and their use as cell reporters. Cell Discov 2023; 9:56. [PMID: 37311750 DOI: 10.1038/s41421-023-00546-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/18/2023] [Indexed: 06/15/2023] Open
Abstract
Naturally occurring fluorescent proteins (FPs) are the most widely used tools for tracking cellular proteins and sensing cellular events. Here, we chemically evolved the self-labeling SNAP-tag into a palette of SNAP-tag mimics of fluorescent proteins (SmFPs) that possess bright, rapidly inducible fluorescence ranging from cyan to infrared. SmFPs are integral chemical-genetic entities based on the same fluorogenic principle as FPs, i.e., induction of fluorescence of non-emitting molecular rotors by conformational locking. We demonstrate the usefulness of these SmFPs in real-time tracking of protein expression, degradation, binding interactions, trafficking, and assembly, and show that these optimally designed SmFPs outperform FPs like GFP in many important ways. We further show that the fluorescence of circularly permuted SmFPs is sensitive to the conformational changes of their fusion partners, and that these fusion partners can be used for the development of single SmFP-based genetically encoded calcium sensors for live cell imaging.
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Affiliation(s)
- Dasheng Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhengda Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zengmin Du
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ni Su
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Yihui Ge
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Lipeng Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yujie Hua
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xin Hua
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Fangting Zuo
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ningfeng Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Li Jiang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chunyan Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
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17
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Pelletier R, Danylchuk DI, Benaissa H, Broch F, Vauchelles R, Gautier A, Klymchenko AS. Genetic Targeting of Solvatochromic Dyes for Probing Nanoscale Environments of Proteins in Organelles. Anal Chem 2023. [PMID: 37229557 DOI: 10.1021/acs.analchem.3c00515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A variety of protein tags are available for genetically encoded protein labeling, which allow their precise localization and tracking inside the cells. A new dimension in protein imaging can be offered by combining protein tags with polarity-sensitive fluorescent probes, which provide information about local nanoscale environments of target proteins within the subcellular compartments (organelles). Here, we designed three fluorescent probes based on solvatochromic nile red dye, conjugated to a HaloTag reactive targeting group through polyethylene glycol linkers of varying lengths. The probe with medium linker length, NR12-Halo, was found to label specifically a large variety of proteins localized in defined cell compartments, such as plasma membranes (outer and inner leaflets), endoplasmic reticulum, Golgi apparatus, cytosol, microtubules, actin, and chromatin. Owing to its polarity-sensitive fluorophore, the probe clearly distinguished the proteins localized within apolar lipid membranes from other proteins. Moreover, it revealed dramatic changes in the environment during the life cycle of proteins from biosynthesis to their expected localization and, finally, to recycling inside lysosomes. Heterogeneity in the local polarity of some membrane proteins also suggested a formation of low-polar protein aggregates, for example, within cell-cell contacts. The approach also showed that mechanical stress (cell shrinking by osmotic shock) induced a general polarity decrease in membrane proteins, probably due to the condensation of biomolecules. Finally, the nanoenvironment of some membrane proteins was affected by a polyunsaturated fatty acid diet, which provided the bridge between organization of lipids and proteins. The developed solvatochromic HaloTag probe constitutes a promising tool for probing nanoscale environments of proteins and their interactions within subcellular structures.
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Affiliation(s)
- Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Hela Benaissa
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Fanny Broch
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Romain Vauchelles
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Arnaud Gautier
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
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18
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Thimaradka V, Utsunomiya H, Tamura T, Hamachi I. Endogenous Cell-Surface Receptor Modification by Metal Chelation-Assisted Pyridinium Oxime Catalyst. Org Lett 2023; 25:2118-2122. [PMID: 36947590 DOI: 10.1021/acs.orglett.3c00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Organocatalyst-mediated acyl transfer reactions hold promise for selective protein labeling in biological milieu. However, they often suffer from off-target reactions and high background signals because of the requirement of high concentrations of substrates. Here, we report a new catalytic protein acylation strategy promoted by the His-tag/NiNTA interaction. The recognition-assisted activation mechanism allows efficient protein labeling even with >10-fold lower substrate concentrations than conventional reactions, thereby enabling highly selective and efficient cell-surface receptor modification in live cells.
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Affiliation(s)
- Vikram Thimaradka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hayata Utsunomiya
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Sanbancho, Chiyodaku, Tokyo 102-0075, Japan
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19
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O WY, Cui JF, Yu Q, Kung KKY, Chung SF, Leung YC, Wong MK. Isoindolium-Based Allenes: Reactivity Studies and Applications in Fluorescence Temperature Sensing and Cysteine Bioconjugation. Angew Chem Int Ed Engl 2023; 62:e202218038. [PMID: 36670048 DOI: 10.1002/anie.202218038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
Abstract
The reaction of a series of electron-deficient isoindolium-based allenes with sulfhydryl compounds has been studied, leading to the formation of isoindolium-based vinyl sulfides. The vinyl sulfides generated could be readily converted into the corresponding indanones and amines upon heating at 30-70 °C with good yields up to 61 %. The thermal cleavage reaction of vinyl sulfides was further studied for developing temperature-sensitive systems. Notably, a novel FRET-based fluorescent temperature sensor was designed and synthesized for temperature sensing at 50 °C, giving a 6.5-fold blue fluorescence enhancement. Moreover, chemoselective bioconjugation of cysteine-containing peptides with the isoindolium-based allenes for the construction of multifunctional peptide bioconjugates was investigated. Thermal cleavage of isoindoliums on the modified peptides at 35-70 °C gave indanone bioconjugates with up to >99 % conversion. These results indicated the biocompatibility of this novel temperature-sensitive reaction.
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Affiliation(s)
- Wa-Yi O
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China.,The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Jian-Fang Cui
- Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, 518055, China
| | - Qiong Yu
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Karen Ka-Yan Kung
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China.,The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Sai-Fung Chung
- Henry Cheng Research Laboratory for Drug Development, Lo Ka Chung Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Yun-Chung Leung
- Henry Cheng Research Laboratory for Drug Development, Lo Ka Chung Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Man-Kin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China.,The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
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20
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Zhang J, Shi H, Huang C, Mei L, Guo Q, Cheng K, Wu P, Su D, Chen Q, Gan S, Wing Chan CK, Shi J, Chen JL, Jonathan Choi CH, Yao SQ, Chen XK, Tang BZ, He J, Sun H. De Novo Designed Self-Assembling Rhodamine Probe for Real-Time, Long-Term and Quantitative Live-Cell Nanoscopy. ACS NANO 2023; 17:3632-3644. [PMID: 36744992 DOI: 10.1021/acsnano.2c10467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Super-resolution imaging provides a powerful approach to image dynamic biomolecule events at nanoscale resolution. An ingenious method involving tuning intramolecular spirocyclization in rhodamine offers an appealing strategy to design cell-permeable fluorogenic probes for super-resolution imaging. Nevertheless, precise control of rhodamine spirocyclization presents a significant challenge. Through detailed study of the structure-activity relationship, we identified that multiple key factors control rhodamime spirocyclization. The findings provide opportunities to create fluorogenic probes with tailored properties. On the basis of our findings, we constructed self-assembling rhodamine probes for no-wash live-cell confocal and super-resolution imaging. The designed self-assembling probe Rho-2CF3 specifically labeled its target proteins and displayed high ring-opening ability, fast labeling kinetics (<1 min), and large turn-on fold (>80 folds), which is very difficult to be realized by the existing methods. Using the probe, we achieved high-contrast super-resolution imaging of nuclei and mitochondria with a spatial resolution of up to 42 nm. The probe also showed excellent photostability and proved ideal for real-time and long-term tracking of mitochondrial fission and fusion events with high spatiotemporal resolution. Furthermore, Rho-2CF3 could resolve the ultrastructure of mitochondrial cristae and quantify their morphological changes under drug treatment at nanoscale. Our strategy thus demonstrates its usefulness in designing self-assembling probes for super-resolution imaging.
