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Poulou E, Hackenberger CPR. Staudinger Ligation and Reactions – From Bioorthogonal Labeling to Next‐Generation Biopharmaceuticals. Isr J Chem 2022. [DOI: 10.1002/ijch.202200057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eleftheria Poulou
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Department of Chemistry Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
- Department of Chemistry Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
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2
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Single-molecule FRET uncovers hidden conformations and dynamics of human Argonaute 2. Nat Commun 2022; 13:3825. [PMID: 35780145 PMCID: PMC9250533 DOI: 10.1038/s41467-022-31480-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 06/10/2022] [Indexed: 11/10/2022] Open
Abstract
Human Argonaute 2 (hAgo2) constitutes the functional core of the RNA interference pathway. Guide RNAs direct hAgo2 to target mRNAs, which ultimately leads to hAgo2-mediated mRNA degradation or translational inhibition. Here, we combine site-specifically labeled hAgo2 with time-resolved single-molecule FRET measurements to monitor conformational states and dynamics of hAgo2 and hAgo2-RNA complexes in solution that remained elusive so far. We observe dynamic anchoring and release of the guide’s 3’-end from the PAZ domain during the stepwise target loading process even with a fully complementary target. We find differences in structure and dynamic behavior between partially and fully paired canonical hAgo2-guide/target complexes and the miRNA processing complex formed by hAgo2 and pre-miRNA451. Furthermore, we detect a hitherto unknown conformation of hAgo2-guide/target complexes that poises them for target-directed miRNA degradation. Taken together, our results show how the conformational flexibility of hAgo2-RNA complexes determines function and the fate of the ribonucleoprotein particle. Single-molecule FRET measurements provide detailed insights into the conformational states and dynamics of human Argonaute 2 that are required for its function at the core of the eukaryotic RNA silencing pathway.
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3
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Meineke B, Heimgärtner J, Craig AJ, Landreh M, Moodie LWK, Elsässer SJ. A Genetically Encoded Picolyl Azide for Improved Live Cell Copper Click Labeling. Front Chem 2021; 9:768535. [PMID: 34858945 PMCID: PMC8632528 DOI: 10.3389/fchem.2021.768535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
Bioorthogonal chemistry allows rapid and highly selective reactivity in biological environments. The copper-catalyzed azide–alkyne cycloaddition (CuAAC) is a classic bioorthogonal reaction routinely used to modify azides or alkynes that have been introduced into biomolecules. Amber suppression is an efficient method for incorporating such chemical handles into proteins on the ribosome, in which noncanonical amino acids (ncAAs) are site specifically introduced into the polypeptide in response to an amber (UAG) stop codon. A variety of ncAA structures containing azides or alkynes have been proven useful for performing CuAAC chemistry on proteins. To improve CuAAC efficiency, biologically incorporated alkyne groups can be reacted with azide substrates that contain copper-chelating groups. However, the direct incorporation of copper-chelating azides into proteins has not been explored. To remedy this, we prepared the ncAA paz-lysine (PazK), which contains a picolyl azide motif. We show that PazK is efficiently incorporated into proteins by amber suppression in mammalian cells. Furthermore, PazK-labeled proteins show improved reactivity with alkyne reagents in CuAAC.
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Affiliation(s)
- Birthe Meineke
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden
| | - Johannes Heimgärtner
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden
| | - Alexander J Craig
- Drug Design and Discovery, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Lindon W K Moodie
- Drug Design and Discovery, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden.,Uppsala Antibiotic Centre, Uppsala University, Uppsala, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden
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4
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Kowalski-Jahn M, Schihada H, Turku A, Huber T, Sakmar TP, Schulte G. Frizzled BRET sensors based on bioorthogonal labeling of unnatural amino acids reveal WNT-induced dynamics of the cysteine-rich domain. SCIENCE ADVANCES 2021; 7:eabj7917. [PMID: 34757789 PMCID: PMC8580317 DOI: 10.1126/sciadv.abj7917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Frizzleds (FZD1–10) are G protein–coupled receptors containing an extracellular cysteine-rich domain (CRD) binding Wingless/Int-1 lipoglycoproteins (WNTs). Despite the role of WNT/FZD signaling in health and disease, our understanding of how WNT binding is translated into receptor activation and transmembrane signaling remains limited. Current hypotheses dispute the roles for conformational dynamics. To clarify how WNT binding to FZD translates into receptor dynamics, we devised conformational FZD-CRD biosensors based on bioluminescence resonance energy transfer (BRET). Using FZD with N-terminal nanoluciferase (Nluc) and fluorescently labeled unnatural amino acids in the linker domain and extracellular loop 3, we show that WNT-3A and WNT-5A induce similar CRD conformational rearrangements despite promoting distinct signaling pathways and that CRD dynamics are not required for WNT/β-catenin signaling. Thus, these FZD-CRD biosensors provide insights into binding, activation, and signaling processes in FZDs. The sensor design is broadly applicable to explore ligand-induced dynamics also in other membrane receptors.
