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Feng Z, Ducos B, Scerbo P, Aujard I, Jullien L, Bensimon D. The Development and Application of Opto-Chemical Tools in the Zebrafish. Molecules 2022; 27:molecules27196231. [PMID: 36234767 PMCID: PMC9572478 DOI: 10.3390/molecules27196231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
The zebrafish is one of the most widely adopted animal models in both basic and translational research. This popularity of the zebrafish results from several advantages such as a high degree of similarity to the human genome, the ease of genetic and chemical perturbations, external fertilization with high fecundity, transparent and fast-developing embryos, and relatively low cost-effective maintenance. In particular, body translucency is a unique feature of zebrafish that is not adequately obtained with other vertebrate organisms. The animal’s distinctive optical clarity and small size therefore make it a successful model for optical modulation and observation. Furthermore, the convenience of microinjection and high embryonic permeability readily allow for efficient delivery of large and small molecules into live animals. Finally, the numerous number of siblings obtained from a single pair of animals offers large replicates and improved statistical analysis of the results. In this review, we describe the development of opto-chemical tools based on various strategies that control biological activities with unprecedented spatiotemporal resolution. We also discuss the reported applications of these tools in zebrafish and highlight the current challenges and future possibilities of opto-chemical approaches, particularly at the single cell level.
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Affiliation(s)
- Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
- Correspondence: (Z.F.); (D.B.)
| | - Bertrand Ducos
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- High Throughput qPCR Core Facility, Ecole Normale Supérieure, Paris Sciences Letters University, 46 Rue d’Ulm, 75005 Paris, France
| | - Pierluigi Scerbo
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Inovarion, 75005 Paris, France
| | - Isabelle Aujard
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - Ludovic Jullien
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - David Bensimon
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Correspondence: (Z.F.); (D.B.)
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2
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Chen TH, Garnir K, Chen CY, Jian CB, Gao HD, Cheng B, Tseng MC, Moucheron C, Kirsch-De Mesmaeker A, Lee HM. A Toolkit for Engineering Proteins in Living Cells: Peptide with a Tryptophan-Selective Ru-TAP Complex to Regioselectively Photolabel Specific Proteins. J Am Chem Soc 2022; 144:18117-18125. [PMID: 36135325 DOI: 10.1021/jacs.2c08342] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using a chemical approach to crosslink functionally versatile bioeffectors (such as peptides) to native proteins of interest (POI) directly inside a living cell is a useful toolbox for chemical biologists. However, this goal has not been reached due to unsatisfactory chemoselectivity, regioselectivity, and protein selectivity in protein labeling within living cells. Herein, we report the proof of concept of a cytocompatible and highly selective photolabeling strategy using a tryptophan-specific Ru-TAP complex as a photocrosslinker. Aside from the high selectivity, the photolabeling is blue light-driven by a photoinduced electron transfer (PeT) and allows the bioeffector to bear an additional UV-responsive unit. The two different photosensitivities are demonstrated by blue light-photocrosslinking a UV-sensitive peptide to POI. Our visible light photolabeling can generate photocaged proteins for subsequent activity manipulation by UV light. Cytoskeletal dynamics regulation is demonstrated in living cells via the unprecedented POI photomanipulation and proves that our methodology opens a new avenue to endogenous protein modification.
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Affiliation(s)
- Tzu-Ho Chen
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.,Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Kevin Garnir
- Laboratoire de Chimie Organique et Photochimie CP160/08, Université libre de Bruxelles, 50 Av. Franklin D. Roosevelt, 1050 Brussels, Belgium
| | - Chong-Yan Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Cheng-Bang Jian
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.,Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.,Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Hua-De Gao
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.,Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Bill Cheng
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung 40227, Taiwan
| | - Mei-Chun Tseng
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Cécile Moucheron
- Laboratoire de Chimie Organique et Photochimie CP160/08, Université libre de Bruxelles, 50 Av. Franklin D. Roosevelt, 1050 Brussels, Belgium
| | - Andrée Kirsch-De Mesmaeker
- Laboratoire de Chimie Organique et Photochimie CP160/08, Université libre de Bruxelles, 50 Av. Franklin D. Roosevelt, 1050 Brussels, Belgium
| | - Hsien-Ming Lee
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
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3
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Recent Advances in Protein Caging Tools for Protein Photoactivation. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12083750] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In biosciences and biotechnologies, it is recently critical to promote research regarding the regulation of the dynamic functions of proteins of interest. Light-induced control of protein activity is a strong tool for a wide variety of applications because light can be spatiotemporally irradiated in high resolutions. Therefore, synthetic, semi-synthetic, and genetic engineering techniques for photoactivation of proteins have been actively developed. In this review, the conventional approaches will be outlined. As a solution for overcoming barriers in conventional ones, our recent approaches in which proteins were chemically modified with biotinylated caging reagents are introduced to photo-activate a variety of proteins without genetic engineering and elaborate optimization. This review mainly focuses on protein caging and describes the concepts underlying the development of reported approaches that can contribute to the emergence of both novel protein photo-regulating methods and their killer applications.
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4
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Mangubat-Medina AE, Ball ZT. Triggering biological processes: methods and applications of photocaged peptides and proteins. Chem Soc Rev 2021; 50:10403-10421. [PMID: 34320043 DOI: 10.1039/d0cs01434f] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There has been a significant push in recent years to deploy fundamental knowledge and methods of photochemistry toward biological ends. Photoreactive groups have enabled chemists to activate biological function using the concept of photocaging. By granting spatiotemporal control over protein activation, these photocaging methods are fundamental in understanding biological processes. Peptides and proteins are an important group of photocaging targets that present conceptual and technical challenges, requiring precise chemoselectivity in complex polyfunctional environments. This review focuses on recent advances in photocaging techniques and methodologies, as well as their use in living systems. Photocaging methods include genetic and chemical approaches that require a deep understanding of structure-function relationships based on subtle changes in primary structure. Successful implementation of these ideas can shed light on important spatiotemporal aspects of living systems.
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Affiliation(s)
| | - Zachary T Ball
- Department of Chemistry, Rice University, Houston, TX, 77005, USA.
