101
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Abstract
Genetic code expansion is commonly used to introduce bioorthogonal reactive functional groups onto proteins for labeling. In recent years, the inverse electron demand Diels-Alder reaction between tetrazines and strained trans-cyclooctenes has increased in popularity as a bioorthogonal ligation for protein labeling due to its fast reaction rate and high in vivo stability. We provide methods for the facile synthesis of a tetrazine containing amino acid, Tet-v2.0, and the site-specific incorporation of Tet-v2.0 into proteins via genetic code expansion. Furthermore, we demonstrate that proteins containing Tet-v2.0 can be quickly and efficiently reacted with strained alkene labels at low concentrations. This chemistry has enabled the labeling of protein surfaces with fluorophores, inhibitors, or common posttranslational modifications such as glycosylation or lipidation.
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102
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Sotokawa S, Kitamura T, Takahashi D, Toshima K. An anthraquinone–enzyme–peptide hybrid as a photo-switchable enzyme. Chem Commun (Camb) 2018; 54:10614-10617. [DOI: 10.1039/c8cc06130k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The purpose-designed anthraquinone–horseradish peroxidase–cell penetrating peptide hybrid1exhibited cell permeability and enzymatic activity without photo-irradiation whereas significant self-degradation and loss of enzymatic activity occurred upon photo-irradiation in living cells.
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Affiliation(s)
- Shota Sotokawa
- Department of Applied Chemistry
- Faculty of Science and Technology
- Keio University
- Yokohama 223-8522
- Japan
| | - Takashi Kitamura
- Department of Applied Chemistry
- Faculty of Science and Technology
- Keio University
- Yokohama 223-8522
- Japan
| | - Daisuke Takahashi
- Department of Applied Chemistry
- Faculty of Science and Technology
- Keio University
- Yokohama 223-8522
- Japan
| | - Kazunobu Toshima
- Department of Applied Chemistry
- Faculty of Science and Technology
- Keio University
- Yokohama 223-8522
- Japan
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103
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Elliott TS, Bianco A, Townsley FM, Fried SD, Chin JW. Tagging and Enriching Proteins Enables Cell-Specific Proteomics. Cell Chem Biol 2017; 23:805-815. [PMID: 27447048 PMCID: PMC4959846 DOI: 10.1016/j.chembiol.2016.05.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/13/2016] [Accepted: 05/23/2016] [Indexed: 01/01/2023]
Abstract
Cell-specific proteomics in multicellular systems and whole animals is a promising approach to understand the differentiated functions of cells and tissues. Here, we extend our stochastic orthogonal recoding of translation (SORT) approach for the co-translational tagging of proteomes with a cyclopropene-containing amino acid in response to diverse codons in genetically targeted cells, and create a tetrazine-biotin probe containing a cleavable linker that offers a way to enrich and identify tagged proteins. We demonstrate that SORT with enrichment, SORT-E, efficiently recovers and enriches SORT tagged proteins and enables specific identification of enriched proteins via mass spectrometry, including low-abundance proteins. We show that tagging at distinct codons enriches overlapping, but distinct sets of proteins, suggesting that tagging at more than one codon enhances proteome coverage. Using SORT-E, we accomplish cell-specific proteomics in the fly. These results suggest that SORT-E will enable the definition of cell-specific proteomes in animals during development, disease progression, and learning and memory. A tetrazine-biotin probe containing a cleavable linker was created Proteomes labeled with cyclopropene amino acids were enriched and identified Proteome coverage is increased by targeting the amino acids to multiple codons Cell-specific proteomics was accomplished in the fly
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Affiliation(s)
- Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ambra Bianco
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Fiona M Townsley
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephen D Fried
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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104
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Chin JW. Expanding and reprogramming the genetic code. Nature 2017; 550:53-60. [PMID: 28980641 DOI: 10.1038/nature24031] [Citation(s) in RCA: 504] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022]
Abstract
Nature uses a limited, conservative set of amino acids to synthesize proteins. The ability to genetically encode an expanded set of building blocks with new chemical and physical properties is transforming the study, manipulation and evolution of proteins, and is enabling diverse applications, including approaches to probe, image and control protein function, and to precisely engineer therapeutics. Underpinning this transformation are strategies to engineer and rewire translation. Emerging strategies aim to reprogram the genetic code so that noncanonical biopolymers can be synthesized and evolved, and to test the limits of our ability to engineer the translational machinery and systematically recode genomes.