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Affiliation(s)
- Maria Kowalski-Jahn
- Karolinska Institutet, Department of Physiology and Pharmacology, Section of Receptor Biology and Signaling, Biomedicum 6D, S-17165 Stockholm, Sweden
| | - Hannes Schihada
- Karolinska Institutet, Department of Physiology and Pharmacology, Section of Receptor Biology and Signaling, Biomedicum 6D, S-17165 Stockholm, Sweden
| | - Ainoleena Turku
- Karolinska Institutet, Department of Physiology and Pharmacology, Section of Receptor Biology and Signaling, Biomedicum 6D, S-17165 Stockholm, Sweden
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
- Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, S-17164 Stockholm, Sweden
| | - Gunnar Schulte
- Karolinska Institutet, Department of Physiology and Pharmacology, Section of Receptor Biology and Signaling, Biomedicum 6D, S-17165 Stockholm, Sweden
- Corresponding author.
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5
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Heiss TK, Dorn RS, Prescher JA. Bioorthogonal Reactions of Triarylphosphines and Related Analogues. Chem Rev 2021; 121:6802-6849. [PMID: 34101453 PMCID: PMC10064493 DOI: 10.1021/acs.chemrev.1c00014] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bioorthogonal phosphines were introduced in the context of the Staudinger ligation over 20 years ago. Since that time, phosphine probes have been used in myriad applications to tag azide-functionalized biomolecules. The Staudinger ligation also paved the way for the development of other phosphorus-based chemistries, many of which are widely employed in biological experiments. Several reviews have highlighted early achievements in the design and application of bioorthogonal phosphines. This review summarizes more recent advances in the field. We discuss innovations in classic Staudinger-like transformations that have enabled new biological pursuits. We also highlight relative newcomers to the bioorthogonal stage, including the cyclopropenone-phosphine ligation and the phospha-Michael reaction. The review concludes with chemoselective reactions involving phosphite and phosphonite ligations. For each transformation, we describe the overall mechanism and scope. We also showcase efforts to fine-tune the reagents for specific functions. We further describe recent applications of the chemistries in biological settings. Collectively, these examples underscore the versatility and breadth of bioorthogonal phosphine reagents.
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6
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Xiong M, Liu Q, Tang D, Liu L, Kong G, Fu X, Yang C, Lyu Y, Meng HM, Ke G, Zhang XB. “Apollo Program” in Nanoscale: Landing and Exploring Cell-Surface with DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2020; 3:2723-2742. [DOI: 10.1021/acsabm.9b01193] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Qin Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Decui Tang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Xiaoyi Fu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Chan Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Hong-Min Meng
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
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7
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Quast RB, Margeat E. Studying GPCR conformational dynamics by single molecule fluorescence. Mol Cell Endocrinol 2019; 493:110469. [PMID: 31163201 DOI: 10.1016/j.mce.2019.110469] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 02/07/2023]
Abstract
Over the last decades, G protein coupled receptors (GPCRs) have experienced a tremendous amount of attention, which has led to a boost of structural and pharmacological insights on this large membrane protein superfamily involved in various essential physiological functions. Recently, evidence has emerged that, rather than being activated by ligands in an on/off manner switching from an inactive to an active state, GPCRs exhibit high structural flexibility in the absence and even in the presence of ligands. So far the physiological as well as pharmacological impact of this structural flexibility remains largely unexplored albeit its potential role in precisely fine-tuning receptor function and regulating the specificity of signal transduction into the cell. By complementing other biophysical approaches, single molecule fluorescence (SMF) offers the advantage of monitoring structural dynamics in biomolecules in real-time, with minimal structural invasiveness and in the context of complex biological environments. In this review a general introduction to GPCR structural dynamics is given followed by a presentation of SMF methods used to explore them. Particular attention is paid to single molecule Förster resonance energy transfer (smFRET), a key method to measure actual distance changes between two probes, and highlight conformational changes occurring at timescales relevant for protein conformational movements. The available literature reporting on GPCR structural dynamics by SMF is discussed with a focus on the newly gained biological insights on receptor activation and signaling, in particular for the β2 adrenergic and the metabotropic glutamate receptors.
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Affiliation(s)
- Robert B Quast
- CBS, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Emmanuel Margeat
- CBS, CNRS, INSERM, Université de Montpellier, Montpellier, France.
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8
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Nödling AR, Spear LA, Williams TL, Luk LYP, Tsai YH. Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells. Essays Biochem 2019; 63:237-266. [PMID: 31092687 PMCID: PMC6610526 DOI: 10.1042/ebc20180042] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.