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5
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Adatia KK, Halbritter T, Reinfelds M, Michele A, Tran M, Laschat S, Heckel A, Tovar GEM, Southan A. Coumarin‐4‐ylmethyl‐ and p‐Hydroxyphenacyl‐Based Photoacid Generators with High Solubility in Aqueous Media: Synthesis, Stability and Photolysis. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.201900258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Karishma K. Adatia
- Institute of Interfacial Process Engineering and Plasma Technology IGVPUniversity of Stuttgart Nobelstr. 12 70569 Stuttgart Germany
| | - Thomas Halbritter
- Institute for Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
- Department of ChemistryUniversity of Iceland Dunhaga 3 107 Reykjavik Iceland
| | - Matiss Reinfelds
- Institute for Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Andre Michele
- Institute of Interfacial Process Engineering and Plasma Technology IGVPUniversity of Stuttgart Nobelstr. 12 70569 Stuttgart Germany
- Institute of Organic Chemistry IOCUniversity of Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Michael Tran
- Institute of Interfacial Process Engineering and Plasma Technology IGVPUniversity of Stuttgart Nobelstr. 12 70569 Stuttgart Germany
- Institute of Organic Chemistry IOCUniversity of Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Sabine Laschat
- Institute of Organic Chemistry IOCUniversity of Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Günter E. M. Tovar
- Institute of Interfacial Process Engineering and Plasma Technology IGVPUniversity of Stuttgart Nobelstr. 12 70569 Stuttgart Germany
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB Nobelstr. 12 70569 Stuttgart Germany
| | - Alexander Southan
- Institute of Interfacial Process Engineering and Plasma Technology IGVPUniversity of Stuttgart Nobelstr. 12 70569 Stuttgart Germany
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6
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Singh AK, Kundu M, Roy S, Roy B, Shah SS, Nair AV, Pal B, Mondal M, Singh NDP. A two-photon responsive naphthyl tagged p-hydroxyphenacyl based drug delivery system: uncaging of anti-cancer drug in the phototherapeutic window with real-time monitoring. Chem Commun (Camb) 2020; 56:9986-9989. [DOI: 10.1039/d0cc01903h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A two-photon responsive drug delivery system having two-photon absorption (TPA) in the phototherapeutic window with a two-photon uncaging cross-section ≥10 GM and exhibiting real-time monitoring of anti-cancer drug release.
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Affiliation(s)
- Amit Kumar Singh
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- 721302 Kharagpur
- India
| | - Moumita Kundu
- School of Medical Science and Technology
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
| | - Samrat Roy
- Department of Physical Sciences
- Indian Institute of Science Education and Research
- Kolkata, Mohanpur, Nadia 741246
- India
| | - Biswajit Roy
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- 721302 Kharagpur
- India
| | - Sk. Sheriff Shah
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- 721302 Kharagpur
- India
| | - Asha V Nair
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- 721302 Kharagpur
- India
| | - Bipul Pal
- Department of Physical Sciences
- Indian Institute of Science Education and Research
- Kolkata, Mohanpur, Nadia 741246
- India
| | - Mahitosh Mondal
- School of Medical Science and Technology
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
| | - N. D. Pradeep Singh
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- 721302 Kharagpur
- India
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7
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Claaßen C, Gerlach T, Rother D. Stimulus-Responsive Regulation of Enzyme Activity for One-Step and Multi-Step Syntheses. Adv Synth Catal 2019; 361:2387-2401. [PMID: 31244574 PMCID: PMC6582597 DOI: 10.1002/adsc.201900169] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/25/2019] [Indexed: 01/20/2023]
Abstract
Multi-step biocatalytic reactions have gained increasing importance in recent years because the combination of different enzymes enables the synthesis of a broad variety of industrially relevant products. However, the more enzymes combined, the more crucial it is to avoid cross-reactivity in these cascade reactions and thus achieve high product yields and high purities. The selective control of enzyme activity, i.e., remote on-/off-switching of enzymes, might be a suitable tool to avoid the formation of unwanted by-products in multi-enzyme reactions. This review compiles a range of methods that are known to modulate enzyme activity in a stimulus-responsive manner. It focuses predominantly on in vitro systems and is subdivided into reversible and irreversible enzyme activity control. Furthermore, a discussion section provides indications as to which factors should be considered when designing and choosing activity control systems for biocatalysis. Finally, an outlook is given regarding the future prospects of the field.
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Affiliation(s)
- Christiane Claaßen
- Institute of Bio- and Geosciences – Biotechnology (IBG-1)Forschungszentrum Jülich GmbH52425JülichGermany
| | - Tim Gerlach
- Institute of Bio- and Geosciences – Biotechnology (IBG-1)Forschungszentrum Jülich GmbH52425JülichGermany
- Aachen Biology and Biotechnology (ABBt)RWTH Aachen University52074AachenGermany
| | - Dörte Rother
- Institute of Bio- and Geosciences – Biotechnology (IBG-1)Forschungszentrum Jülich GmbH52425JülichGermany
- Aachen Biology and Biotechnology (ABBt)RWTH Aachen University52074AachenGermany
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8
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Dedkova LM, Hecht SM. Expanding the Scope of Protein Synthesis Using Modified Ribosomes. J Am Chem Soc 2019; 141:6430-6447. [PMID: 30901982 DOI: 10.1021/jacs.9b02109] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The ribosome produces all of the proteins and many of the peptides present in cells. As a macromolecular complex composed of both RNAs and proteins, it employs a constituent RNA to catalyze the formation of peptide bonds rapidly and with high fidelity. Thus, the ribosome can be argued to represent the key link between the RNA World, in which RNAs were the primary catalysts, and present biological systems in which protein catalysts predominate. In spite of the well-known phylogenetic conservation of rRNAs through evolutionary history, rRNAs can be altered readily when placed under suitable pressure, e.g. in the presence of antibiotics which bind to functionally critical regions of rRNAs. While the structures of rRNAs have been altered intentionally for decades to enable the study of their role(s) in the mechanism of peptide bond formation, it is remarkable that the purposeful alteration of rRNA structure to enable the elaboration of proteins and peptides containing noncanonical amino acids has occurred only recently. In this Perspective, we summarize the history of rRNA modifications, and demonstrate how the intentional modification of 23S rRNA in regions critical for peptide bond formation now enables the direct ribosomal incorporation of d-amino acids, β-amino acids, dipeptides and dipeptidomimetic analogues of the normal proteinogenic l-α-amino acids. While proteins containing metabolically important functional groups such as carbohydrates and phosphate groups are normally elaborated by the post-translational modification of nascent polypeptides, the use of modified ribosomes to produce such polymers directly is also discussed. Finally, we describe the elaboration of such modified proteins both in vitro and in bacterial cells, and suggest how such novel biomaterials may be exploited in future studies.