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Affiliation(s)
- Jie Zhang
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong, 999077, China
| | - Heng Shi
- Departments of Neuroscience and Biomedical Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong Province 510530, China
| | - Chen Huang
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Le Mei
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Qiang Guo
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- Department of Science, School of Science and Technology, Hong Kong Metropolitan University, Good Shepherd Street, Ho Man Tin, Hong Kong SAR, 999077, China
| | - Ke Cheng
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Pingzhou Wu
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Dan Su
- Departments of Neuroscience and Biomedical Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Qingxin Chen
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Shenglong Gan
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Cecilia Ka Wing Chan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, 999077, China
| | - Jiahai Shi
- Departments of Neuroscience and Biomedical Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Jian Lin Chen
- Department of Science, School of Science and Technology, Hong Kong Metropolitan University, Good Shepherd Street, Ho Man Tin, Hong Kong SAR, 999077, China
| | - Chung Hang Jonathan Choi
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, 999077, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Xian-Kai Chen
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
| | - Ben Zhong Tang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, 999077, China
| | - Jufang He
- Departments of Neuroscience and Biomedical Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong, 999077, China
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, 999077, China
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21
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Wang Y, Li Z, Mo F, Chen-Mayfield TJ, Saini A, LaMere AM, Hu Q. Chemically engineering cells for precision medicine. Chem Soc Rev 2023; 52:1068-1102. [PMID: 36633324 DOI: 10.1039/d2cs00142j] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cell-based therapy holds great potential to address unmet medical needs and revolutionize the healthcare industry, as demonstrated by several therapeutics such as CAR-T cell therapy and stem cell transplantation that have achieved great success clinically. Nevertheless, natural cells are often restricted by their unsatisfactory in vivo trafficking and lack of therapeutic payloads. Chemical engineering offers a cost-effective, easy-to-implement engineering tool that allows for strengthening the inherent favorable features of cells and confers them new functionalities. Moreover, in accordance with the trend of precision medicine, leveraging chemical engineering tools to tailor cells to accommodate patients individual needs has become important for the development of cell-based treatment modalities. This review presents a comprehensive summary of the currently available chemically engineered tools, introduces their application in advanced diagnosis and precision therapy, and discusses the current challenges and future opportunities.
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Affiliation(s)
- Yixin Wang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA. .,Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.,Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zhaoting Li
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA. .,Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.,Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Fanyi Mo
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Ting-Jing Chen-Mayfield
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Aryan Saini
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Afton Martin LaMere
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA. .,Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.,Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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22
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Barber LJ, Yates NDJ, Fascione MA, Parkin A, Hemsworth GR, Genever PG, Spicer CD. Selectivity and stability of N-terminal targeting protein modification chemistries. RSC Chem Biol 2023; 4:56-64. [PMID: 36685256 PMCID: PMC9811658 DOI: 10.1039/d2cb00203e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
Protein N-termini provide uniquely reactive motifs for single site protein modification. Though a number of reactions have been developed to target this site, the selectivity, generality, and stability of the conjugates formed has not been studied. We have therefore undertaken a comprehensive comparative study of the most promising methods for N-terminal protein modification, and find that there is no 'one size fits all' approach, necessitating reagent screening for a particular protein or application. Moreover, we observed limited stability in all cases, leading to a need for continued innovation and development in the bioconjugation field.
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Affiliation(s)
- Lydia J. Barber
- Department of Chemistry, University of YorkHeslingtonYO10 5DDUK,York Biomedical Research Institute, University of YorkHeslingtonYO10 5DDUK,Department of Biology, University of YorkHeslingtonYO10 5DDUK
| | - Nicholas D. J. Yates
- Department of Chemistry, University of YorkHeslingtonYO10 5DDUK,York Biomedical Research Institute, University of YorkHeslingtonYO10 5DDUK
| | - Martin A. Fascione
- Department of Chemistry, University of YorkHeslingtonYO10 5DDUK,York Biomedical Research Institute, University of YorkHeslingtonYO10 5DDUK
| | - Alison Parkin
- Department of Chemistry, University of YorkHeslingtonYO10 5DDUK
| | - Glyn R. Hemsworth
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds LS2 9JTUK
| | - Paul G. Genever
- York Biomedical Research Institute, University of YorkHeslingtonYO10 5DDUK,Department of Biology, University of YorkHeslingtonYO10 5DDUK
| | - Christopher D. Spicer
- Department of Chemistry, University of YorkHeslingtonYO10 5DDUK,York Biomedical Research Institute, University of YorkHeslingtonYO10 5DDUK,Department of Biology, University of YorkHeslingtonYO10 5DDUK
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23
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Bulovaite E, Qiu Z, Kratschke M, Zgraj A, Fricker DG, Tuck EJ, Gokhale R, Koniaris B, Jami SA, Merino-Serrais P, Husi E, Mendive-Tapia L, Vendrell M, O'Dell TJ, DeFelipe J, Komiyama NH, Holtmaat A, Fransén E, Grant SGN. A brain atlas of synapse protein lifetime across the mouse lifespan. Neuron 2022; 110:4057-4073.e8. [PMID: 36202095 PMCID: PMC9789179 DOI: 10.1016/j.neuron.2022.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 07/01/2022] [Accepted: 09/07/2022] [Indexed: 11/12/2022]
Abstract
The lifetime of proteins in synapses is important for their signaling, maintenance, and remodeling, and for memory duration. We quantified the lifetime of endogenous PSD95, an abundant postsynaptic protein in excitatory synapses, at single-synapse resolution across the mouse brain and lifespan, generating the Protein Lifetime Synaptome Atlas. Excitatory synapses have a wide range of PSD95 lifetimes extending from hours to several months, with distinct spatial distributions in dendrites, neurons, and brain regions. Synapses with short protein lifetimes are enriched in young animals and in brain regions controlling innate behaviors, whereas synapses with long protein lifetimes accumulate during development, are enriched in the cortex and CA1 where memories are stored, and are preferentially preserved in old age. Synapse protein lifetime increases throughout the brain in a mouse model of autism and schizophrenia. Protein lifetime adds a further layer to synapse diversity and enriches prevailing concepts in brain development, aging, and disease.