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Affiliation(s)
| | - Luke A Spear
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Thomas L Williams
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
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9
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Serfling R, Seidel L, Bock A, Lohse MJ, Annibale P, Coin I. Quantitative Single-Residue Bioorthogonal Labeling of G Protein-Coupled Receptors in Live Cells. ACS Chem Biol 2019; 14:1141-1149. [PMID: 31074969 DOI: 10.1021/acschembio.8b01115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
High-end microscopy studies of G protein-coupled receptors (GPCRs) require installing onto the receptors bright and photostable dyes. Labeling must occur in quantitative yields, to allow stoichiometric data analysis, and in a minimally invasive fashion, to avoid perturbing GPCR function. We demonstrate here that the genetic incorporation of trans-cyclooct-2-ene lysine (TCO*) allows achieving quantitative single-residue labeling of the extracellular loops of the β2-adrenergic and the muscarinic M2 class A GPCRs, as well as of the corticotropin releasing factor class B GPCR. Labeling occurs within a few minutes by reaction with dye-tetrazine conjugates on the surface of live cells and preserves the functionality of the receptors. To precisely quantify the labeling yields, we devise a method based on fluorescence fluctuation microscopy that extracts the number of labeling sites at the single-cell level. Further, we show that single-residue labeling is better suited for studies of GPCR diffusion than fluorescent-protein tags, since the latter can affect the mobility of the receptor. Finally, by performing dual-color competitive labeling on a single TCO* site, we devise a method to estimate the oligomerization state of a GPCR without the need for a biological monomeric reference, which facilitates the application of fluorescence methods to oligomerization studies. As TCO* and the dye-tetrazines used in this study are commercially available and the described microscopy techniques can be performed on a commercial microscope, we expect our approach to be widely applicable to fluorescence microscopy studies of membrane proteins in general.
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Affiliation(s)
- Robert Serfling
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
| | - Lisa Seidel
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
| | - Andreas Bock
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Martin J. Lohse
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Paolo Annibale
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Irene Coin
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
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10
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Krause BS, Kaufmann JCD, Kuhne J, Vierock J, Huber T, Sakmar TP, Gerwert K, Bartl FJ, Hegemann P. Tracking Pore Hydration in Channelrhodopsin by Site-Directed Infrared-Active Azido Probes. Biochemistry 2019; 58:1275-1286. [DOI: 10.1021/acs.biochem.8b01211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Benjamin S. Krause
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Joel C. D. Kaufmann
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
- Institut für medizinische Physik und Biophysik, Charité-Universitätsmedizin, Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jens Kuhne
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Johannes Vierock
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Thomas Huber
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Alfred Nobels Allé 23, 141 57 Huddinge, Sweden
| | - Klaus Gerwert
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Franz J. Bartl
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
- Institut für medizinische Physik und Biophysik, Charité-Universitätsmedizin, Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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11
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Cheng L, Kang X, Wang D, Gao Y, Yi L, Xi Z. The one-pot nonhydrolysis Staudinger reaction and Staudinger or SPAAC ligation. Org Biomol Chem 2019; 17:5675-5679. [DOI: 10.1039/c9ob00528e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The one-pot nonhydrolysis Staudinger reaction and Staudinger or SPAAC ligation were used for producing a FRET-based dyad in living cells as a proof-of-concept study.
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Affiliation(s)
- Longhuai Cheng
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology
- National Engineering Research Center of Pesticide (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Xueying Kang
- State Key Laboratory of Organic–Inorganic Composites and Beijing Key Laboratory of Bioprocess
- Beijing University of Chemical Technology (BUCT)
- Beijing 100029
- China
| | - Dan Wang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology
- National Engineering Research Center of Pesticide (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Yasi Gao
- State Key Laboratory of Organic–Inorganic Composites and Beijing Key Laboratory of Bioprocess
- Beijing University of Chemical Technology (BUCT)
- Beijing 100029
- China
| | - Long Yi
- State Key Laboratory of Organic–Inorganic Composites and Beijing Key Laboratory of Bioprocess
- Beijing University of Chemical Technology (BUCT)
- Beijing 100029
- China
- Collaborative Innovation Center of Chemical Science and Engineering
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology
- National Engineering Research Center of Pesticide (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
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12
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Evaluation and optimisation of unnatural amino acid incorporation and bioorthogonal bioconjugation for site-specific fluorescent labelling of proteins expressed in mammalian cells. Biochem Biophys Rep 2018; 17:1-9. [PMID: 30450427 PMCID: PMC6226565 DOI: 10.1016/j.bbrep.2018.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/08/2018] [Accepted: 10/18/2018] [Indexed: 11/21/2022] Open
Abstract
Many biophysical techniques that are available to study the structure, function and dynamics of cellular constituents require modification of the target molecules. Site-specific labelling of a protein is of particular interest for fluorescence-based single-molecule measurements including single-molecule FRET or super-resolution microscopy. The labelling procedure should be highly specific but minimally invasive to preserve sensitive biomolecules. The modern molecular engineering toolkit provides elegant solutions to achieve the site-specific modification of a protein of interest often necessitating the incorporation of an unnatural amino acid to introduce a unique reactive moiety. The Amber suppression strategy allows the site-specific incorporation of unnatural amino acids into a protein of interest. Recently, this approach has been transferred to the mammalian expression system. Here, we demonstrate how the combination of unnatural amino acid incorporation paired with current bioorthogonal labelling strategies allow the site-specific engineering of fluorescent dyes into proteins produced in the cellular environment of a human cell. We describe in detail which parameters are important to ensure efficient incorporation of unnatural amino acids into a target protein in human expression systems. We furthermore outline purification and bioorthogonal labelling strategies that allow fast protein preparation and labelling of the modified protein. This way, the complete eukaryotic proteome becomes available for single-molecule fluorescence assays. Optimal conditions for incorporation of unnatural amino acids in mammalian cells. Fast small scale purification/labelling for unnatural amino acid-carrying proteins. Evaluation of biorthogonal labelling reactions for dye engineering into proteins.