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Affiliation(s)
- Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.,Department of Chemistry, Cambridge University, Cambridge CB2 1EW, UK
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105
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Leippe P, Koehler Leman J, Trauner D. Specificity and Speed: Tethered Photopharmacology. Biochemistry 2017; 56:5214-5220. [DOI: 10.1021/acs.biochem.7b00687] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Philipp Leippe
- Department
of Chemistry and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Julia Koehler Leman
- Center
for Computational Biology, Flatiron Institute, Simons Foundation, 162 Fifth Avenue, New York, New York 10010, United States
- Department
of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 10003, United States
| | - Dirk Trauner
- Department
of Chemistry and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 Munich, Germany
- Department
of Chemistry, New York University, Silver Center, 100 Washington Square
East, Room 712, New York, New York 10003, United States
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106
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Lebraud H, Wright DJ, East CE, Holding FP, O'Reilly M, Heightman TD. In-gel activity-based protein profiling of a clickable covalent ERK1/2 inhibitor. MOLECULAR BIOSYSTEMS 2017; 12:2867-74. [PMID: 27385078 DOI: 10.1039/c6mb00367b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In-gel activity-based protein profiling (ABPP) offers rapid assessment of the proteome-wide selectivity and target engagement of a chemical tool. Here we demonstrate the use of the inverse electron demand Diels Alder (IEDDA) click reaction for in-gel ABPP by evaluating the selectivity profile and target engagement of a covalent ERK1/2 probe tagged with a trans-cyclooctene group. The chemical probe was shown to bind covalently to Cys166 of ERK2 using protein MS and X-ray crystallography, and displayed submicromolar GI50s in A375 and HCT116 cells. In both cell lines, the probe demonstrated target engagement and a good selectivity profile at low concentrations, which was lost at higher concentrations. The IEDDA cycloaddition enabled fast and quantitative fluorescent tagging for readout with a high background-to-noise ratio and thereby provides a promising alternative to the commonly used copper catalysed alkyne-azide cycloaddition.
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Affiliation(s)
- Honorine Lebraud
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
| | - David J Wright
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
| | - Charlotte E East
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
| | - Finn P Holding
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
| | - Marc O'Reilly
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
| | - Tom D Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
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107
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Mogaki R, Okuro K, Aida T. Adhesive Photoswitch: Selective Photochemical Modulation of Enzymes under Physiological Conditions. J Am Chem Soc 2017; 139:10072-10078. [DOI: 10.1021/jacs.7b05151] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Rina Mogaki
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-8656, Japan
| | - Kou Okuro
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-8656, Japan
| | - Takuzo Aida
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-8656, Japan
- Riken Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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108
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Zheng S, Fan X, Wang J, Zhao J, Chen PR. Dissection of Kinase Isoforms through Orthogonal and Chemical Inducible Signaling Cascades. Chembiochem 2017; 18:1593-1598. [DOI: 10.1002/cbic.201700255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Siqi Zheng
- Beijing National Laboratory for Molecular Sciences; Synthetic and Functional Biomolecules Center; Key Laboratory of Bioorganic Chemistry and; Molecular Engineering of the Ministry of Education; College of Chemistry and Molecular Engineering; Peking University; Haidian District Beijing 100871 China
| | - Xinyuan Fan
- Academy for Advanced Interdisciplinary Studies; Peking-Tsinghua Center for Life Sciences; Peking University; Haidian District Beijing 100871 China
| | - Jie Wang
- Academy for Advanced Interdisciplinary Studies; Peking-Tsinghua Center for Life Sciences; Peking University; Haidian District Beijing 100871 China
| | - Jingyi Zhao
- Academy for Advanced Interdisciplinary Studies; Peking-Tsinghua Center for Life Sciences; Peking University; Haidian District Beijing 100871 China
| | - Peng R. Chen
- Beijing National Laboratory for Molecular Sciences; Synthetic and Functional Biomolecules Center; Key Laboratory of Bioorganic Chemistry and; Molecular Engineering of the Ministry of Education; College of Chemistry and Molecular Engineering; Peking University; Haidian District Beijing 100871 China
- Academy for Advanced Interdisciplinary Studies; Peking-Tsinghua Center for Life Sciences; Peking University; Haidian District Beijing 100871 China
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109
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Kang K, Park J, Kim E. Tetrazine ligation for chemical proteomics. Proteome Sci 2017; 15:15. [PMID: 28674480 PMCID: PMC5485739 DOI: 10.1186/s12953-017-0121-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/15/2017] [Indexed: 12/12/2022] Open
Abstract
Determining small molecule-target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding first-class molecular tools. Chemical probes can provide great spatiotemporal control to elucidate biological functions of proteins as well as for interrogating biological pathways. The invention of bioorthogonal chemistry has revolutionized the field of chemical biology by providing superior chemical tools and has been widely used for investigating the dynamics and function of biomolecules in live condition. Among 20 different bioorthogonal reactions, tetrazine ligation has been spotlighted as the most advanced bioorthogonal chemistry because of their extremely faster kinetics and higher specificity than others. Therefore, tetrazine ligation has a tremendous potential to enhance the proteomic research. This review highlights the current status of tetrazine ligation reaction as a molecular tool for the chemical proteomics.