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Affiliation(s)
- Edita Bulovaite
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Zhen Qiu
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Maximilian Kratschke
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Adrianna Zgraj
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - David G Fricker
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Eleanor J Tuck
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Ragini Gokhale
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Babis Koniaris
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; School of Computing, Edinburgh Napier University, Edinburgh EH10 5DT, UK
| | - Shekib A Jami
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Paula Merino-Serrais
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, UPM, 28223 Madrid, Spain; Instituto Cajal, CSIC, 28002 Madrid, Spain
| | - Elodie Husi
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Lorena Mendive-Tapia
- Centre for Inflammation Research, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Marc Vendrell
- Centre for Inflammation Research, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Thomas J O'Dell
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Javier DeFelipe
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, UPM, 28223 Madrid, Spain; Instituto Cajal, CSIC, 28002 Madrid, Spain
| | - Noboru H Komiyama
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK; The Patrick Wild Centre for Research into Autism, Fragile X Syndrome & Intellectual Disabilities, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK; Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Anthony Holtmaat
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Erik Fransén
- Department of Computational Science and Technology, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 10044 Stockholm, Sweden; Science for Life Laboratory, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Seth G N Grant
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK.
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24
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Hu Y, Zhang RQ, Wang ZG, Liu SL. In Situ Quantification of Lipids in Live Cells by Using Lipid-Binding Domain-Based Biosensors. Bioconjug Chem 2022; 33:2076-2087. [DOI: 10.1021/acs.bioconjchem.2c00469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yusi Hu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Centre for New Organic Matter, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Rui-Qiao Zhang
- Qingdao Academy of Agricultural Sciences, Qingdao 266100, P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Centre for New Organic Matter, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Centre for New Organic Matter, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry and School of Medicine, Nankai University, Tianjin 300071, P. R. China
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25
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Hanaoka K, Iwaki S, Yagi K, Myochin T, Ikeno T, Ohno H, Sasaki E, Komatsu T, Ueno T, Uchigashima M, Mikuni T, Tainaka K, Tahara S, Takeuchi S, Tahara T, Uchiyama M, Nagano T, Urano Y. General Design Strategy to Precisely Control the Emission of Fluorophores via a Twisted Intramolecular Charge Transfer (TICT) Process. J Am Chem Soc 2022; 144:19778-19790. [PMID: 36191139 DOI: 10.1021/jacs.2c06397] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorogenic probes for bioimaging have become essential tools for life science and medicine, and the key to their development is a precise understanding of the mechanisms available for fluorescence off/on control, such as photoinduced electron transfer (PeT) and Förster resonance energy transfer (FRET). Here we establish a new molecular design strategy to rationally develop activatable fluorescent probes, which exhibit a fluorescence off/on change in response to target biomolecules, by controlling the twisted intramolecular charge transfer (TICT) process. This approach was developed on the basis of a thorough investigation of the fluorescence quenching mechanism of N-phenyl rhodamine dyes (commercially available as the QSY series) by means of time-dependent density functional theory (TD-DFT) calculations and photophysical evaluation of their derivatives. To illustrate and validate this TICT-based design strategy, we employed it to develop practical fluorogenic probes for HaloTag and SNAP-tag. We further show that the TICT-controlled fluorescence off/on mechanism is generalizable by synthesizing a Si-rhodamine-based fluorogenic probe for HaloTag, thus providing a palette of chemical dyes that spans the visible and near-infrared range.
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Affiliation(s)
- Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minoto-ku, Tokyo105-8512, Japan
| | | | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
| | | | | | - Hisashi Ohno
- Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minoto-ku, Tokyo105-8512, Japan
| | - Eita Sasaki
- Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minoto-ku, Tokyo105-8512, Japan
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26
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Yu H, Wang S, Huang J, Fu Y, Wagner M, Weil T, Zhong F, Zhao W, Wu Y. Light-Controlled Traceless Protein Labeling via Decaging Thio- o-naphthoquinone Methide Chemistry. Org Lett 2022; 24:6816-6821. [PMID: 36099167 DOI: 10.1021/acs.orglett.2c02742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the molecular design of a novel multifunctional reagent and its application for light-controlled selective protein labeling. This molecule integrates functions of protein-ligand recognition, bioconjugation, ligand cleavage, and photoactivation by merging the photochemistries of 2-nitrophenylpropyloxycarbonyl and 3-hydroxymethyl-2-naphthol with an affinity ligand and fluorescein. Highly electrophilic o-naphthoquinone methide was photochemically released and underwent proximity-driven selective labeling with the protein of interest (e.g., carbonic anhydrases), which retains its native function after labeling.
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Affiliation(s)
- Huaibin Yu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Shuangshuang Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Jianjian Huang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Yu Fu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Fangrui Zhong
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Weining Zhao
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Yuzhou Wu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
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27
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Chen TH, Garnir K, Chen CY, Jian CB, Gao HD, Cheng B, Tseng MC, Moucheron C, Kirsch-De Mesmaeker A, Lee HM. A Toolkit for Engineering Proteins in Living Cells: Peptide with a Tryptophan-Selective Ru-TAP Complex to Regioselectively Photolabel Specific Proteins. J Am Chem Soc 2022; 144:18117-18125. [PMID: 36135325 DOI: 10.1021/jacs.2c08342] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using a chemical approach to crosslink functionally versatile bioeffectors (such as peptides) to native proteins of interest (POI) directly inside a living cell is a useful toolbox for chemical biologists. However, this goal has not been reached due to unsatisfactory chemoselectivity, regioselectivity, and protein selectivity in protein labeling within living cells. Herein, we report the proof of concept of a cytocompatible and highly selective photolabeling strategy using a tryptophan-specific Ru-TAP complex as a photocrosslinker. Aside from the high selectivity, the photolabeling is blue light-driven by a photoinduced electron transfer (PeT) and allows the bioeffector to bear an additional UV-responsive unit. The two different photosensitivities are demonstrated by blue light-photocrosslinking a UV-sensitive peptide to POI. Our visible light photolabeling can generate photocaged proteins for subsequent activity manipulation by UV light. Cytoskeletal dynamics regulation is demonstrated in living cells via the unprecedented POI photomanipulation and proves that our methodology opens a new avenue to endogenous protein modification.