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13
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Caldwell TA, Baoukina S, Brock AT, Oliver RC, Root KT, Krueger JK, Glover KJ, Tieleman DP, Columbus L. Low- q Bicelles Are Mixed Micelles. J Phys Chem Lett 2018; 9:4469-4473. [PMID: 30024762 PMCID: PMC6353637 DOI: 10.1021/acs.jpclett.8b02079] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bicelles are used in many membrane protein studies because they are thought to be more bilayer-like than micelles. We investigated the properties of "isotropic" bicelles by small-angle neutron scattering, small-angle X-ray scattering, fluorescence anisotropy, and molecular dynamics. All data suggest that bicelles with a q value below 1 deviate from the classic bicelle that contains lipids in the core and detergent in the rim. Thus not all isotropic bicelles are bilayer-like.
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Affiliation(s)
- Tracy A. Caldwell
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Svetlana Baoukina
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ashton T. Brock
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ryan C. Oliver
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Kyle T. Root
- Department of Chemistry, Lock Haven University, Lock Haven, Pennsylvania 17745, United States
| | - Joanna K. Krueger
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kerney Jebrell Glover
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - D. Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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14
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Xie Y, Cheng L, Gao Y, Cai X, Yang X, Yi L, Xi Z. Tetrafluorination of Aromatic Azide Yields a Highly Efficient Staudinger Reaction: Kinetics and Biolabeling. Chem Asian J 2018; 13:1791-1796. [PMID: 29714052 DOI: 10.1002/asia.201800503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/30/2018] [Indexed: 02/28/2024]
Abstract
The development of highly efficient bioorthogonal reactions is of paramount importance for the research fields of biomaterials and chemical biology. We found that the o,o'-difluorinated aromatic azide was able to react with triphenylphosphine to produce water-stable phosphanimine. To further improve the efficiency of this kind of nonhydrolysis Staudinger reaction, a tetrafluorinated aromatic azide was employed to develop a faster nonhydrolysis Staudinger reaction with a rate of up to 51 m-1 s-1 , as revealed by high-performance liquid chromatography (HPLC) analysis and fluorescence kinetics. As a proof-of-concept study, the highly efficient Staudinger reaction was successfully used for chemoselective fluorescence labeling of proteins and nucleic acids (DNA and RNA) as well as for protein polyethyleneglycol (PEG)ylation. We believe that this bioorthogonal reaction can provide a broadly useful tool for various bioconjugations.
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Affiliation(s)
- Yonghui Xie
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, National Pesticide Engineering Research Center (Tianjin), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, China
| | - Longhuai Cheng
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, National Pesticide Engineering Research Center (Tianjin), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, China
| | - Yasi Gao
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology (BUCT), Beijing, 100029, China
| | - Xuekang Cai
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology (BUCT), Beijing, 100029, China
- Department of Nuclear Medicine, Peking University First Hospital, Beijing, 100034, China
| | - Xing Yang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing, 100034, China
| | - Long Yi
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology (BUCT), Beijing, 100029, China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, National Pesticide Engineering Research Center (Tianjin), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, China
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15
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Gust A, Jakob L, Zeitler DM, Bruckmann A, Kramm K, Willkomm S, Tinnefeld P, Meister G, Grohmann D. Site-Specific Labelling of Native Mammalian Proteins for Single-Molecule FRET Measurements. Chembiochem 2018; 19:780-783. [PMID: 29394002 DOI: 10.1002/cbic.201700696] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 12/31/2022]
Abstract
Human cells are complex entities in which molecular recognition and selection are critical for cellular processes often driven by structural changes and dynamic interactions. Biomolecules appear in different chemical states, and modifications, such as phosphorylation, affect their function. Hence, using proteins in their chemically native state in biochemical and biophysical assays is essential. Single-molecule FRET measurements allow exploration of the structure, function and dynamics of biomolecules but cannot be fully exploited for the human proteome, as a method for the site-specific coupling of organic dyes into native, non-recombinant mammalian proteins is lacking. We address this issue showing the site-specific engineering of fluorescent dyes into human proteins on the basis of bioorthogonal reactions. We show the applicability of the method to study functional and post-translationally modified proteins on the single-molecule level, among them the hitherto inaccessible human Argonaute 2.