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Affiliation(s)
- Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi 17104 Republic of Korea
| | - Jongmin Park
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge St, CPZN 5206, Boston, Massachusetts 02114 USA
| | - Eunha Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499 Republic of Korea
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110
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Abstract
The formation of well-defined protein bioconjugates is critical for many studies and technologies in chemical biology. Tried-and-true methods for accomplishing this typically involve the targeting of cysteine residues, but the rapid growth of contemporary bioconjugate applications has required an expanded repertoire of modification techniques. One very powerful set of strategies involves the modification of proteins at their N termini, as these positions are typically solvent exposed and provide chemically distinct sites for many protein targets. Several chemical techniques can be used to modify N-terminal amino acids directly or convert them into unique functional groups for further ligations. A growing number of N-terminus-specific enzymatic ligation strategies have provided additional possibilities. This Perspective provides an overview of N-terminal modification techniques and the chemical rationale governing each. Examples of specific N-terminal protein conjugates are provided, along with their uses in a number of diverse biological applications.
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111
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Expanding the genetic code of mammalian cells. Biochem Soc Trans 2017; 45:555-562. [PMID: 28408495 DOI: 10.1042/bst20160336] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 12/27/2022]
Abstract
In the last two decades, unnatural amino acid (UAA) mutagenesis has emerged as a powerful new method to probe and engineer protein structure and function. This technology enables precise incorporation of a rapidly expanding repertoire of UAAs into predefined sites of a target protein expressed in living cells. Owing to the small footprint of these genetically encoded UAAs and the large variety of enabling functionalities they offer, this technology has tremendous potential for deciphering the delicate and complex biology of the mammalian cells. Over the last few years, exciting progress has been made toward expanding the toolbox of genetically encoded UAAs in mammalian cells, improving the efficiency of their incorporation and developing innovative applications. Here, we provide our perspective on these recent developments and highlight the current challenges that must be overcome to realize the full potential of this technology.
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112
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Long MJC, Parvez S, Zhao Y, Surya SL, Wang Y, Zhang S, Aye Y. Akt3 is a privileged first responder in isozyme-specific electrophile response. Nat Chem Biol 2017; 13:333-338. [PMID: 28114274 PMCID: PMC5586141 DOI: 10.1038/nchembio.2284] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/29/2016] [Indexed: 12/25/2022]
Abstract
Isozyme-specific post-translational regulation fine tunes signaling events. However, redundancy in sequence or activity renders links between isozyme-specific modifications and downstream functions uncertain. Methods to study this phenomenon are underdeveloped. Here we use a redox-targeting screen to reveal that Akt3 is a first-responding isozyme sensing native electrophilic lipids. Electrophile modification of Akt3 modulated downstream pathway responses in cells and Danio rerio (zebrafish) and markedly differed from Akt2-specific oxidative regulation. Digest MS sequencing identified Akt3 C119 as the privileged cysteine that senses 4-hydroxynonenal. A C119S Akt3 mutant was hypomorphic for all downstream phenotypes shown by wild-type Akt3. This study documents isozyme-specific and chemical redox signal-personalized physiological responses.
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Affiliation(s)
- Marcus J. C. Long
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
| | - Saba Parvez
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
| | - Yi Zhao
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
| | - Sanjna L. Surya
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
| | - Yiran Wang
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
| | - Sheng Zhang
- Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14850, United States
| | - Yimon Aye
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, United States
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113
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Acar H, Srivastava S, Chung EJ, Schnorenberg MR, Barrett JC, LaBelle JL, Tirrell M. Self-assembling peptide-based building blocks in medical applications. Adv Drug Deliv Rev 2017; 110-111:65-79. [PMID: 27535485 PMCID: PMC5922461 DOI: 10.1016/j.addr.2016.08.006] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/01/2016] [Accepted: 08/05/2016] [Indexed: 12/22/2022]
Abstract
Peptides and peptide-conjugates, comprising natural and synthetic building blocks, are an increasingly popular class of biomaterials. Self-assembled nanostructures based on peptides and peptide-conjugates offer advantages such as precise selectivity and multifunctionality that can address challenges and limitations in the clinic. In this review article, we discuss recent developments in the design and self-assembly of various nanomaterials based on peptides and peptide-conjugates for medical applications, and categorize them into two themes based on the driving forces of molecular self-assembly. First, we present the self-assembled nanostructures driven by the supramolecular interactions between the peptides, with or without the presence of conjugates. The studies where nanoassembly is driven by the interactions between the conjugates of peptide-conjugates are then presented. Particular emphasis is given to in vivo studies focusing on therapeutics, diagnostics, immune modulation and regenerative medicine. Finally, challenges and future perspectives are presented.
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Affiliation(s)
- Handan Acar
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA.
| | - Samanvaya Srivastava
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA; Institute for Molecular Engineering, Argonne National Laboratory, Argonne, IL 60439, USA.
| | - Eun Ji Chung
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA; Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Mathew R Schnorenberg
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA; Medical Scientist Training Program, University of Chicago, Chicago, IL 60637, USA.
| | - John C Barrett
- Biophysical Sciences Graduate Program, University of Chicago, Chicago, IL 60637, USA.
| | - James L LaBelle
- Department of Pediatrics, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA.
| | - Matthew Tirrell
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA; Institute for Molecular Engineering, Argonne National Laboratory, Argonne, IL 60439, USA.