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Affiliation(s)
- Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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9
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Fleming CL, Grøtli M, Andréasson J. On‐Command Regulation of Kinase Activity using Photonic Stimuli. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201800253] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Cassandra L. Fleming
- Department of Chemistry and Molecular BiologyUniversity of Gothenburg SE-41296 Göteborg Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular BiologyUniversity of Gothenburg SE-41296 Göteborg Sweden
| | - Joakim Andréasson
- Department of Chemistry and Chemical Engineering, Chemistry and BiochemistryChalmers University of Technology SE-41296 Göteborg Sweden
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10
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Schultz C. The Life Science Toolbox Provided by Chemical Biology. Isr J Chem 2019. [DOI: 10.1002/ijch.201900020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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11
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Traven V, Cheptsov D, Vershinina G, Solovjeva N, Chibisova T, Dolotov S, Ivanov I. (7-Dialkylamino-3-coumarinyl)pyrazolines – new effective push-pull photogenerators of acidity. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.09.072] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Biswas S, Mengji R, Barman S, Venugopal V, Jana A, Singh NDP. ‘AIE + ESIPT’ assisted photorelease: fluorescent organic nanoparticles for dual anticancer drug delivery with real-time monitoring ability. Chem Commun (Camb) 2018; 54:168-171. [DOI: 10.1039/c7cc07692d] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
‘Aggregation Induced Emission + Excited State Intramolecular Proton Transfer (AIE + ESIPT)’-assisted photorelease of an anticancer drug by a p-hydroxyphenacyl (pHP) phototrigger with real-time monitoring has been demonstrated.
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Affiliation(s)
- Sandipan Biswas
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur-721302
- India
| | - Rakesh Mengji
- Division of Chemical Biology
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
| | - Shrabani Barman
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur-721302
- India
| | - Vangala Venugopal
- Division of Chemical Biology
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Academic of Scientific and Innovative Research (AcSIR)
| | - Avijit Jana
- Division of Chemical Biology
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Division of Natural Products Chemistry
| | - N. D. Pradeep Singh
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur-721302
- India
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13
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Chen S, Maini R, Bai X, Nangreave RC, Dedkova LM, Hecht SM. Incorporation of Phosphorylated Tyrosine into Proteins: In Vitro Translation and Study of Phosphorylated IκB-α and Its Interaction with NF-κB. J Am Chem Soc 2017; 139:14098-14108. [PMID: 28898075 PMCID: PMC5901656 DOI: 10.1021/jacs.7b05168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphorylated proteins play important roles in the regulation of many different cell networks. However, unlike the preparation of proteins containing unmodified proteinogenic amino acids, which can be altered readily by site-directed mutagenesis and expressed in vitro and in vivo, the preparation of proteins phosphorylated at predetermined sites cannot be done easily and in acceptable yields. To enable the synthesis of phosphorylated proteins for in vitro studies, we have explored the use of phosphorylated amino acids in which the phosphate moiety bears a chemical protecting group, thus eliminating the negative charges that have been shown to have a negative effect on protein translation. Bis-o-nitrobenzyl protection of tyrosine phosphate enabled its incorporation into DHFR and IκB-α using wild-type ribosomes, and the elaborated proteins could subsequently be deprotected by photolysis. Also investigated in parallel was the re-engineering of the 23S rRNA of Escherichia coli, guided by the use of a phosphorylated puromycin, to identify modified ribosomes capable of incorporating unprotected phosphotyrosine into proteins from a phosphotyrosyl-tRNACUA by UAG codon suppression during in vitro translation. Selection of a library of modified ribosomal clones with phosphorylated puromycin identified six modified ribosome variants having mutations in nucleotides 2600-2605 of 23S rRNA; these had enhanced sensitivity to the phosphorylated puromycin. The six clones demonstrated some sequence homology in the region 2600-2605 and incorporated unprotected phosphotyrosine into IκB-α using a modified gene having a TAG codon in the position corresponding to amino acid 42 of the protein. The purified phosphorylated protein bound to a phosphotyrosine specific antibody and permitted NF-κB binding to a DNA duplex sequence corresponding to its binding site in the IL-2 gene promoter. Unexpectedly, phosphorylated IκB-α also mediated the exchange of exogenous DNA into an NF-κB-cellular DNA complex isolated from the nucleus of activated Jurkat cells.
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Affiliation(s)
- Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Rumit Maini
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Ryan C. Nangreave
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M. Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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14
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Luo X, Wu J, Lv T, Lai Y, Zhang H, Lu JJ, Zhang Y, Huang Z. Synthesis and evaluation of novel O2-derived diazeniumdiolates as photochemical and real-time monitoring nitric oxide delivery agents. Org Chem Front 2017. [DOI: 10.1039/c7qo00695k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
3, a new photochemical theranostic agent, wherein light-triggered nitric oxide release can be controlled and real-time monitored at the cellular level.