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Affiliation(s)
- Alexander Gust
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Leonhard Jakob
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Daniela M Zeitler
- Department for Biochemistry I, Biochemistry Centre University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Centre University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Kevin Kramm
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Sarah Willkomm
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Gunter Meister
- Department for Biochemistry I, Biochemistry Centre University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
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16
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Calebiro D, Sungkaworn T. Single-Molecule Imaging of GPCR Interactions. Trends Pharmacol Sci 2018; 39:109-122. [DOI: 10.1016/j.tips.2017.10.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 02/07/2023]
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17
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Ramil CP, Dong M, An P, Lewandowski TM, Yu Z, Miller LJ, Lin Q. Spirohexene-Tetrazine Ligation Enables Bioorthogonal Labeling of Class B G Protein-Coupled Receptors in Live Cells. J Am Chem Soc 2017; 139:13376-13386. [PMID: 28876923 DOI: 10.1021/jacs.7b05674] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A new bioorthogonal reactant pair, spiro[2.3]hex-1-ene (Sph) and 3,6-di(2-pyridyl)-s-tetrazine (DpTz), for the strain-promoted inverse electron-demand Diels-Alder cycloaddition, that is, tetrazine ligation, is reported. As compared to the previously reported strained alkenes such as trans-cyclooctene (TCO) and 1,3-disubstituted cyclopropene, Sph exhibits balanced reactivity and stability in tetrazine ligation with the protein substrates. A lysine derivative of Sph, SphK, was site-selectively incorporated into the extracellular loop regions (ECLs) of GCGR and GLP-1R, two members of class B G protein-coupled receptors (GPCRs) in mammalian cells with the incorporation efficiency dependent on the location. Subsequent bioorthogonal reactions with the fluorophore-conjugated DpTz reagents afforded the fluorescently labeled GCGR and GLP-1R ECL mutants with labeling yield as high as 68%. A multitude of functional assays were performed with these GPCR mutants, including ligand binding, ligand-induced receptor internalization, and ligand-stimulated intracellular cAMP accumulation. Several positions in the ECL3s of GCGR and GLP-1R were identified that tolerate SphK mutagenesis and subsequent bioorthogonal labeling. The generation of functional, fluorescently labeled ECL3 mutants of GCGR and GLP-1R should allow biophysical studies of conformation dynamics of this important class of GPCRs in their native environment in live cells.
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Affiliation(s)
- Carlo P Ramil
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Maoqing Dong
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States
| | - Peng An
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Tracey M Lewandowski
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Zhipeng Yu
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Laurence J Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
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18
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Tian H, Sakmar TP, Huber T. The Energetics of Chromophore Binding in the Visual Photoreceptor Rhodopsin. Biophys J 2017; 113:60-72. [PMID: 28700926 DOI: 10.1016/j.bpj.2017.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 01/06/2023] Open
Abstract
The visual photoreceptor rhodopsin is a prototypical G-protein-coupled receptor (GPCR) that stabilizes its inverse agonist ligand, 11-cis-retinal (11CR), by a covalent, protonated Schiff base linkage. In the visual dark adaptation, the fundamental molecular event after photobleaching of rhodopsin is the recombination reaction between its apoprotein opsin and 11CR. Here we present a detailed analysis of the kinetics and thermodynamics of this reaction, also known as the "regeneration reaction". We compared the regeneration of purified rhodopsin reconstituted into phospholipid/detergent bicelles with rhodopsin reconstituted into detergent micelles. We found that the lipid bilayer of bicelles stabilized the chromophore-free opsin over the long timescale required for the regeneration experiments, and also facilitated the ligand reuptake binding reaction. We utilized genetic code expansion and site-specific bioorthogonal labeling of rhodopsin with Alexa488 to enable, to our knowledge, a novel fluorescence resonance energy transfer-based measurement of the binding kinetics between opsin and 11CR. Based on these results, we report a complete energy diagram for the regeneration reaction of rhodopsin. We show that the dissociation reaction of rhodopsin to 11CR and opsin has a 25-pM equilibrium dissociation constant, which corresponds to only 0.3 kcal/mol stabilization compared to the noncovalent, tightly bound antagonist-GPCR complex of iodopindolol and β-adrenergic receptor. However, 11CR dissociates four orders-of-magnitude slower than iodopindolol, which corresponds to a 6-kcal/mol higher dissociation free energy barrier. We further used isothermal titration calorimetry to show that ligand binding in rhodopsin is enthalpy driven with -22 kcal/mol, which is 12 kcal/mol more stable than the antagonist-GPCR complex. Our data provide insights into the ligand-receptor binding reaction for rhodopsin in particular, and for GPCRs more broadly.
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Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden.
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York.
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19
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Tian H, Sakmar TP, Huber T. Measurement of Slow Spontaneous Release of 11-cis-Retinal from Rhodopsin. Biophys J 2017; 112:153-161. [PMID: 28076806 DOI: 10.1016/j.bpj.2016.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/08/2016] [Accepted: 12/05/2016] [Indexed: 01/05/2023] Open
Abstract
The vertebrate visual photoreceptor rhodopsin (Rho) is a unique G protein-coupled receptor as it utilizes a covalently tethered inverse agonist (11-cis-retinal) as the native ligand. Previously, electrophysiological studies showed that ligand binding of 11-cis-retinal in dark-adapted Rho was essentially irreversible with a half-life estimated to be 420 years, until after thermal isomerization to all-trans-retinal, which then slowly dissociates. This long lifetime of 11-cis-retinal binding was considered to be physiologically important for minimizing background signal (dark noise) of the visual system. However, in vitro biochemical studies on the thermal stability of Rho showed that Rho decays with a half-life on the order of days. In this study, we resolve the discrepancy by measuring the chromophore exchange rate of the bound 11-cis-retinal chromophore with free 9-cis-retinal from Rho in an in vitro phospholipid/detergent bicelle system. We conclude that the thermal decay of Rho primarily proceeds through spontaneous breaking of the covalent linkage between opsin and 11-cis-retinal, which was overlooked in the electrophysiological recording. We estimate that this slow spontaneous release of 11-cis-retinal from Rho should result in 104 to 105 free opsin molecules in a dark-adapted rod cell-a number that is three orders of magnitude higher than previously expected. We also discuss the physiological implications of these findings on the basal activity of opsins and the associated dark noise in the visual system.