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Affiliation(s)
- Tzu-Ho Chen
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.,Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Kevin Garnir
- Laboratoire de Chimie Organique et Photochimie CP160/08, Université libre de Bruxelles, 50 Av. Franklin D. Roosevelt, 1050 Brussels, Belgium
| | - Chong-Yan Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Cheng-Bang Jian
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.,Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Hua-De Gao
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.,Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Bill Cheng
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung 40227, Taiwan
| | - Mei-Chun Tseng
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Cécile Moucheron
- Laboratoire de Chimie Organique et Photochimie CP160/08, Université libre de Bruxelles, 50 Av. Franklin D. Roosevelt, 1050 Brussels, Belgium
| | - Andrée Kirsch-De Mesmaeker
- Laboratoire de Chimie Organique et Photochimie CP160/08, Université libre de Bruxelles, 50 Av. Franklin D. Roosevelt, 1050 Brussels, Belgium
| | - Hsien-Ming Lee
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
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28
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Jin G, Sun D, Xia X, Jiang Z, Cheng B, Ning Y, Wang F, Zhao Y, Chen X, Zhang J. Bioorthogonal Lanthanide Molecular Probes for Near‐Infrared Fluorescence and Mass Spectrometry Imaging. Angew Chem Int Ed Engl 2022; 61:e202208707. [DOI: 10.1002/anie.202208707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Guo‐Qing Jin
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
| | - De‐en Sun
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
- Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 P. R. China
| | - Xiaoqian Xia
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
- Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 P. R. China
| | - Zhi‐Fan Jiang
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
- Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 P. R. China
| | - Yingying Ning
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences CAS Research/Education Center for Excellence in Molecular Sciences National Centre for Mass Spectrometry in Beijing CAS Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences CAS Research/Education Center for Excellence in Molecular Sciences National Centre for Mass Spectrometry in Beijing CAS Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Xing Chen
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
- Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 P. R. China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 P. R. China
| | - Jun‐Long Zhang
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
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29
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Jin GQ, Sun DE, Xia X, Jiang ZF, Cheng B, Ning Y, Wang F, Zhao Y, Chen X, Zhang JL. Bioorthogonal Lanthanide Molecular Probes for Near‐Infrared Fluorescence and Mass Spectrometry Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Guo-Qing Jin
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - De-en Sun
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Xiaoqian Xia
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Zhi-Fan Jiang
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Bo Cheng
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Yingying Ning
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Fuyi Wang
- Institute of Chemistry Chinese Academy of Sciences Beijing National Laboratory for Molecular Sciences CHINA
| | - Yao Zhao
- Institute of Chemistry Chinese Academy of Sciences Beijing National Laboratory for Molecular Sciences CHINA
| | - Xing Chen
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Jun-Long Zhang
- Peking University College of Chemistry and Molecular Engineering Chengfu Road 202 100871 Beijing CHINA
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30
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Roßmann K, Akkaya KC, Poc P, Charbonnier C, Eichhorst J, Gonschior H, Valavalkar A, Wendler N, Cordes T, Dietzek-Ivanšić B, Jones B, Lehmann M, Broichhagen J. N-Methyl deuterated rhodamines for protein labelling in sensitive fluorescence microscopy. Chem Sci 2022; 13:8605-8617. [PMID: 35974762 PMCID: PMC9337740 DOI: 10.1039/d1sc06466e] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/02/2022] [Indexed: 11/21/2022] Open
Abstract
Rhodamine fluorophores are setting benchmarks in fluorescence microscopy. Herein, we report the deuterium (d12) congeners of tetramethyl(silicon)rhodamine, obtained by isotopic labelling of the four methyl groups, show improved photophysical parameters (i.e. brightness, lifetimes) and reduced chemical bleaching. We explore this finding for SNAP- and Halo-tag labelling in live cells, and highlight enhanced properties in several applications, such as fluorescence activated cell sorting, fluorescence lifetime microscopy, stimulated emission depletion nanoscopy and single-molecule Förster-resonance energy transfer. We finally extend this idea to other dye families and envision deuteration as a generalizable concept to improve existing and to develop new chemical biology probes.
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Affiliation(s)
- Kilian Roßmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Kerem C Akkaya
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Pascal Poc
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | | | - Jenny Eichhorst
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Hannes Gonschior
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Abha Valavalkar
- Leibniz Institute for Photonic Technology Jena e.V. (Leibniz-IPHT), Research Department Functional Interfaces Jena Germany
| | - Nicolas Wendler
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München Großhaderner Str. 2-4, Planegg-Martinsried 82152 Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München Großhaderner Str. 2-4, Planegg-Martinsried 82152 Germany
| | - Benjamin Dietzek-Ivanšić
- Leibniz Institute for Photonic Technology Jena e.V. (Leibniz-IPHT), Research Department Functional Interfaces Jena Germany
| | - Ben Jones
- Section of Endocrinology and Investigative Medicine, Imperial College London London W12 0NN UK
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
- Department of Chemical Biology, Max Planck Institute for Medical Research Heidelberg Germany
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31
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Lincoln R, Bossi ML, Remmel M, D'Este E, Butkevich AN, Hell SW. A general design of caging-group-free photoactivatable fluorophores for live-cell nanoscopy. Nat Chem 2022; 14:1013-1020. [PMID: 35864152 PMCID: PMC9417988 DOI: 10.1038/s41557-022-00995-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
The controlled switching of fluorophores between non-fluorescent and fluorescent states is central to every super-resolution fluorescence microscopy (nanoscopy) technique, and the exploration of radically new switching mechanisms remains critical to boosting the performance of established, as well as emerging super-resolution methods. Photoactivatable dyes offer substantial improvements to many of these techniques, but often rely on photolabile protecting groups that limit their applications. Here we describe a general method to transform 3,6-diaminoxanthones into caging-group-free photoactivatable fluorophores. These photoactivatable xanthones (PaX) assemble rapidly and cleanly into highly fluorescent, photo- and chemically stable pyronine dyes upon irradiation with light. The strategy is extendable to carbon- and silicon-bridged xanthone analogues, yielding a family of photoactivatable labels spanning much of the visible spectrum. Our results demonstrate the versatility and utility of PaX dyes in fixed and live-cell labelling for conventional microscopy, as well as the coordinate-stochastic and deterministic nanoscopies STED, PALM and MINFLUX. ![]()
The design of photoactivatable fluorophores—which are required for some super-resolution fluorescence microscopy methods—usually relies on light-sensitive protecting groups imparting lipophilicity and generating reactive by-products. Now, it has been shown that by exploiting a unique intramolecular photocyclization, bright and highly photostable fluorophores can be rapidly generated in situ from appropriately substituted 1-alkenyl-3,6-diaminoxanthone precursors.
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Affiliation(s)
- Richard Lincoln
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Mariano L Bossi
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Michael Remmel
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Elisa D'Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Alexey N Butkevich
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany.