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Affiliation(s)
- Xiaojun Luo
- State Key Laboratory of Natural Medicines
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases
- Jiangsu Key Laboratory of Drug Screening
- China Pharmaceutical University
- Nanjing 210009
| | - Jianbing Wu
- State Key Laboratory of Natural Medicines
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases
- Jiangsu Key Laboratory of Drug Screening
- China Pharmaceutical University
- Nanjing 210009
| | - Tian Lv
- State Key Laboratory of Natural Medicines
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases
- Jiangsu Key Laboratory of Drug Screening
- China Pharmaceutical University
- Nanjing 210009
| | - Yisheng Lai
- State Key Laboratory of Natural Medicines
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases
- Jiangsu Key Laboratory of Drug Screening
- China Pharmaceutical University
- Nanjing 210009
| | - Honghua Zhang
- Foreign Languages Department
- China Pharmaceutical University
- Nanjing 210009
- PR China
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
| | - Yihua Zhang
- State Key Laboratory of Natural Medicines
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases
- Jiangsu Key Laboratory of Drug Screening
- China Pharmaceutical University
- Nanjing 210009
| | - Zhangjian Huang
- State Key Laboratory of Natural Medicines
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases
- Jiangsu Key Laboratory of Drug Screening
- China Pharmaceutical University
- Nanjing 210009
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15
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Barman S, Mukhopadhyay SK, Biswas S, Nandi S, Gangopadhyay M, Dey S, Anoop A, Pradeep Singh ND. A p
-Hydroxyphenacyl-Benzothiazole-Chlorambucil Conjugate as a Real-Time-Monitoring Drug-Delivery System Assisted by Excited-State Intramolecular Proton Transfer. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201508901] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shrabani Barman
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Sourav K. Mukhopadhyay
- Department of Biotechnology; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Sandipan Biswas
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Surajit Nandi
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Moumita Gangopadhyay
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Satyahari Dey
- Department of Biotechnology; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Anakuthil Anoop
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - N. D. Pradeep Singh
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
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16
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Barman S, Mukhopadhyay SK, Biswas S, Nandi S, Gangopadhyay M, Dey S, Anoop A, Pradeep Singh ND. A p
-Hydroxyphenacyl-Benzothiazole-Chlorambucil Conjugate as a Real-Time-Monitoring Drug-Delivery System Assisted by Excited-State Intramolecular Proton Transfer. Angew Chem Int Ed Engl 2016; 55:4194-8. [PMID: 26919455 DOI: 10.1002/anie.201508901] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/16/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Shrabani Barman
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Sourav K. Mukhopadhyay
- Department of Biotechnology; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Sandipan Biswas
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Surajit Nandi
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Moumita Gangopadhyay
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Satyahari Dey
- Department of Biotechnology; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - Anakuthil Anoop
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
| | - N. D. Pradeep Singh
- Department of Chemistry; Indian Institute of Technology; Kharagpur 721302 West Bengal India
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17
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Wang X, Feng M, Xiao L, Tong A, Xiang Y. Postsynthetic Modification of DNA Phosphodiester Backbone for Photocaged DNAzyme. ACS Chem Biol 2016; 11:444-51. [PMID: 26669486 DOI: 10.1021/acschembio.5b00867] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photocaged (photoactivatable) biomolecules are powerful tools for noninvasive control of biochemical activities by light irradiation. DNAzymes (deoxyribozymes) are single-stranded oligonucleotides with a broad range of enzymatic activities. In this work, to construct photocaged DNAzymes, we developed a facile and mild postsynthetic method to incorporate an interesting photolabile modification (thioether-enol phosphate, phenol substituted, TEEP-OH) into readily available phosphorothioate DNA. Upon light irradiation, TEEP-OH transformed into a native DNA phosphodiester, and accordingly the DNAzymes with RNA-cleaving activities were turned "on" from its inactive and caged form. Activation of the TEEP-OH-caged DNAzyme by light was also successful inside live cells.
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Affiliation(s)
- Xiaoyan Wang
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Mengli Feng
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Lu Xiao
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
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18
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Wang M, Sun S, Neufeld CI, Perez-Ramirez B, Xu Q. Reactive Oxygen Species-Responsive Protein Modification and Its Intracellular Delivery for Targeted Cancer Therapy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407234] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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19
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Wang M, Sun S, Neufeld CI, Perez-Ramirez B, Xu Q. Reactive oxygen species-responsive protein modification and its intracellular delivery for targeted cancer therapy. Angew Chem Int Ed Engl 2014; 53:13444-8. [PMID: 25287050 DOI: 10.1002/anie.201407234] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/19/2014] [Indexed: 12/11/2022]
Abstract
Herein we report a convenient chemical approach to reversibly modulate protein (RNase A) function and develop a protein that is responsive to reactive oxygen species (ROS) for targeted cancer therapy. The conjugation of RNase A with 4-nitrophenyl 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl) benzyl carbonate (NBC) blocks protein lysine and temporarily deactivates the protein. However, the treatment of RNase A-NBC with hydrogen peroxide (one major intracellular ROS) efficiently cleaves the NBC conjugation and restores the RNase A activity. Thus, RNase A-NBC can be reactivated inside tumor cells by high levels of intracellular ROS, thereby restoring the cytotoxicity of RNase A for cancer therapy. Due to higher ROS levels inside tumor cells compared to healthy cells, and the resulting different levels of RNase A-NBC reactivation, RNase A-NBC shows a significant specific cytotoxicity against tumor cells.