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Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden.
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY.
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20
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Cai Y, Liu Y, Culhane KJ, DeVree BT, Yang Y, Sunahara RK, Yan ECY. Purification of family B G protein-coupled receptors using nanodiscs: Application to human glucagon-like peptide-1 receptor. PLoS One 2017; 12:e0179568. [PMID: 28609478 PMCID: PMC5469476 DOI: 10.1371/journal.pone.0179568] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/31/2017] [Indexed: 12/16/2022] Open
Abstract
Family B G protein-coupled receptors (GPCRs) play vital roles in hormone-regulated homeostasis. They are drug targets for metabolic diseases, including type 2 diabetes and osteoporosis. Despite their importance, the signaling mechanisms for family B GPCRs at the molecular level remain largely unexplored due to the challenges in purification of functional receptors in sufficient amount for biophysical characterization. Here, we purified the family B GPCR human glucagon-like peptide-1 (GLP-1) receptor (GLP1R), whose agonists, e.g. exendin-4, are used for the treatment of type 2 diabetes mellitus. The receptor was expressed in HEK293S GnTl- cells using our recently developed protocol. The protocol incorporates the receptor into the native-like lipid environment of reconstituted high density lipoprotein (rHDL) particles, also known as nanodiscs, immediately after the membrane solubilization step followed by chromatographic purification, minimizing detergent contact with the target receptor to reduce denaturation and prolonging stabilization of receptor in lipid bilayers without extra steps of reconstitution. This method yielded purified GLP1R in nanodiscs that could bind to GLP-1 and exendin-4 and activate Gs protein. This nanodisc purification method can potentially be a general strategy to routinely obtain purified family B GPCRs in the 10s of microgram amounts useful for spectroscopic analysis of receptor functions and activation mechanisms.
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Affiliation(s)
- Yingying Cai
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Yuting Liu
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Kelly J. Culhane
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Brian T. DeVree
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yang Yang
- Nanobiology Institute, Yale University, New Haven, Connecticut, United States of America
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Roger K. Sunahara
- Department of Pharmacology, University of California at San Diego, La Jolla, California, United States of America
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
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21
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Tian H, Sakmar TP, Huber T. A simple method for enhancing the bioorthogonality of cyclooctyne reagent. Chem Commun (Camb) 2016; 52:5451-4. [PMID: 27009873 DOI: 10.1039/c6cc01321j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cross-reactivity between some cyclooctynes and thiols limits the bioorthogonality of the strain-promoted azide-alkyne cycloaddition reaction. We show that a low concentration of β-mercaptoethanol significantly reduces the undesirable side reaction between bicyclononyne (BCN) and cysteine and while preserving free cysteines. We site-specifically label a genetically-encoded azido group in the visual photoreceptor rhodopsin to demonstrate the utility of the strategy.
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Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA.
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA. and Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, 141 57 Huddinge, Sweden
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA.
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22
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Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
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23
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Thompson DA, Ng R, Dawson PE. Arginine selective reagents for ligation to peptides and proteins. J Pept Sci 2016; 22:311-9. [DOI: 10.1002/psc.2867] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Darren A. Thompson
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. San Diego CA 92037 USA
| | - Raymond Ng
- University of California, San Diego; 9500 Gilman Dr San Diego CA 92093 USA
| | - Philip E. Dawson
- Department of Chemistry; The Scripps Research Institute; 10550 N. Torrey Pines Rd. San Diego CA 92037 USA
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24
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Bioorthogonal Labeling of Ghrelin Receptor to Facilitate Studies of Ligand-Dependent Conformational Dynamics. ACTA ACUST UNITED AC 2015; 22:1431-1436. [DOI: 10.1016/j.chembiol.2015.09.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/21/2015] [Accepted: 09/28/2015] [Indexed: 01/09/2023]
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25
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Tian H, Sakmar TP, Huber T. Micelle-Enhanced Bioorthogonal Labeling of Genetically Encoded Azido Groups on the Lipid-Embedded Surface of a GPCR. Chembiochem 2015; 16:1314-22. [PMID: 25962668 PMCID: PMC5287413 DOI: 10.1002/cbic.201500030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Indexed: 12/21/2022]
Abstract
Genetically encoded p-azido-phenylalanine (azF) residues in G protein-coupled receptors (GPCRs) can be targeted with dibenzocyclooctyne-modified (DIBO-modified) fluorescent probes by means of strain-promoted [3+2] azide-alkyne cycloaddition (SpAAC). Here we show that azF residues situated on the transmembrane surfaces of detergent-solubilized receptors exhibit up to 1000-fold rate enhancement relative to azF residues on water-exposed surfaces. We show that the amphipathic moment of the labeling reagent, consisting of hydrophobic DIBO coupled to hydrophilic Alexa dye, results in strong partitioning of the DIBO group into the hydrocarbon core of the detergent micelle and consequently high local reactant concentrations. The observed rate constant for the micelleenhanced SpAAC is comparable with those of the fastest bioorthogonal labeling reactions known. Targeting hydrophobic regions of membrane proteins by use of micelle-enhanced SpAAC should expand the utility of bioorthogonal labeling strategies.