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany. .,Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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32
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Ahangarpour M, Kavianinia I, Hume PA, Harris PWR, Brimble MA. N-Vinyl Acrylamides: Versatile Heterobifunctional Electrophiles for Thiol-Thiol Bioconjugations. J Am Chem Soc 2022; 144:13652-13662. [PMID: 35858283 DOI: 10.1021/jacs.2c04146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Herein we report the first examples of thiol-selective heterobifunctional electrophiles, N-vinyl acrylamides, that enable efficient highly selective thiol-thiol bioconjugations and cysteine modification of peptides. We demonstrate that these new classes of thiol-selective scaffolds can readily undergo a thia-Michael addition and an orthogonal radical induced thiol-ene "click" reaction under biocompatible conditions. Furthermore, the formation of an unexpected Markovnikov N,S-acetal hydrothiolation was explained using computational studies. We also reveal that N-methylation of the N-vinyl acrylamide scaffold changes the regioselectivity of the reaction. We demonstrate that use of N-vinyl acrylamides shows promise as an efficient, mild, and exquisite cysteine-selective protocol for facile construction of fluorophore-labeled peptides and proteins and that the resultant conjugates are resistant to degradation and thiol exchange, thus significantly improving their biophysical properties.
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Affiliation(s)
- Marzieh Ahangarpour
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Iman Kavianinia
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Paul A Hume
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Paul W R Harris
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
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33
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Enhanced incorporation of subnanometer tags into cellular proteins for fluorescence nanoscopy via optimized genetic code expansion. Proc Natl Acad Sci U S A 2022; 119:e2201861119. [PMID: 35858298 PMCID: PMC9304028 DOI: 10.1073/pnas.2201861119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With few-nanometer resolution recently achieved by a new generation of fluorescence nanoscopes (MINFLUX and MINSTED), the size of the tags used to label proteins will increasingly limit the ability to dissect nanoscopic biological structures. Bioorthogonal (click) chemical groups are powerful tools for the specific detection of biomolecules. Through the introduction of an engineered aminoacyl–tRNA synthetase/tRNA pair (tRNA: transfer ribonucleic acid), genetic code expansion allows for the site-specific introduction of amino acids with “clickable” side chains into proteins of interest. Well-defined label positions and the subnanometer scale of the protein modification provide unique advantages over other labeling approaches for imaging at molecular-scale resolution. We report that, by pairing a new N-terminally optimized pyrrolysyl–tRNA synthetase (chPylRS
2020
) with a previously engineered orthogonal tRNA, clickable amino acids are incorporated with improved efficiency into bacteria and into mammalian cells. The resulting enhanced genetic code expansion machinery was used to label β-actin in U2OS cell filopodia for MINFLUX imaging with minimal separation of fluorophores from the protein backbone. Selected data were found to be consistent with previously reported high-resolution information from cryoelectron tomography about the cross-sectional filament bundling architecture. Our study underscores the need for further improvements to the degree of labeling with minimal-offset methods in order to fully exploit molecular-scale optical three-dimensional resolution.
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34
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Abstract
![]()
There is a continuous demand to improve our
understanding of fundamental
processes that underlie human health and disease. Therefore, novel
strategies that can assist in these efforts are required. For example,
molecular biology and genetic approaches have revolutionized our understanding
of protein-mediated processes by facilitating their direct visualization
and analyses in living cells. Despite these developments, genetic
manipulation has limitations in controlling events that occur after
translation such as posttranslational modifications (PTMs), which
are imperative regulatory elements. As a result, developing new methods
to study PTMs in live cells is a major bottleneck in deciphering their
exact roles in the myriad cellular processes. Synthetic and
semisynthetic proteins are prepared by combining
solid phase peptide synthesis (SPPS) and chemoselective ligation approaches
with synthetic or recombinant peptides. Employing protein synthesis
allows chemists to incorporate natural and unnatural modifications
with virtually unlimited number of functional groups into the protein’s
sequence, such as PTMs and their mimics. In addition, synthetic proteins
can include additional elements such as fluorescent tags, reactive
groups, caged units, and enrichment handles. Therefore, harnessing
the power of chemical protein synthesis offers great opportunities
to study fundamental biological processes. Unfortunately, the
low cell permeability of proteins limits their
applications mainly to in vitro settings, excluding
live cell studies. As a result, chemical biologists have been attempting
to overcome these limitations by developing protein delivery methods
that would enable the study of custom-made proteins in a biological
context. Success with these strategies should enable accurate determination
of protein localization, degradation, folding, interactions, and involvement
in the assembly of membrane-less organelles formed by liquid–liquid
phase separation inside cells. Importantly, protein delivery approaches
are complementary to genetic manipulations, and combining these approaches
should pave the way to new discoveries. In this Account, we
describe recent developments in protein delivery
methods, with emphasis on those most compatible with synthetic proteins.
We highlight experimental approaches and conceptual adaptations required
to design and study synthetic proteins in live cells, with or without
genetic manipulation. In addition, we highlight the strength and weakness
of these approaches for both the delivery and the subsequent studies.
We also describe our endeavors to deliver synthetic proteins to cells
via cell penetrating peptides (CPPs) and multiplexed bead loading
(MBL), as showcases of the applications of these methods to shed light
on biological processes. Lastly, we contemplate other future applications
of synthetic proteins to answer questions that are currently unapproachable.
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Affiliation(s)
- Guy Mann
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Pradeep Sadhu
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
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35
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Istrate A, Geeson MB, Navo CD, Sousa BB, Marques MC, Taylor RJ, Journeaux T, Oehler SR, Mortensen MR, Deery MJ, Bond AD, Corzana F, Jiménez-Osés G, Bernardes GJL. Platform for Orthogonal N-Cysteine-Specific Protein Modification Enabled by Cyclopropenone Reagents. J Am Chem Soc 2022; 144:10396-10406. [PMID: 35658467 PMCID: PMC9490850 DOI: 10.1021/jacs.2c02185] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein conjugates are valuable tools for studying biological processes or producing therapeutics, such as antibody-drug conjugates. Despite the development of several protein conjugation strategies in recent years, the ability to modify one specific amino acid residue on a protein in the presence of other reactive side chains remains a challenge. We show that monosubstituted cyclopropenone (CPO) reagents react selectively with the 1,2-aminothiol groups of N-terminal cysteine residues to give a stable 1,4-thiazepan-5-one linkage under mild, biocompatible conditions. The CPO-based reagents, all accessible from a common activated ester CPO-pentafluorophenol (CPO-PFP), allow selective modification of N-terminal cysteine-containing peptides and proteins even in the presence of internal, solvent-exposed cysteine residues. This approach enabled the preparation of a dual protein conjugate of 2×cys-GFP, containing both internal and N-terminal cysteine residues, by first modifying the N-terminal residue with a CPO-based reagent followed by modification of the internal cysteine with a traditional cysteine-modifying reagent. CPO-based reagents enabled a copper-free click reaction between two proteins, producing a dimer of a de novo protein mimic of IL2 that binds to the β-IL2 receptor with low nanomolar affinity. Importantly, the reagents are compatible with the common reducing agent dithiothreitol (DTT), a useful property for working with proteins prone to dimerization. Finally, quantum mechanical calculations uncover the origin of selectivity for CPO-based reagents for N-terminal cysteine residues. The ability to distinguish and specifically target N-terminal cysteine residues on proteins facilitates the construction of elaborate multilabeled bioconjugates with minimal protein engineering.