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Affiliation(s)
- Ming Wang
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA (USA)
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20
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Li J, Yu J, Zhao J, Wang J, Zheng S, Lin S, Chen L, Yang M, Jia S, Zhang X, Chen PR. Palladium-triggered deprotection chemistry for protein activation in living cells. Nat Chem 2014; 6:352-61. [DOI: 10.1038/nchem.1887] [Citation(s) in RCA: 289] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 02/05/2014] [Indexed: 02/07/2023]
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21
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Kohse S, Neubauer A, Pazidis A, Lochbrunner S, Kragl U. Photoswitching of Enzyme Activity by Laser-Induced pH-Jump. J Am Chem Soc 2013; 135:9407-11. [DOI: 10.1021/ja400700x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Stefanie Kohse
- Department of Chemistry, University of Rostock, Albert-Einstein-Straße
3a, D-18059 Rostock, Germany
- Faculty
of Interdisciplinary Research, University of Rostock, Wismarsche Straße 8, D-18057
Rostock, Germany
| | - Antje Neubauer
- Institute of Physics, University of Rostock, Universitaetsplatz 3, D-18055
Rostock, Germany
| | - Alexandra Pazidis
- Institute of Physics, University of Rostock, Universitaetsplatz 3, D-18055
Rostock, Germany
| | - Stefan Lochbrunner
- Institute of Physics, University of Rostock, Universitaetsplatz 3, D-18055
Rostock, Germany
- Faculty
of Interdisciplinary Research, University of Rostock, Wismarsche Straße 8, D-18057
Rostock, Germany
| | - Udo Kragl
- Department of Chemistry, University of Rostock, Albert-Einstein-Straße
3a, D-18059 Rostock, Germany
- Faculty
of Interdisciplinary Research, University of Rostock, Wismarsche Straße 8, D-18057
Rostock, Germany
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22
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Klán P, Šolomek T, Bochet CG, Blanc A, Givens R, Rubina M, Popik V, Kostikov A, Wirz J. Photoremovable protecting groups in chemistry and biology: reaction mechanisms and efficacy. Chem Rev 2013; 113:119-91. [PMID: 23256727 PMCID: PMC3557858 DOI: 10.1021/cr300177k] [Citation(s) in RCA: 1229] [Impact Index Per Article: 111.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Petr Klán
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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23
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Matsuo K, Kioi Y, Yasui R, Takaoka Y, Miki T, Fujishima SH, Hamachi I. One-step construction of caged carbonic anhydrase I using a ligand-directed acyl imidazole-based protein labeling method. Chem Sci 2013. [DOI: 10.1039/c3sc50560j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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24
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Givens RS, Rubina M, Wirz J. Applications of p-hydroxyphenacyl (pHP) and coumarin-4-ylmethyl photoremovable protecting groups. Photochem Photobiol Sci 2012; 11:472-88. [PMID: 22344608 PMCID: PMC3422890 DOI: 10.1039/c2pp05399c] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 01/20/2012] [Indexed: 12/12/2022]
Abstract
Most applications of photoremovable protecting groups have used o-nitrobenzyl compounds and their (often commercially available) derivatives that, however, have several disadvantages. The focus of this review is on applications of the more recently developed title compounds, which are especially well suited for time-resolved biochemical and physiological investigations, because they release the caged substrates in high yield within a few nanoseconds or less. Together, these two chromophores cover the action spectrum for photorelease from >700 nm to 250 nm.
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Affiliation(s)
- Richard S. Givens
- Department of Chemistry, University of Kansas, Kansas, USA; Tel: +1 785 864 3846
| | - Marina Rubina
- Department of Chemistry, University of Kansas, Kansas, USA; Tel: +1 785 864 1574
| | - Jakob Wirz
- Department of Chemistry, Klingelbergstrasse 80, CH-4056 Basel, Switzerland; Tel: +41 76 413 47 48
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25
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Stanton-Humphreys MN, Taylor RDT, McDougall C, Hart ML, Brown CTA, Emptage NJ, Conway SJ. Wavelength-orthogonal photolysis of neurotransmittersin vitro. Chem Commun (Camb) 2012; 48:657-9. [DOI: 10.1039/c1cc15135e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Givens RS, Stensrud K, Conrad PG, Yousef AL, Perera C, Senadheera SN, Heger D, Wirz J. p-Hydroxyphenacyl photoremovable protecting groups - Robust photochemistry despite substituent diversity. CAN J CHEM 2011; 89:364-384. [PMID: 24436496 PMCID: PMC3891043 DOI: 10.1139/v10-143] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A broadly based investigation of the effects of a diverse array of substituents on the photochemical rearrangement of p-hydroxyphenacyl esters has demonstrated that common substituents such as F, MeO, CN, CO2R, CONH2, and CH3 have little effect on the rate and quantum efficiencies for the photo-Favorskii rearrangement and the release of the acid leaving group or on the lifetimes of the reactive triplet state. A decrease in the quantum yields across all substituents was observed for the release and rearrangement when the photolyses were carried out in buffered aqueous media at pHs that exceeded the ground-state pKa of the chromophore where the conjugate base is the predominant form. Otherwise, substituents have only a very modest effect on the photoreaction of these robust chromophores.
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Affiliation(s)
- Richard S. Givens
- Department of Chemistry, University of Kansas Lawrence, Lawrence, KS 66045, USA
| | - Kenneth Stensrud
- Department of Chemistry, University of Kansas Lawrence, Lawrence, KS 66045, USA
| | - Peter G. Conrad
- Department of Chemistry, University of Kansas Lawrence, Lawrence, KS 66045, USA
| | - Abraham L. Yousef
- Department of Chemistry, University of Kansas Lawrence, Lawrence, KS 66045, USA
| | - Chamani Perera
- Department of Chemistry, University of Kansas Lawrence, Lawrence, KS 66045, USA
| | | | - Dominik Heger
- Research Centre for Toxic Compounds in the Environment (RECETOX) and Department of Chemistry, Faculty of Science, Masaryk University, Kamenice3, 625 00 Brno, Czech Republic
| | - Jakob Wirz
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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27
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Agnes RS, Jernigan F, Shell JR, Sharma V, Lawrence DS. Suborganelle sensing of mitochondrial cAMP-dependent protein kinase activity. J Am Chem Soc 2010; 132:6075-80. [PMID: 20380406 DOI: 10.1021/ja909652q] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A fluorescent sensor of protein kinase activity has been developed and used to characterize the compartmentalized location of cAMP-dependent protein kinase activity in mitochondria. The sensor functions via a phosphorylation-induced release of a quencher from a peptide-based substrate, producing a 150-fold enhancement in fluorescence. The quenching phenomenon transpires via interaction of the quencher with Arg residues positioned on the peptide substrate. Although the cAMP-dependent protein kinase is known to be present in mitochondria, the relative amount of enzyme positioned in the major compartments (outer membrane, intermembrane space, and the matrix) of the organelle is unclear. The fluorescent sensor developed in this study was used to reveal the relative matrix/intermembrane space/outer membrane (85:6:9) distribution of PKA in bovine heart mitochondria.
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Affiliation(s)
- Richard S Agnes
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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28
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Kageyama Y, Ohshima R, Sakurama K, Fujiwara Y, Tanimoto Y, Yamada Y, Aoki S. Photochemical cleavage reactions of 8-quinolinyl sulfonates in aqueous solution. Chem Pharm Bull (Tokyo) 2010; 57:1257-66. [PMID: 19881278 DOI: 10.1248/cpb.57.1257] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Photochemical cleavage reactions of 8-quinolinyl benzenesulfonate derivatives and related sulfonates in aqueous solutions are reported. The 8-quinolinyl benzenesulfonates undergo photolysis upon photoirradiation at 300-330 nm to give the corresponding 8-quinolinols and benzenesulfonic acids with the production of only negligible amounts of byproducts. The effects of substituent groups of the 8-quinolinyl moiety and the benzene ring on the photolysis reactions were examined. Based on steady-state mechanistic studies using a triplet sensitizer, a triplet quencher, and electron donors, it was suggested that the photolysis proceeds mainly via the homolytic cleavage of S-O bonds in the excited triplet state.