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114
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Xiao H, Wu R. Quantitative investigation of human cell surface N-glycoprotein dynamics. Chem Sci 2017; 8:268-277. [PMID: 28616130 PMCID: PMC5458730 DOI: 10.1039/c6sc01814a] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/13/2016] [Indexed: 12/21/2022] Open
Abstract
Surface glycoproteins regulate nearly every extracellular event and they are dynamic for cells to adapt to the ever-changing extracellular environment. These glycoproteins contain a wealth of information on cellular development and disease states, and have significant biomedical implications. Systematic investigation of surface glycoproteins will result in a better understanding of surface protein functions, cellular activities and the molecular mechanisms of disease. However, it is extraordinarily challenging to specifically and globally analyze surface glycoproteins. Here we designed the first method to systematically analyze surface glycoprotein dynamics and measure their half-lives by integrating pulse-chase labeling, selective enrichment of surface glycoproteins, and multiplexed proteomics. The current results clearly demonstrated that surface glycoproteins with catalytic activities were more stable than those with binding and receptor activities. Glycosylation sites located outside of any domain had a notably longer median half-life than those within domains, which strongly suggests that glycans within domains regulate protein interactions with other molecules while those outside of domains mainly play a role in protecting the protein from degradation. This method can be extensively applied to biological and biomedical research.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry , The Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , USA . ; ; Tel: +1-404-385-1515
| | - Ronghu Wu
- School of Chemistry and Biochemistry , The Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , USA . ; ; Tel: +1-404-385-1515
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115
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Lebraud H, Wright DJ, Johnson CN, Heightman TD. Protein Degradation by In-Cell Self-Assembly of Proteolysis Targeting Chimeras. ACS CENTRAL SCIENCE 2016; 2:927-934. [PMID: 28058282 PMCID: PMC5200928 DOI: 10.1021/acscentsci.6b00280] [Citation(s) in RCA: 240] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 05/03/2023]
Abstract
Selective degradation of proteins by proteolysis targeting chimeras (PROTACs) offers a promising potential alternative to protein inhibition for therapeutic intervention. Current PROTAC molecules incorporate a ligand for the target protein, a linker, and an E3 ubiquitin ligase recruiting group, which bring together target protein and ubiquitinating machinery. Such hetero-bifunctional molecules require significant linker optimization and possess high molecular weight, which can limit cellular permeation, solubility, and other drug-like properties. We show here that the hetero-bifunctional molecule can be formed intracellularly by bio-orthogonal click combination of two smaller precursors. We designed a tetrazine tagged thalidomide derivative which reacts rapidly with a trans-cyclo-octene tagged ligand of the target protein in cells to form a cereblon E3 ligase recruiting PROTAC molecule. The in-cell click-formed proteolysis targeting chimeras (CLIPTACs) were successfully used to degrade two key oncology targets, BRD4 and ERK1/2. ERK1/2 degradation was achieved using a CLIPTAC based on a covalent inhibitor. We expect this approach to be readily extendable to other inhibitor-protein systems because the tagged E3 ligase recruiter is capable of undergoing the click reaction with a suitably tagged ligand of any protein of interest to elicit its degradation.
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116
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Proteomics approaches to decipher new signaling pathways. Curr Opin Struct Biol 2016; 41:128-134. [DOI: 10.1016/j.sbi.2016.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/11/2016] [Indexed: 01/01/2023]
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117
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Hu Y, Zou W, Julita V, Ramanathan R, Tabor RF, Nixon-Luke R, Bryant G, Bansal V, Wilkinson BL. Photomodulation of bacterial growth and biofilm formation using carbohydrate-based surfactants. Chem Sci 2016; 7:6628-6634. [PMID: 28567253 PMCID: PMC5450525 DOI: 10.1039/c6sc03020c] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/03/2016] [Indexed: 01/06/2023] Open
Abstract
Naturally occurring and synthetic carbohydrate amphiphiles have emerged as a promising class of antimicrobial and antiadhesive agents that act through a number of dynamic and often poorly understood mechanisms. In this paper, we provide the first report on the application of azobenzene trans-cis photoisomerization for effecting spatial and temporal control over bacterial growth and biofilm formation using carbohydrate-based surfactants. Photocontrollable surface tension studies and small angle neutron scattering (SANS) revealed the diverse geometries and dimensions of self-assemblies (micelles) made possible through variation of the head group and UV-visible light irradiation. Using these light-addressable amphiphiles, we demonstrate optical control over the antibacterial activity and formation of biofilms against multi-drug resistant (MDR) Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus (MRSA) and Gram-negative Escherichia coli. To probe the mechanism of bioactivity further, we evaluated the impact of trans-cis photoisomerization in these surfactants on bacterial motility and revealed photomodulated enhancement in swarming motility in P. aeruginosa. These light-responsive amphiphiles should attract significant interest as a new class of antibacterial agents and as investigational tools for probing the complex mechanisms underpinning bacterial adhesion and biofilm formation.