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Affiliation(s)
- Alena Istrate
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Michael B Geeson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Barbara B Sousa
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marta C Marques
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ross J Taylor
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Toby Journeaux
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Sebastian R Oehler
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Michael R Mortensen
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Michael J Deery
- Cambridge Centre for Proteomics, Gleeson Building, University of Cambridge, Tennis Court Road, CB2 1QR Cambridge, United Kingdom
| | - Andrew D Bond
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006 Logroño, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Gonçalo J L Bernardes
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom.,Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
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36
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Lee Y, Kim D, Park SB. Systematic Exploration of Furoindolizine‐Based Molecular Frameworks towards a Versatile Fluorescent Platform. Chemistry 2022; 28:e202200533. [DOI: 10.1002/chem.202200533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Youngjun Lee
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Dahham Kim
- CRI Center for Chemical Proteomics, Department of Chemistry Seoul National University Seoul 08826 Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics, Department of Chemistry Seoul National University Seoul 08826 Korea
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37
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Farrants H, Tebo AG. Fluorescent chemigenetic actuators and indicators for use in living animals. Curr Opin Pharmacol 2022; 62:159-167. [DOI: 10.1016/j.coph.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/03/2021] [Accepted: 12/12/2021] [Indexed: 11/28/2022]
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38
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Magg V, Klein P, Ruggieri A. Monitoring Virus-Induced Stress Granule Dynamics Using Long-Term Live-Cell Imaging. Methods Mol Biol 2022; 2428:325-348. [PMID: 35171489 DOI: 10.1007/978-1-0716-1975-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The integrated stress response is a highly regulated signaling cascade that allows cells to react to a variety of external and internal stimuli. Activation of different stress-responsive kinases leads to the phosphorylation of their common downstream target, the eukaryotic translation initiation factor 2 alpha (eIF2α), which is a critical component of functional translation preinitiation complexes. As a consequence, stalled ribonucleoprotein complexes accumulate in the cytoplasm and condense into microscopically visible cytoplasmic stress granules (SGs). Over the past years, numerous microscopy approaches have been developed to study the spatiotemporal control of SG formation in response to a variety of stressors. Here, we apply long-term live-cell microscopy to monitor the dynamic cellular stress response triggered by infection with chronic hepatitis C virus (HCV) at single-cell level and study the behavior of infected cells that repeatedly switch between a stressed and unstressed state. We describe in detail the engineering of fluorescent SG-reporter cells expressing enhanced yellow fluorescent protein (YFP)-tagged T cell internal antigen 1 (TIA-1) using lentiviral delivery, as well as the production of mCherry-tagged HCV trans-complemented particles, which allow live tracking of SG assembly and disassembly, SG number and size in single infected cells over time.
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Affiliation(s)
- Vera Magg
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany
| | - Philipp Klein
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany.
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39
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Reddi RN, Rogel A, Resnick E, Gabizon R, Prasad PK, Gurwicz N, Barr H, Shulman Z, London N. Site-Specific Labeling of Endogenous Proteins Using CoLDR Chemistry. J Am Chem Soc 2021; 143:20095-20108. [PMID: 34817989 PMCID: PMC8662641 DOI: 10.1021/jacs.1c06167] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Chemical modifications
of native proteins can affect their stability,
activity, interactions, localization, and more. However, there are
few nongenetic methods for the installation of chemical modifications
at a specific protein site in cells. Here we report a covalent ligand
directed release (CoLDR) site-specific labeling strategy, which enables
the installation of a variety of functional tags on a target protein
while releasing the directing ligand. Using this approach, we were
able to label various proteins such as BTK, K-RasG12C,
and SARS-CoV-2 PLpro with different tags. For BTK we have
shown selective labeling in cells of both alkyne and fluorophores
tags. Protein labeling by traditional affinity methods often inhibits
protein activity since the directing ligand permanently occupies the
target binding pocket. We have shown that using CoLDR chemistry, modification
of BTK by these probes in cells preserves its activity. We demonstrated
several applications for this approach including determining the half-life
of BTK in its native environment with minimal perturbation, as well
as quantification of BTK degradation by a noncovalent proteolysis
targeting chimera (PROTAC) by in-gel fluorescence. Using an environment-sensitive
“turn-on” fluorescent probe, we were able to monitor
ligand binding to the active site of BTK. Finally, we have demonstrated
efficient CoLDR-based BTK PROTACs (DC50 < 100 nM), which
installed a CRBN binder onto BTK. This approach joins very few available
labeling strategies that maintain the target protein activity and
thus makes an important addition to the toolbox of chemical biology.
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Affiliation(s)
- Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Efrat Resnick
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Pragati Kishore Prasad
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Neta Gurwicz
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Barr
- Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ziv Shulman
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
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40
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Selective and predicable amine conjugation sites by kinetic characterization under excess reagents. Sci Rep 2021; 11:21222. [PMID: 34707190 PMCID: PMC8551328 DOI: 10.1038/s41598-021-00743-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/12/2021] [Indexed: 11/09/2022] Open
Abstract
The site selectivity for lysine conjugation on a native protein is difficult to control and characterize. Here, we applied mass spectrometry to examine the conjugation kinetics of Trastuzumab-IgG (Her-IgG) and α-lactalbumin under excess linker concentration ([L]0) based on the modified Michaelis–Menten equation, in which the initial rate constant per amine (kNH2 = Vmax/NH2/KM) was determined by the maximum reaction rate (Vmax/NH2) under saturated accessible sites and initial amine–linker affinity (1/KM). Reductive amination (RA) displayed 3–4 times greater Vmax/NH2 and a different panel of conjugation sites than that observed for N-hydroxysuccinimide ester (NHS) chemistry using the same length of polyethylene glycol (PEG) linkers. Moreover, faster conversion power rendered RA site selectivity among accessible amine groups and a greater tunable range of linker/protein ratio for aldehyde-linkers compared to those of the same length of NHS-linkers. Single conjugation with high yield or poly-conjugations with site homogeneity was demonstrated by controlling [L]0 or gradual addition to minimize the [L]0/KM ratio. Formaldehyde, the shortest aldehyde-linker with the greatest 1/KM, exhibited the highest selectivity and was shown to be a suitable probe to predict conjugation profile of aldehyde-linkers. Four linkers on the few probe-predicted hot spots were elucidated by kinetically controlled RA with conserved drug efficacy when conjugated with the payload. This study provides insights into controlling factors for homogenous and predictable amine bioconjugation.