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Affiliation(s)
- Yoshiyuki Kageyama
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
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29
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Shao Q, Xing B. Photoactive molecules for applications in molecular imaging and cell biology. Chem Soc Rev 2010; 39:2835-46. [DOI: 10.1039/b915574k] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Kotzur N, Briand B, Beyermann M, Hagen V. Wavelength-Selective Photoactivatable Protecting Groups for Thiols. J Am Chem Soc 2009; 131:16927-31. [DOI: 10.1021/ja907287n] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nico Kotzur
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Benoît Briand
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Michael Beyermann
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Volker Hagen
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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31
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Priestman MA, Lawrence DS. Light-mediated remote control of signaling pathways. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:547-58. [PMID: 19765679 DOI: 10.1016/j.bbapap.2009.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Accepted: 09/08/2009] [Indexed: 01/25/2023]
Abstract
Cell signaling networks display an extraordinary range of temporal and spatial plasticity. Our programmatic approach focuses on the construction of intracellular probes, including sensors, inhibitors, and functionally unique proteins that can be temporally and spatially controlled by the investigator even after they have entered the cell. We have designed and evaluated protein kinase sensors that furnish a fluorescent readout upon phosphorylation. In addition, since the sensors are inert (i.e., cannot be phosphorylated) until activated by light, they can be carried through the various stages of any given cell-based behavior without being consumed. Using this strategy, we have shown that PKCbeta is essential for nuclear envelope breakdown and thus the transition from prophase to metaphase in actively dividing cells. Photoactivatable proteins furnish the means to initiate cellular signaling pathways with a high degree of spatial and temporal control. We have used this approach to demonstrate that cofilin serves as a component of the steering apparatus of the cell. Finally, inhibitors are commonly used to assess the participation of specific enzymes in signaling pathways that control cellular behavior. We have constructed a photo-deactivatable inhibitor, an inhibitory species that can be switched off with light. In the absence of light, the target enzyme is inactive due to the presence of the potent inhibitory molecule. Upon photolysis, the inhibitory molecule is destroyed and enzymatic activity is released.
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Affiliation(s)
- Melanie A Priestman
- Department of Chemistry, The University of North Carolina at Chapel Hill, Kenan Laboratories, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
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32
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Stensrud K, Noh J, Kandler K, Wirz J, Heger D, Givens RS. Competing pathways in the photo-Favorskii rearrangement and release of esters: studies on fluorinated p-hydroxyphenacyl-caged GABA and glutamate phototriggers. J Org Chem 2009; 74:5219-27. [PMID: 19572582 PMCID: PMC3422889 DOI: 10.1021/jo900139h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three new trifluoromethylated p-hydroxyphenacyl (pHP)-caged gamma-aminobutyric acid (GABA) and glutamate (Glu) derivatives have been examined for their efficacy as photoremovable protecting groups in aqueous solution. Through the replacement of hydrogen with fluorine, e.g., a m-trifluoromethyl or a m-trifluoromethoxy versus m-methoxy substituents on the pHP chromophore, modest increases in the quantum yields for the release of amino acids GABA and glutamate as well as improved lipophilicity were realized. The pHP triplet undergoes a photo-Favorskii rearrangement with concomitant release of the amino acid substrate. Deprotonation competes with the rearrangement from the triplet excited state and yields the pHP conjugate base that, upon reprotonation, regenerates the starting ketoester, a chemically unproductive or "energy-wasting" process. When picosecond pump-probe spectroscopy is employed, GABA derivatives 2-5 are characterized by short triplet lifetimes, a manifestation of their rapid release of GABA. The bioavailability of released GABA at the GABA(A) receptor improved when the release took place from m-OCF3 (2) but decreased for m-CF3 (3) when compared with the parent pHP derivative. These studies demonstrate that pKa and lipophilicity exert significant but sometimes opposing influences on the photochemistry and biological activity of pHP phototriggers.
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Affiliation(s)
- Kenneth Stensrud
- Department of Chemistry,1251 Wescoe Hall Drive, University of Kansas, Lawrence, KS 66045
| | - Jihyun Noh
- Department of Otolaryngology, 3500 Terrace St., University of Pittsburgh, Pittsburgh, PA 15208
| | - Karl Kandler
- Department of Otolaryngology, 3500 Terrace St., University of Pittsburgh, Pittsburgh, PA 15208
| | - Jakob Wirz
- Departement Chemie, Universität Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Dominik Heger
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Richard S. Givens
- Department of Chemistry,1251 Wescoe Hall Drive, University of Kansas, Lawrence, KS 66045
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33
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Lee HM, Larson DR, Lawrence DS. Illuminating the chemistry of life: design, synthesis, and applications of "caged" and related photoresponsive compounds. ACS Chem Biol 2009; 4:409-27. [PMID: 19298086 DOI: 10.1021/cb900036s] [Citation(s) in RCA: 369] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Biological systems are characterized by a level of spatial and temporal organization that often lies beyond the grasp of present day methods. Light-modulated bioreagents, including analogs of low molecular weight compounds, peptides, proteins, and nucleic acids, represent a compelling strategy to probe, perturb, or sample biological phenomena with the requisite control to address many of these organizational complexities. Although this technology has created considerable excitement in the chemical community, its application to biological questions has been relatively limited. We describe the challenges associated with the design, synthesis, and use of light-responsive bioreagents; the scope and limitations associated with the instrumentation required for their application; and recent chemical and biological advances in this field.