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Affiliation(s)
- Yingxue Hu
- School of Chemistry , Monash University , Victoria 3800 , Australia
| | - Wenyue Zou
- Ian Potter NanoBioSensing Facility , NanoBiotechnology Research Laboratory , School of Science , RMIT University , Victoria 3000 , Australia .
| | - Villy Julita
- School of Chemistry , Monash University , Victoria 3800 , Australia
| | - Rajesh Ramanathan
- Ian Potter NanoBioSensing Facility , NanoBiotechnology Research Laboratory , School of Science , RMIT University , Victoria 3000 , Australia .
| | - Rico F Tabor
- School of Chemistry , Monash University , Victoria 3800 , Australia
| | - Reece Nixon-Luke
- Centre for Molecular and Nanoscale Physics , School of Science , RMIT University , Victoria 3000 , Australia
| | - Gary Bryant
- Centre for Molecular and Nanoscale Physics , School of Science , RMIT University , Victoria 3000 , Australia
| | - Vipul Bansal
- Ian Potter NanoBioSensing Facility , NanoBiotechnology Research Laboratory , School of Science , RMIT University , Victoria 3000 , Australia .
| | - Brendan L Wilkinson
- School of Science and Technology , The University of New England , New South Wales 2351 , Australia .
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118
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Kozma E, Nikić I, Varga BR, Aramburu IV, Kang JH, Fackler OT, Lemke EA, Kele P. Hydrophilic trans-Cyclooctenylated Noncanonical Amino Acids for Fast Intracellular Protein Labeling. Chembiochem 2016; 17:1518-24. [PMID: 27223658 DOI: 10.1002/cbic.201600284] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Indexed: 01/02/2023]
Abstract
Introduction of bioorthogonal functionalities (e.g., trans-cyclooctene-TCO) into a protein of interest by site-specific genetic encoding of non-canonical amino acids (ncAAs) creates uniquely targetable platforms for fluorescent labeling schemes in combination with tetrazine-functionalized dyes. However, fluorescent labeling of an intracellular protein is usually compromised by high background, arising from the hydrophobicity of ncAAs; this is typically compensated for by hours-long washout to remove excess ncAAs from the cellular interior. To overcome these problems, we designed, synthesized, and tested new, hydrophilic TCO-ncAAs. One derivative, DOTCO-lysine was genetically incorporated into proteins with good yield. The increased hydrophilicity shortened the excess ncAA washout time from hours to minutes, thus permitting rapid labeling and subsequent fluorescence microscopy.
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Affiliation(s)
- Eszter Kozma
- Hungarian Academy of Sciences, Research Centre for Natural Sciences, Institute of Organic Chemistry, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Ivana Nikić
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Balázs R Varga
- Hungarian Academy of Sciences, Research Centre for Natural Sciences, Institute of Organic Chemistry, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Iker Valle Aramburu
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jun Hee Kang
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Oliver T Fackler
- Center of Infectious Diseases, Integrative Virology, University of Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
| | - Péter Kele
- Hungarian Academy of Sciences, Research Centre for Natural Sciences, Institute of Organic Chemistry, Magyar tudósok krt. 2, 1117, Budapest, Hungary.
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119
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Neumann-Staubitz P, Neumann H. The use of unnatural amino acids to study and engineer protein function. Curr Opin Struct Biol 2016; 38:119-28. [DOI: 10.1016/j.sbi.2016.06.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/02/2016] [Accepted: 06/04/2016] [Indexed: 12/21/2022]
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120
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Komatsu T, Virdee S. ICBS and ECBS Chemical Biology Meeting 2015 - Let Them Come to Berlin! ACS Chem Biol 2016; 11:1159-66. [PMID: 27198933 DOI: 10.1021/acschembio.6b00268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Toru Komatsu
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- JST PRESTO, Tokyo, Japan
| | - Satpal Virdee
- MRC
Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
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121
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Long MC, Poganik JR, Aye Y. On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry. J Am Chem Soc 2016; 138:3610-22. [PMID: 26907082 PMCID: PMC4805449 DOI: 10.1021/jacs.5b12608] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 11/28/2022]
Abstract
Proximity enhancement is a central chemical tenet underpinning an exciting suite of small-molecule toolsets that have allowed us to unravel many biological complexities. The leitmotif of this opus is "tethering"-a strategy in which a multifunctional small molecule serves as a template to bring proteins/biomolecules together. Scaffolding approaches have been powerfully applied to control diverse biological outcomes such as protein-protein association, protein stability, activity, and improve imaging capabilities. A new twist on this strategy has recently appeared, in which the small-molecule probe is engineered to unleash controlled amounts of reactive chemical signals within the microenvironment of a target protein. Modification of a specific target elicits a precisely timed and spatially controlled gain-of-function (or dominant loss-of-function) signaling response. Presented herein is a unique personal outlook conceptualizing the powerful proximity-enhanced chemical biology toolsets into two paradigms: "multifunctional scaffolding" versus "on-demand targeting". By addressing the latest advances and challenges in the established yet constantly evolving multifunctional scaffolding strategies as well as in the emerging on-demand precision targeting (and related) systems, this Perspective is aimed at choosing when it is best to employ each of the two strategies, with an emphasis toward further promoting novel applications and discoveries stemming from these innovative chemical biology platforms.