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Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA)
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA).
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Alfred Nobels Allé 23, 141 57 Huddinge (Sweden).
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA).
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26
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Sleno R, Pétrin D, Devost D, Goupil E, Zhang A, Hébert TE. Designing BRET-based conformational biosensors for G protein-coupled receptors. Methods 2015; 92:11-8. [PMID: 25962643 DOI: 10.1016/j.ymeth.2015.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/30/2015] [Accepted: 05/02/2015] [Indexed: 12/16/2022] Open
Abstract
Ligand-biased signaling is starting to have significant impact on drug discovery programs in the pharmaceutical industry and has reinvigorated our understanding of pharmacological efficacy. As such, many investigators and screening campaigns are now being directed at a larger section of the signaling responses downstream of an individual G protein-coupled receptor. Many biosensor-based platforms have been developed to capture signaling signatures. Despite our growing ability to use such signaling signatures, we remain hampered by the fact that signaling signatures may be particular to an individual cell type and thus our platforms may not be portable from cell to cell, necessitating further cell-specific biosensor development. Here, we provide a complementary strategy based on capturing receptor-proximal conformational profiles using intra-molecular BRET-based sensors composed of a Renilla luciferase donor engineered into the carboxy-terminus and CCPGCC motifs which bind fluorescent hairpin arsenical dyes engineered into different positions in intracellular loop 3 of FP, the receptor for PGF2α. We discuss the design and optimization of such sensors for orthosteric and allosteric ligands.
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Affiliation(s)
- Rory Sleno
- Department of Pharmacology and Therapeutics, McGill University, Canada
| | - Darlaine Pétrin
- Department of Pharmacology and Therapeutics, McGill University, Canada
| | - Dominic Devost
- Department of Pharmacology and Therapeutics, McGill University, Canada
| | - Eugénie Goupil
- Department of Pharmacology and Therapeutics, McGill University, Canada
| | - Alice Zhang
- Department of Pharmacology and Therapeutics, McGill University, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Canada.
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27
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Ghrelin receptor conformational dynamics regulate the transition from a preassembled to an active receptor:Gq complex. Proc Natl Acad Sci U S A 2015; 112:1601-6. [PMID: 25605885 DOI: 10.1073/pnas.1414618112] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
How G protein-coupled receptor conformational dynamics control G protein coupling to trigger signaling is a key but still open question. We addressed this question with a model system composed of the purified ghrelin receptor assembled into lipid discs. Combining receptor labeling through genetic incorporation of unnatural amino acids, lanthanide resonance energy transfer, and normal mode analyses, we directly demonstrate the occurrence of two distinct receptor:Gq assemblies with different geometries whose relative populations parallel the activation state of the receptor. The first of these assemblies is a preassembled complex with the receptor in its basal conformation. This complex is specific of Gq and is not observed with Gi. The second one is an active assembly in which the receptor in its active conformation triggers G protein activation. The active complex is present even in the absence of agonist, in a direct relationship with the high constitutive activity of the ghrelin receptor. These data provide direct evidence of a mechanism for ghrelin receptor-mediated Gq signaling in which transition of the receptor from an inactive to an active conformation is accompanied by a rearrangement of a preassembled receptor:G protein complex, ultimately leading to G protein activation and signaling.
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28
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Naganathan S, Ray-Saha S, Park M, Tian H, Sakmar TP, Huber T. Multiplex detection of functional G protein-coupled receptors harboring site-specifically modified unnatural amino acids. Biochemistry 2015; 54:776-86. [PMID: 25524496 PMCID: PMC4310623 DOI: 10.1021/bi501267x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
We developed a strategy for identifying
positions in G protein-coupled
receptors that are amenable to bioorthogonal modification with a peptide
epitope tag under cell culturing conditions. We introduced the unnatural
amino acid p-azido-l-phenylalanine (azF)
into human CC chemokine receptor 5 (CCR5) at site-specific amber codon
mutations. We then used strain-promoted azide–alkyne [3+2]
cycloaddition to label the azF-CCR5 variants with a FLAG peptide epitope-conjugated
aza-dibenzocyclooctyne (DBCO) reagent. A microtiter plate-based sandwich
fluorophore-linked immunosorbent assay was used to probe simultaneously
the FLAG epitope and the receptor using infrared dye-conjugated antibodies
so that the extent of DBCO incorporation, corresponding nominally
to labeling efficiency, could be quantified ratiometrically. The extent
of incorporation of DBCO at the various sites was evaluated in the
context of a recent crystal structure of maraviroc-bound CCR5. We
observed that labeling efficiency varied dramatically depending on
the topological location of the azF in CCR5. Interestingly, position
109 in transmembrane helix 3, located in a hydrophobic cavity on the
extracellular side of the receptor, was labeled most efficiently.