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Affiliation(s)
- Hsien-Ming Lee
- Departments of Chemistry, Medicinal Chemistry & Natural Products, and Pharmacology, The University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Daniel R. Larson
- Department of Anatomy and Structural Biology, The Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - David S. Lawrence
- Departments of Chemistry, Medicinal Chemistry & Natural Products, and Pharmacology, The University of North Carolina, Chapel Hill, North Carolina 27599-3290
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34
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Mizuno T, Suzuki K, Imai T, Kitade Y, Furutani Y, Kudou M, Oda M, Kandori H, Tsumoto K, Tanaka T. Manipulation of protein-complex function by using an engineered heterotrimeric coiled-coil switch. Org Biomol Chem 2009. [DOI: 10.1039/b901118h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Szewczuk LM, Tarrant MK, Cole PA. Protein phosphorylation by semisynthesis: from paper to practice. Methods Enzymol 2009; 462:1-24. [PMID: 19632467 DOI: 10.1016/s0076-6879(09)62001-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Deconvolution of specific phosphorylation events can be complicated by the reversibility of modification. Protein semisynthesis with phosphonate analogues offers an attractive approach to functional analysis of signaling pathways. In this technique, N- and C-terminal synthetic peptides containing nonhydrolyzable phosphonates at target residues can be ligated to recombinant proteins of interest. The resultant semisynthetic proteins contain site specific, stoichiometric phosphonate modifications and are completely resistant to phosphatases. Control of stoichiometry, specificity, and reversibility allows for complex signaling systems to be broken down into individual events and discretely examined. This chapter outlines the general methods and considerations for designing and carrying out phosphoprotein semisynthetic projects.
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Affiliation(s)
- Lawrence M Szewczuk
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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36
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Tanabe K, Ebihara M, Hirata N, Nishimoto SI. Radiolytic one-electron reduction characteristics of tyrosine derivative caged by 2-oxopropyl group. Bioorg Med Chem Lett 2008; 18:6126-9. [PMID: 18930655 DOI: 10.1016/j.bmcl.2008.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 10/02/2008] [Accepted: 10/03/2008] [Indexed: 10/21/2022]
Abstract
We employed X-irradiation to activate a caged amino acid with a 2-oxoalkyl group. We designed and synthesized tyrosine derivative caged by a 2-oxoalkyl group (Tyr(Oxo)) to evaluate its radiolytic one-electron reduction characteristics in aqueous solution. Upon hypoxic X-irradiation, Tyr(Oxo) released a 2-oxopropyl group to form the corresponding uncaged tyrosine. In addition, radiolysis of dipeptides containing Tyr(Oxo) revealed that the efficiency of radiolytic removal of 2-oxopropyl group increased significantly by the presence of neighboring aromatic amino acids.
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Affiliation(s)
- Kazuhito Tanabe
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan.
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37
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Li H, Hah JM, Lawrence DS. Light-mediated liberation of enzymatic activity: "small molecule" caged protein equivalents. J Am Chem Soc 2008; 130:10474-5. [PMID: 18642802 DOI: 10.1021/ja803395d] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light-activatable ("caged") proteins have been used to correlate, with exquisite temporal and spatial control, intracellular biochemical action with global cellular behavior. However, the chemical or genetic construction of caged proteins is nontrivial, with subsequent laborious introduction into living cells, potentially problematic competition with natural endogenous counterparts, and challenging intracellular incorporation at levels equivalent to the natural enzymes. We describe the design, synthesis, and characterization of small molecular equivalents of a caged Src kinase. These compounds are easy to prepare and function by inhibiting the action of the natural unmodified enzyme.
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Affiliation(s)
- Haishan Li
- Department of Biochemistry, The Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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38
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Kawakami T, Cheng H, Hashiro S, Nomura Y, Tsukiji S, Furuta T, Nagamune T. A Caged Phosphopeptide‐Based Approach for Photochemical Activation of Kinases in Living Cells. Chembiochem 2008; 9:1583-6. [DOI: 10.1002/cbic.200800116] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Abstract
A caged molecule is an inert but photosensitive molecule that is transformed by photolysis into a biologically active molecule at high speed (typically 1 msec). The process is referred to as photorelease. The spatial resolution of photorelease is limited by the properties of light; submicrometer resolution is potentially achievable. Therefore, focal photorelease of caged molecules enables one to control biological processes with high spatio-temporal precision. The principles underlying caged molecules as well as practical considerations for their use are discussed in this unit.
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Affiliation(s)
- Joseph P Y Kao
- University of Maryland Biotechnology Institute, Baltimore, Maryland, USA
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40
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Hahn ME, Pellois JP, Vila-Perelló M, Muir TW. Tunable photoactivation of a post-translationally modified signaling protein and its unmodified counterpart in live cells. Chembiochem 2008; 8:2100-5. [PMID: 17907120 DOI: 10.1002/cbic.200700404] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An ideal technology for direct imaging of post-translationally modified proteins would be one in which the appearance of a fluorescent signal is linked to a modification dependent protein-activation event. Herein, we utilize the protein semisynthesis technique, expressed protein ligation (EPL), to prepare caged analogues of the signaling protein Smad2; the function and fluorescence of the analogues were then photocontrolled in a correlated fashion. We show that this strategy permits titration of the cellular levels of active phosphorylated Smad2 in its biologically relevant, full-length form. We also prepared a nonphosphorylated, caged full-length Smad2 analogue labeled with an orthogonal fluorophore, and simultaneously imaged the phosphorylated and nonphosphorylated forms of the protein in the same cell. This strategy should enable the dissection of the cellular consequences of post-translational modifications (PTMs) by direct comparison of the behavior of the modified and unmodified forms of the protein following uncaging.
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Affiliation(s)
- Michael E Hahn
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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Givens RS, Heger D, Hellrung B, Kamdzhilov Y, Mac M, Conrad PG, Cope E, Lee JI, Mata-Segreda JF, Schowen RL, Wirz J. The photo-Favorskii reaction of p-hydroxyphenacyl compounds is initiated by water-assisted, adiabatic extrusion of a triplet biradical. J Am Chem Soc 2008; 130:3307-9. [PMID: 18290649 DOI: 10.1021/ja7109579] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Richard S Givens
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA.