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41
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Lardon N, Wang L, Tschanz A, Hoess P, Tran M, D'Este E, Ries J, Johnsson K. Systematic Tuning of Rhodamine Spirocyclization for Super-resolution Microscopy. J Am Chem Soc 2021; 143:14592-14600. [PMID: 34460256 DOI: 10.1021/jacs.1c05004] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Rhodamines are the most important class of fluorophores for applications in live-cell fluorescence microscopy. This is mainly because rhodamines exist in a dynamic equilibrium between a fluorescent zwitterion and a nonfluorescent but cell-permeable spirocyclic form. Different imaging applications require different positions of this dynamic equilibrium, and an adjustment of the equilibrium poses a challenge for the design of suitable probes. We describe here how the conversion of the ortho-carboxy moiety of a given rhodamine into substituted acyl benzenesulfonamides and alkylamides permits the systematic tuning of the equilibrium of spirocyclization with unprecedented accuracy and over a large range. This allows one to transform the same rhodamine into either a highly fluorogenic and cell-permeable probe for live-cell-stimulated emission depletion (STED) microscopy or a spontaneously blinking dye for single-molecule localization microscopy (SMLM). We used this approach to generate differently colored probes optimized for different labeling systems and imaging applications.
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Affiliation(s)
- Nicolas Lardon
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Faculty of Chemistry and Earth Sciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Lu Wang
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Zhangheng Road 826, 201203 Shanghai, China
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | - Philipp Hoess
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | - Mai Tran
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Elisa D'Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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42
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Gautier A, Jullien L, Li C, Plamont MA, Tebo AG, Thauvin M, Volovitch M, Vriz S. Versatile On-Demand Fluorescent Labeling of Fusion Proteins Using Fluorescence-Activating and Absorption-Shifting Tag (FAST). Methods Mol Biol 2021; 2350:253-265. [PMID: 34331290 DOI: 10.1007/978-1-0716-1593-5_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Observing the localization, the concentration, and the distribution of proteins in cells or organisms is essential to understand theirs functions. General and versatile methods allowing multiplexed imaging of proteins under a large variety of experimental conditions are thus essential for deciphering the inner workings of cells and organisms. Here, we present a general method based on the non-covalent labeling of a small protein tag, named FAST (fluorescence-activating and absorption-shifting tag), with various fluorogenic ligands that light up upon labeling, which makes the simple, robust, and versatile on-demand labeling of fusion proteins in a wide range of experimental systems possible.
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Affiliation(s)
- Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, Paris, France.
- Institut Universitaire de France, Paris, France.
| | - Ludovic Jullien
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, Paris, France
| | - Chenge Li
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, Paris, France
- Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Marie-Aude Plamont
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, Paris, France
| | - Alison G Tebo
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, Paris, France
- Janelia Farms Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Marion Thauvin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Michel Volovitch
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
- Department of Biology, École Normale Supérieure, Université PSL, Paris, France
| | - Sophie Vriz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
- Faculty of Science, Université de Paris, Paris, France
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43
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Wilhelm J, Kühn S, Tarnawski M, Gotthard G, Tünnermann J, Tänzer T, Karpenko J, Mertes N, Xue L, Uhrig U, Reinstein J, Hiblot J, Johnsson K. Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag. Biochemistry 2021; 60:2560-2575. [PMID: 34339177 PMCID: PMC8388125 DOI: 10.1021/acs.biochem.1c00258] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/23/2021] [Indexed: 01/16/2023]
Abstract
The self-labeling protein tags (SLPs) HaloTag7, SNAP-tag, and CLIP-tag allow the covalent labeling of fusion proteins with synthetic molecules for applications in bioimaging and biotechnology. To guide the selection of an SLP-substrate pair and provide guidelines for the design of substrates, we report a systematic and comparative study of the labeling kinetics and substrate specificities of HaloTag7, SNAP-tag, and CLIP-tag. HaloTag7 reaches almost diffusion-limited labeling rate constants with certain rhodamine substrates, which are more than 2 orders of magnitude higher than those of SNAP-tag for the corresponding substrates. SNAP-tag labeling rate constants, however, are less affected by the structure of the label than those of HaloTag7, which vary over 6 orders of magnitude for commonly employed substrates. Determining the crystal structures of HaloTag7 and SNAP-tag labeled with fluorescent substrates allowed us to rationalize their substrate preferences. We also demonstrate how these insights can be exploited to design substrates with improved labeling kinetics.
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Affiliation(s)
- Jonas Wilhelm
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Stefanie Kühn
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein
Expression and Characterization Facility, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Guillaume Gotthard
- Structural
Biology Group, European Synchrotron Radiation
Facility (ESRF), 38043 Grenoble, France
| | - Jana Tünnermann
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Timo Tänzer
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Julie Karpenko
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Nicole Mertes
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Lin Xue
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Ulrike Uhrig
- Chemical
Biology Core Facility, European Molecular
Biology Laboratory, 69117 Heidelberg, Germany
| | - Jochen Reinstein
- Department
of Biomolecular Mechanisms, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Julien Hiblot
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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44
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Gavins GC, Gröger K, Reimann M, Bartoschek MD, Bultmann S, Seitz O. Orthogonal coiled coils enable rapid covalent labelling of two distinct membrane proteins with peptide nucleic acid barcodes. RSC Chem Biol 2021; 2:1291-1295. [PMID: 34458843 PMCID: PMC8341593 DOI: 10.1039/d1cb00126d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 12/13/2022] Open
Abstract
Templated chemistry offers the prospect of addressing specificity challenges occurring in bioconjugation reactions. Here, we show two peptide-templated amide-bond forming reactions that enable the concurrent labelling of two different membrane proteins with two different peptide nucleic acid (PNA) barcodes. The reaction system is based on the mutually selective coiled coil interaction between two thioester-linked PNA–peptide conjugates and two cysteine peptides serving as genetically encoded peptide tags. Orthogonal coiled coil templated covalent labelling is highly specific, quantitative and proceeds within a minute. To demonstrate the usefulness, we evaluated receptor internalisation of two membranous receptors EGFR (epidermal growth factor) and ErbB2 (epidermal growth factor receptor 2) by first staining PNA-tagged proteins with fluorophore–DNA conjugates and then erasing signals from non-internalized receptors via toehold-mediated strand displacement. A pair of orthogonal coiled coils templates highly specific live cell bioconjugation of two different proteins. PNA tagging and hybridisation with fluorophore–DNA reporters enables rapid dual receptor internalisation analysis of EGFR and ErbB2.![]()
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Affiliation(s)
- Georgina C Gavins
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
| | - Katharina Gröger
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
| | - Marc Reimann
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
| | - Michael D Bartoschek
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstr. 1 Munich 81377 Germany
| | - Sebastian Bultmann
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstr. 1 Munich 81377 Germany
| | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 Berlin 12489 Germany
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45
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Broichhagen J, Kilian N. Chemical Biology Tools To Investigate Malaria Parasites. Chembiochem 2021; 22:2219-2236. [PMID: 33570245 PMCID: PMC8360121 DOI: 10.1002/cbic.202000882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/10/2021] [Indexed: 02/06/2023]
Abstract
Parasitic diseases like malaria tropica have been shaping human evolution and history since the beginning of mankind. After infection, the response of the human host ranges from asymptomatic to severe and may culminate in death. Therefore, proper examination of the parasite's biology is pivotal to deciphering unique molecular, biochemical and cell biological processes, which in turn ensure the identification of treatment strategies, such as potent drug targets and vaccine candidates. However, implementing molecular biology methods for genetic manipulation proves to be difficult for many parasite model organisms. The development of fast and straightforward applicable alternatives, for instance small-molecule probes from the field of chemical biology, is essential. In this review, we will recapitulate the highlights of previous molecular and chemical biology approaches that have already created insight and understanding of the malaria parasite Plasmodium falciparum. We discuss current developments from the field of chemical biology and explore how their application could advance research into this parasite in the future. We anticipate that the described approaches will help to close knowledge gaps in the biology of P. falciparum and we hope that researchers will be inspired to use these methods to gain knowledge - with the aim of ending this devastating disease.