Because the bioorthogonal labeling and detection strategy described
might be used to introduce a variety of different peptide epitopes
or fluorophores into engineered expressed receptors, it might prove
to be useful for a wide range of applications, including single-molecule
detection studies of receptor trafficking and signaling mechanism.
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Affiliation(s)
- Saranga Naganathan
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University , New York, New York 10065, United States
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29
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Park M, Tian H, Naganathan S, Sakmar TP, Huber T. Quantitative Multi-color Detection Strategies for Bioorthogonally Labeled GPCRs. Methods Mol Biol 2015; 1335:67-93. [PMID: 26260595 DOI: 10.1007/978-1-4939-2914-6_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe multiple bioorthogonal approaches to label G protein-coupled receptors (GPCRs) heterologously expressed in mammalian cells. The use of genetically encoded unnatural amino acids as bioorthogonal tags results in receptors that are expressed at lower levels than even their low abundance wild-type counterparts. Therefore, reproducible and sensitive quantification of the labeled GPCRs is extremely important and conventional methods are simply not sufficiently accurate and precise. Silver stains lack reproducibility, spectroscopic methods using fluorescent ligands are limited to quantifying only functional receptor molecules, and immunoassays using epitope tags derived from rhodopsin are particularly variable for low-abundance GPCRs. To avoid these shortcomings, we employ near infrared (NIR) imaging-based methods that enable simultaneous multi-color detection of two different antigens, thus facilitating the ratiometric analysis of bioorthogonally modified GPCRs. We anticipate that these multi-color detection strategies will provide new tools for quantitatively assessing stoichiometrically labeled GPCRs for studies of signalosomes and for structure-function relationships at a single molecule level.
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Affiliation(s)
- Minyoung Park
- Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University, New York, NY, 10065, USA
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30
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Zhang J, Men Y, Lv S, Yi L, Chen JF. Protein tetrazinylation via diazonium coupling for covalent and catalyst-free bioconjugation. Org Biomol Chem 2015; 13:11422-5. [DOI: 10.1039/c5ob02053k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work reports an efficient reagent 1 for direct and covalent introduction of tetrazines onto the surface of proteins and viruses under mild conditions.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Yuwen Men
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Shanshan Lv
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Long Yi
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
- Collaborative Innovation Center of Chemical Science and Engineering
| | - Jian-Feng Chen
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
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Schafer CT, Farrens DL. Conformational selection and equilibrium governs the ability of retinals to bind opsin. J Biol Chem 2014; 290:4304-18. [PMID: 25451936 DOI: 10.1074/jbc.m114.603134] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Despite extensive study, how retinal enters and exits the visual G protein-coupled receptor rhodopsin remains unclear. One clue may lie in two openings between transmembrane helix 1 (TM1) and TM7 and between TM5 and TM6 in the active receptor structure. Recently, retinal has been proposed to enter the inactive apoprotein opsin (ops) through these holes when the receptor transiently adopts the active opsin conformation (ops*). Here, we directly test this "transient activation" hypothesis using a fluorescence-based approach to measure rates of retinal binding to samples containing differing relative fractions of ops and ops*. In contrast to what the transient activation hypothesis model would predict, we found that binding for the inverse agonist, 11-cis-retinal (11CR), slowed when the sample contained more ops* (produced using M257Y, a constitutively activating mutation). Interestingly, the increased presence of ops* allowed for binding of the agonist, all-trans-retinal (ATR), whereas WT opsin showed no binding. Shifting the conformational equilibrium toward even more ops* using a G protein peptide mimic (either free in solution or fused to the receptor) accelerated the rate of ATR binding and slowed 11CR binding. An arrestin peptide mimic showed little effect on 11CR binding; however, it stabilized opsin · ATR complexes. The TM5/TM6 hole is apparently not involved in this conformational selection. Increasing its size by mutagenesis did not enable ATR binding but instead slowed 11CR binding, suggesting that it may play a role in trapping 11CR. In summary, our results indicate that conformational selection dictates stable retinal binding, which we propose involves ATR and 11CR binding to different states, the latter a previously unidentified, open-but-inactive conformation.
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Affiliation(s)
- Christopher T Schafer
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098
| | - David L Farrens
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098
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Zhang J, Ma D, Du D, Xi Z, Yi L. An efficient reagent for covalent introduction of alkynes into proteins. Org Biomol Chem 2014; 12:9528-31. [DOI: 10.1039/c4ob01873g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Huber T, Sakmar T. Chemical Biology Methods for Investigating G Protein-Coupled Receptor Signaling. ACTA ACUST UNITED AC 2014; 21:1224-37. [DOI: 10.1016/j.chembiol.2014.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/21/2014] [Accepted: 08/20/2014] [Indexed: 11/26/2022]
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Abstract
Blowing up: Rapid expansion of the genetic code, beyond what nature initially intended, has given chemical biologists innumerable tools for protein engineering and biological studies. This special issue highlights some of the most recent applications of these techniques in in vivo systems.
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Affiliation(s)
- Edward A Lemke
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg (Germany).
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