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Affiliation(s)
- Marcus
J. C. Long
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Jesse R. Poganik
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Yimon Aye
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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122
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Varon Silva D. ECBS & ICBS 2015 Joint Meeting: Bringing Chemistry to Life. Chembiochem 2016; 17:447-52. [PMID: 26710339 DOI: 10.1002/cbic.201500684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Indexed: 01/11/2023]
Abstract
The European Chemical Biology Society (ECBS) and the International Chemical Biology Society (ICBS) recently organized a joint meeting in Berlin. This meeting had more than 250 participants. Four keynote lectures were given by Timothy Mitchison, David Tirrell, Carolyn Bertozzi and Jason Chin; in addition there were 13 invited speakers, 20 selected oral talks and 30 talks selected from 90 posters. The meeting was divided into six topics: chemoproteomics, epigenetics, conjugates for target delivering, anti-infectives, molecular imaging and probing the structure, and function of post-translational modifications. The highlights of the meeting are presented in this report.
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Affiliation(s)
- Daniel Varon Silva
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 01, 14476, Potsdam, Germany.
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123
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Abstract
Over the years, there have been remarkable efforts in the development of selective protein labeling strategies. In this review, we deliver a comprehensive overview of the currently available bioorthogonal and chemoselective reactions. The ability to introduce bioorthogonal handles to proteins is essential to carry out bioorthogonal reactions for protein labeling in living systems. We therefore summarize the techniques that allow for site-specific "installation" of bioorthogonal handles into proteins. We also highlight the biological applications that have been achieved by selective chemical labeling of proteins.
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Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
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124
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Choi C, Simon AL, Chirot F, Kulesza A, Knight G, Daly S, MacAleese L, Antoine R, Dugourd P. Charge, Color, and Conformation: Spectroscopy on Isomer-Selected Peptide Ions. J Phys Chem B 2016; 120:709-14. [PMID: 26756462 PMCID: PMC4819951 DOI: 10.1021/acs.jpcb.5b11919] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 01/10/2016] [Indexed: 11/28/2022]
Abstract
Monitoring the chromism induced by intramolecular hydrogen and charge transfers within proteins as well as the isomerization of both protein and cofactor is essential not only to understand photoactive signaling pathways but also to design targeted opto-switchable proteins. We used a dual-ion mobility drift tube coupled to a tunable picosecond laser to explore the optical and structural properties of a peptide chain bound to a chromophore-a prototype system allowing for a proton transfer coupled to conformational change. With the support of molecular dynamics and DFT calculations, we show how proton transfer between the peptide and its cofactor can dramatically modify the optical properties of the system and demonstrate that these changes can be triggered by collisional activation in the gas phase.
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Affiliation(s)
- Chang
Min Choi
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Anne-Laure Simon
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Fabien Chirot
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Alexander Kulesza
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Geoffrey Knight
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Steven Daly
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Luke MacAleese
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Rodolphe Antoine
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
| | - Philippe Dugourd
- Institut Lumière Matière and Institut des Sciences Analytiques, Université Lyon 1—CNRS, Université
de Lyon, 69622 Villeurbanne Cedex, France
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125
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Broichhagen J, Klingl YE, Trauner D, Mayer P. 6-[6-(Pyridin-2-yl)-1,2,4,5-tetra-zin-3-yl]pyridin-3-amine monohydrate. Acta Crystallogr E Crystallogr Commun 2016; 72:238-40. [PMID: 26958397 PMCID: PMC4770950 DOI: 10.1107/s2056989016000608] [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: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 11/25/2022]
Abstract
The packing of the title compound, C12H9N7·H2O, is dominated by hydrogen bonding and π-stacking. Layers parallel to [010] are established by hydrogen bonds involving all amine donor functions and one of the water donor functions, while the remaining water donor function enables the stacking of the layers along [10-1], which is accompanied by π-stacking. In the molecule, the plane of the central tetra-zine ring forms angles of 5.33 (7) and 19.84 (8)° with the adjacent 3-amine-pyridine and pyridine rings, respectively.