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Affiliation(s)
- Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Roessle-Strasse 1013125BerlinGermany
| | - Nicole Kilian
- Centre for Infectious DiseasesParasitologyHeidelberg University HospitalIm Neuenheimer Feld 32469120HeidelbergGermany
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46
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Mariam J, Hoskere Ashoka A, Gaded V, Ali F, Malvi H, Das A, Anand R. Deciphering protein microenvironment by using a cysteine specific switch-ON fluorescent probe. Org Biomol Chem 2021; 19:5161-5168. [PMID: 34037063 DOI: 10.1039/d1ob00698c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescent probes provide an unparalleled opportunity to visualize and quantify dynamic events. Here, we employ a medium-size, cysteine specific coumarin based switch-ON fluorescent probe 'L' to track protein unfolding profiles and accessibility of cysteine residues in proteins. It was established that 'L' is highly selective and exhibits no artifact due to interaction with other bystander species. 'L' is able to gauge subtle changes in protein microenvironment and proved to be effective in delineating early unfolding events that are difficult to otherwise discern by classic techniques such as circular dichroism. By solving the X-ray structure of TadA and probing the temperature dependent fluorescence-ON response with native TadA and its cysteine mutants, it was revealed that unfolding occurs in a stage-wise manner and the regions that are functionally important form compact sub-domains and unfold at later stages. Our results assert that probe 'L' serves as an efficient tool to monitor subtle changes in protein structure and can be employed as a generic dye to study processes such as protein unfolding.
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Affiliation(s)
- Jessy Mariam
- Department of Chemistry, IIT Bombay, Mumbai-400076, India.
| | - Anila Hoskere Ashoka
- Analytical Science Discipline, CSIR-Central Salt and Marine Chemicals Research Institute, G.B. Marg, Bhavnagar: 364002, Gujarat, India
| | - Vandana Gaded
- Department of Chemistry, IIT Bombay, Mumbai-400076, India.
| | - Firoj Ali
- Analytical Science Discipline, CSIR-Central Salt and Marine Chemicals Research Institute, G.B. Marg, Bhavnagar: 364002, Gujarat, India
| | - Harshada Malvi
- Department of Chemistry, IIT Bombay, Mumbai-400076, India.
| | - Amitava Das
- Analytical Science Discipline, CSIR-Central Salt and Marine Chemicals Research Institute, G.B. Marg, Bhavnagar: 364002, Gujarat, India and Department of Chemical Sciences, Indian Institute of Science and Education Research, Kolkata, Mohanpur: 742246, India.
| | - Ruchi Anand
- Department of Chemistry, IIT Bombay, Mumbai-400076, India.
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47
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De Rosa L, Di Stasi R, Romanelli A, D’Andrea LD. Exploiting Protein N-Terminus for Site-Specific Bioconjugation. Molecules 2021; 26:3521. [PMID: 34207845 PMCID: PMC8228110 DOI: 10.3390/molecules26123521] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022] Open
Abstract
Although a plethora of chemistries have been developed to selectively decorate protein molecules, novel strategies continue to be reported with the final aim of improving selectivity and mildness of the reaction conditions, preserve protein integrity, and fulfill all the increasing requirements of the modern applications of protein conjugates. The targeting of the protein N-terminal alpha-amine group appears a convenient solution to the issue, emerging as a useful and unique reactive site universally present in each protein molecule. Herein, we provide an updated overview of the methodologies developed until today to afford the selective modification of proteins through the targeting of the N-terminal alpha-amine. Chemical and enzymatic strategies enabling the selective labeling of the protein N-terminal alpha-amine group are described.
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Affiliation(s)
- Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy; (L.D.R.); (R.D.S.)
| | - Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy; (L.D.R.); (R.D.S.)
| | - Alessandra Romanelli
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy;
| | - Luca Domenico D’Andrea
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR Via M. Bianco 9, 20131 Milano, Italy
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48
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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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49
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Tuang S, Dieppa-Matos D, Zhang C, Shugrue CR, Dai P, Loas A, Pentelute BL. A reactive peptide interface for site-selective cysteine bioconjugation. Chem Commun (Camb) 2021; 57:3227-3230. [PMID: 33645592 DOI: 10.1039/d1cc00095k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report aqueous, site-selective modification of proteins using a reactive peptide interface comprising a nine-residue sequence. This interface is the fastest (second-order rate constant of 152 M-1 s-1) catalyst-free, cysteine-based method for modifying proteins available to date, and enables near-quantitative labeling of antibodies in cell lysate.
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Affiliation(s)
- Suan Tuang
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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50
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Laxman P, Ansari S, Gaus K, Goyette J. The Benefits of Unnatural Amino Acid Incorporation as Protein Labels for Single Molecule Localization Microscopy. Front Chem 2021; 9:641355. [PMID: 33842432 PMCID: PMC8027105 DOI: 10.3389/fchem.2021.641355] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/26/2021] [Indexed: 01/07/2023] Open
Abstract
Single Molecule Localization Microscopy (SMLM) is an imaging method that allows for the visualization of structures smaller than the diffraction limit of light (~200 nm). This is achieved through techniques such as stochastic optical reconstruction microscopy (STORM) and photoactivated localization microscopy (PALM). A large part of obtaining ideal imaging of single molecules is the choice of the right fluorescent label. An upcoming field of protein labeling is incorporating unnatural amino acids (UAAs) with an attached fluorescent dye for precise localization and visualization of individual molecules. For this technique, fluorescent probes are conjugated to UAAs and are introduced into the protein of interest (POI) as a label. Here we contrast this labeling method with other commonly used protein-based labeling methods such as fluorescent proteins (FPs) or self-labeling tags such as Halotag, SNAP-tags, and CLIP-tags, and highlight the benefits and shortcomings of the site-specific incorporation of UAAs coupled with fluorescent dyes in SMLM.
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Affiliation(s)
| | | | | | - Jesse Goyette
- European Molecular Biology Laboratory (EMBL) Australia Node in Single Molecule Sciences, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
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