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Affiliation(s)
- Johannes Broichhagen
- Ludwig-Maximilians-Universität, Department, Butenandtstrasse 5–13, 81377 München, Germany
| | - Yvonne E. Klingl
- Ludwig-Maximilians-Universität, Department, Butenandtstrasse 5–13, 81377 München, Germany
| | - Dirk Trauner
- Ludwig-Maximilians-Universität, Department, Butenandtstrasse 5–13, 81377 München, Germany
| | - Peter Mayer
- Ludwig-Maximilians-Universität, Department, Butenandtstrasse 5–13, 81377 München, Germany
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126
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Elsässer SJ, Ernst RJ, Walker OS, Chin JW. Genetic code expansion in stable cell lines enables encoded chromatin modification. Nat Methods 2016; 13:158-64. [PMID: 26727110 DOI: 10.1038/nmeth.3701] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/25/2015] [Indexed: 12/15/2022]
Abstract
Genetically encoded unnatural amino acids provide powerful strategies for modulating the molecular functions of proteins in mammalian cells. However, this approach has not been coupled to genome-wide measurements, because efficient incorporation of unnatural amino acids is limited to transient expression settings that lead to very heterogeneous expression. We demonstrate that stable integration of the Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS)/tRNA(Pyl)CUA pair (and its derivatives) into the mammalian genome enables efficient, homogeneous incorporation of unnatural amino acids into target proteins in diverse mammalian cells, and we reveal the distinct transcriptional responses of embryonic stem cells and mouse embryonic fibroblasts to amber codon suppression. Genetically encoding N-ɛ-acetyl-lysine in place of six lysine residues in histone H3 enables deposition of pre-acetylated histones into cellular chromatin, via a pathway that is orthogonal to enzymatic modification. After synthetically encoding lysine-acetylation at natural modification sites, we determined the consequences of acetylation at specific amino acids in histones for gene expression.
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Affiliation(s)
- Simon J Elsässer
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Department of Chemistry, Cambridge University, Cambridge, UK.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Russell J Ernst
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Olivia S Walker
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Department of Chemistry, Cambridge University, Cambridge, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Department of Chemistry, Cambridge University, Cambridge, UK
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127
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Hu R, Yap HK, Fung YH, Wang Y, Cheong WL, So LY, Tsang CS, Lee LYS, Lo WKC, Yuan J, Sun N, Leung YC, Yang G, Wong KY. ‘Light up’ protein–protein interaction through bioorthogonal incorporation of a turn-on fluorescent probe into β-lactamase. MOLECULAR BIOSYSTEMS 2016; 12:3544-3549. [DOI: 10.1039/c6mb00566g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aggregation induced emissive compound EPB can detect protein–protein interaction.
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128
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John AA, Ramil CP, Tian Y, Cheng G, Lin Q. Synthesis and Site-Specific Incorporation of Red-Shifted Azobenzene Amino Acids into Proteins. Org Lett 2015; 17:6258-61. [PMID: 26650435 PMCID: PMC4685939 DOI: 10.1021/acs.orglett.5b03268] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
A series of red-shifted azobenzene
amino acids were synthesized
in moderate-to-excellent yields via a two-step procedure in which
tyrosine derivatives were first oxidized to the corresponding quinonoidal
spirolactones followed by ceric ammonium nitrate-catalyzed azo formation
with the substituted phenylhydrazines. The resulting azobenzene–alanine
derivatives exhibited efficient trans/cis photoswitching upon irradiation with a blue (448 nm) or green (530
nm) LED light. Moreover, nine superfolder green fluorescent protein
(sfGFP) mutants carrying the azobenzene–alanine analogues were
expressed in E. coli in good yields via amber codon
suppression with an orthogonal tRNA/PylRS pair, and one of the mutants
showed durable photoswitching with the LED light.
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Affiliation(s)
- Alford A John
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Carlo P Ramil
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Yulin Tian
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Gang Cheng
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, 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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129
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Wang X, Hu J, Liu G, Tian J, Wang H, Gong M, Liu S. Reversibly Switching Bilayer Permeability and Release Modules of Photochromic Polymersomes Stabilized by Cooperative Noncovalent Interactions. J Am Chem Soc 2015; 137:15262-75. [DOI: 10.1021/jacs.5b10127] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaorui Wang
- CAS
Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory
for Physical Sciences at the Microscale, iChem (Collaborative Innovation
Center of Chemistry for Energy Materials), Department of Polymer Science
and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jinming Hu
- CAS
Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory
for Physical Sciences at the Microscale, iChem (Collaborative Innovation
Center of Chemistry for Energy Materials), Department of Polymer Science
and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Guhuan Liu
- CAS
Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory
for Physical Sciences at the Microscale, iChem (Collaborative Innovation
Center of Chemistry for Energy Materials), Department of Polymer Science
and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jie Tian
- Engineering
and Materials Science Experiment Center, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Huijuan Wang
- Engineering
and Materials Science Experiment Center, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ming Gong
- Engineering
and Materials Science Experiment Center, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Shiyong Liu
- CAS
Key Laboratory of Soft Matter Chemistry, Hefei National Laboratory
for Physical Sciences at the Microscale, iChem (Collaborative Innovation
Center of Chemistry for Energy Materials), Department of Polymer Science
and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
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130
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Imaging and manipulating proteins in live cells through covalent labeling. Nat Chem Biol 2015; 11:917-23. [PMID: 26575238 DOI: 10.1038/nchembio.1959] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/14/2015] [Indexed: 12/19/2022]
Abstract
The past 20 years have witnessed the advent of numerous technologies to specifically and covalently label proteins in cellulo and in vivo with synthetic probes. These technologies range from self-labeling proteins tags to non-natural amino acids, and the question is no longer how we can specifically label a given protein but rather with what additional functionality we wish to equip it. In addition, progress in fields such as super-resolution microscopy and genome editing have either provided additional motivation to label proteins with advanced synthetic probes or removed some of the difficulties of conducting such experiments. By focusing on two particular applications, live-cell imaging and the generation of reversible protein switches, we outline the opportunities and challenges of the field and how the synergy between synthetic chemistry and protein engineering will make it possible to conduct experiments that are not feasible with conventional approaches.
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131
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Broichhagen J, Damijonaitis A, Levitz J, Sokol KR, Leippe P, Konrad D, Isacoff EY, Trauner D. Orthogonal Optical Control of a G Protein-Coupled Receptor with a SNAP-Tethered Photochromic Ligand. ACS CENTRAL SCIENCE 2015; 1:383-393. [PMID: 27162996 PMCID: PMC4827557 DOI: 10.1021/acscentsci.5b00260] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Indexed: 05/30/2023]
Abstract
The covalent attachment of synthetic photoswitches is a general approach to impart light sensitivity onto native receptors. It mimics the logic of natural photoreceptors and significantly expands the reach of optogenetics. Here we describe a novel photoswitch design-the photoswitchable orthogonal remotely tethered ligand (PORTL)-that combines the genetically encoded SNAP-tag with photochromic ligands connected to a benzylguanine via a long flexible linker. We use the method to convert the G protein-coupled receptor mGluR2, a metabotropic glutamate receptor, into a photoreceptor (SNAG-mGluR2) that provides efficient optical control over the neuronal functions of mGluR2: presynaptic inhibition and control of excitability. The PORTL approach enables multiplexed optical control of different native receptors using distinct bioconjugation methods. It should be broadly applicable since SNAP-tags have proven to be reliable, many SNAP-tagged receptors are already available, and photochromic ligands on a long leash are readily designed and synthesized.
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Affiliation(s)
- Johannes Broichhagen
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - Arunas Damijonaitis
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - Joshua Levitz
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - Kevin R. Sokol
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - Philipp Leippe
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - David Konrad
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - Ehud Y. Isacoff
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Helen
Wills Neuroscience Institute, University
of California, Berkeley, California 94720, United States
- Physical
Bioscience Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Dirk Trauner
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
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132
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Dong M, Babalhavaeji A, Samanta S, Beharry AA, Woolley GA. Red-Shifting Azobenzene Photoswitches for in Vivo Use. Acc Chem Res 2015; 48:2662-70. [PMID: 26415024 DOI: 10.1021/acs.accounts.5b00270] [Citation(s) in RCA: 417] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recently, there has been a great deal of interest in using the photoisomerization of azobenzene compounds to control specific biological targets in vivo. These azo compounds can be used as research tools or, in principle, could act as optically controlled drugs. Such "photopharmaceuticals" offer the prospect of targeted drug action and an unprecedented degree of temporal control. A key feature of azo compounds designed to photoswitch in vivo is the wavelength of light required to cause the photoisomerization. To pass through tissue such as the human hand, wavelengths in the red, far-red, or ideally near infrared region are required. This Account describes our attempts to produce such azo compounds. Introducing electron-donating or push/pull substituents at the para positions delocalizes the azobenzene chromophore and leads to long wavelength absorption but usually also lowers the thermal barrier to interconversion of the isomers. Fast thermal relaxation means it is difficult to produce a large steady state fraction of the cis isomer. Thus, specifically activating or inhibiting a biological process with the cis isomer would require an impractically bright light source. We have found that introducing substituents at all four ortho positions leads to azo compounds with a number of unusual properties that are useful for in vivo photoswitching. When the para substituents are amide groups, these tetra-ortho substituted azo compounds show unusually slow thermal relaxation rates and enhanced separation of n-π* transitions of cis and trans isomers compared to analogues without ortho substituents. When para positions are substituted with amino groups, ortho methoxy groups greatly stabilize the azonium form of the compounds, in which the azo group is protonated. Azonium ions absorb strongly in the red region of the spectrum and can reach into the near-IR. These azonium ions can exhibit robust cis-trans isomerization in aqueous solutions at neutral pH. By varying the nature of ortho substituents, together with the number and nature of meta and para substituents, long wavelength switching, stability to photobleaching, stability to hydrolysis, and stability to reduction by thiols can all be crafted into a photoswitch. Some of these newly developed photoswitches can be used in whole blood and show promise for effective use in vivo. It is hoped they can be combined with appropriate bioactive targets to realize the potential of photopharmacology.
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Affiliation(s)
- Mingxin Dong
- Department
of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S
3H6, Canada
| | | | - Subhas Samanta
- Department
of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S
3H6, Canada
- Department
of Chemistry, University of Pittsburgh, Chevron Science Center, 219 Parkman
Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Andrew A. Beharry
- Department
of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S
3H6, Canada
- Department
of Chemistry, Stanford University, 333 Campus Drive, Mudd Building, Stanford, California 94305-4401, United States
| | - G. Andrew Woolley
- Department
of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S
3H6, Canada
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