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42
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Schultz C. Molecular tools for cell and systems biology. HFSP JOURNAL 2007; 1:230-48. [PMID: 19404424 DOI: 10.2976/1.2812442] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 10/24/2007] [Indexed: 01/25/2023]
Abstract
The sequencing of the genomes of key organisms and the subsequent identification of genes merely leads us to the next real challenge in modern biology-revealing the precise functions of these genes. Further, detailed knowledge of how the products of these genes behave in space and time is required, including their interactions with other molecules. In order to tackle these considerable tasks, a large and continuously expanding toolbox is required to probe the functions of proteins on a cellular level. Here, the currently available tools are described and future developments are projected. There is no doubt that only the close interplay between the life science disciplines in addition to advances in engineering will be able to meet the challenge.
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Affiliation(s)
- Carsten Schultz
- Gene Expression Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Lemke EA, Summerer D, Geierstanger BH, Brittain SM, Schultz PG. Control of protein phosphorylation with a genetically encoded photocaged amino acid. Nat Chem Biol 2007; 3:769-72. [PMID: 17965709 DOI: 10.1038/nchembio.2007.44] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 09/20/2007] [Indexed: 01/15/2023]
Abstract
We genetically encoded the photocaged amino acid 4,5-dimethoxy-2-nitrobenzylserine (DMNB-Ser) in Saccharomyces cerevisiae in response to the amber nonsense codon TAG. This amino acid was converted to serine in living cells by irradiation with relatively low-energy blue light and was used to noninvasively photoactivate phosphorylation of the transcription factor Pho4, which controls the cellular response to inorganic phosphate. When substituted at phosphoserine sites that control nuclear export of Pho4, blocks phosphorylation and subsequent export by the receptor Msn5 (ref. 2). We triggered phosphorylation of individual serine residues with a visible laser pulse and monitored nuclear export of Pho4-GFP fusion constructs in real time. We observed distinct export kinetics for differentially phosphorylated Pho4 mutants, which demonstrates dynamic regulation of Pho4 function. This methodology should also facilitate the analysis of other cellular processes involving free serine residues, including catalysis, biomolecular recognition and ion transport.
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Affiliation(s)
- Edward A Lemke
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road SR202, La Jolla, California 92037, USA
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Chen X, Ma C, Kwok WM, Guan X, Du Y, Phillips DL. A Theoretical Investigation of P-Hydroxyphenacyl Caged Phototrigger Compounds: How Water Induces the Photodeprotection and Subsequent Rearrangement Reactions. J Phys Chem B 2007; 111:11832-42. [PMID: 17867669 DOI: 10.1021/jp073529s] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Complete active-space self-consistent field (CASSCF) calculations with a (14,11) active space and density functional theory calculations followed by Car-Parrinello molecular dynamic simulations are reported for the p-hydroxyphenacyl acetate, diethyl phosphate, and diphenyl phosphate phototrigger compounds. These calculations considered the explicit hydrogen bonding of water molecules to the phototrigger compound and help reveal the role of water in promoting the photodeprotection and subsequent rearrangement reactions for the p-hydroxyphenacyl caged phototrigger compounds experimentally observed in the presence of appreciable amounts of water but not observed in neat nonproton solvents like acetonitrile. The 267 nm excitation of the phototrigger compounds leads to an instantaneous population of the S3(1pipi*) state Franck-Condon region, which is followed by an internal conversion deactivation route to the S1(1npi*) state via a 1pipi*/1npi* vibronic coupling. The shorter lifetime of the S1(1npi*) state (approximately 1 ps) starting from the FC geometry is terminated by a fast intersystem crossing at a 3pipi*/3npi* intersection with a structure of mixed pipi*/npi* excitation in the triplet state. The deprotection reaction is triggered by a proton (or hydrogen atom) transfer assisted by water bridges and emanates from this pipi*/npi* triplet state intersection. With the departure of the leaving group, the reaction evolves into a water-mediated post-deprotection phase where the spin inversion of pQM (X, 3A) leads to a spiroketone in the ground state by a cyclization process that is followed by an attack of water to produce a 1,1'-di-hydroxyl-spiroketone. Finally, the H atom of the hydroxyl in 1,1'-di-hydroxyl-spiroketon transfers back to the p-O atom aided by water molecules to generate the p-hydroxyphenyl-acetic acid final rearrangement product.
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Affiliation(s)
- Xuebo Chen
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, PR China
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45
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Abstract
Biologically active compounds which are light-responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with "small molecules", proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as "caged compounds") or reversibly switched between an active and an inactive state.
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Affiliation(s)
- Günter Mayer
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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Sohma Y, Yoshiya T, Taniguchi A, Kimura T, Hayashi Y, Kiso Y. Development of O-acyl isopeptide method. Biopolymers 2007; 88:253-62. [PMID: 17236207 DOI: 10.1002/bip.20683] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
During over a decade of study on aspartic protease inhibitors and water-soluble prodrugs, in 2003, we discovered that the presence of an O-acyl instead of N-acyl residue within the peptide backbone significantly changed the secondary structure of the native peptide. In addition, the target peptide was subsequently generated by an O-N intramolecular acyl migration reaction. These findings led to the development of a novel method, called "O-acyl isopeptide method," for the synthesis of peptides containing difficult sequence. Further application of the method to Alzheimer's Abeta1-42 revealed that the O-acyl isopeptide of Abeta1-42 could be effectively synthesized and stored without spontaneous self-assembly. Intact monomer Abeta1-42 could then be obtained from the isopeptide under physiological experimental conditions. We named the O-acyl isopeptide as "Click Peptide," because of its "quick and easy one-way conversion" to the parent Abeta1- 42. Application of the click peptide has provided a new basis for the investigation of the biological functions of Abeta1-42 by inducible activation of its self-assembly. The O-acyl isopeptide method has further evolved as a general method for peptides synthesis with our recent developments of "O-acyl isodipeptide units" and "racemization-free segment condensation methodology." Isodipeptide units have enabled routine use of the O-acyl isopeptide method by avoiding the often difficult esterification reaction on resin. "Racemizationfree segment condensation methodology" has been achieved by employing N-segments possessing a C-terminal urethaneprotected O-acyl Ser/Thr residues. The synthesis of long peptides/proteins by racemization-free segment condensation has thus become possible at Ser/Thr residues instead of Cterminal Gly/Pro residues. As the O-acyl isopeptide method becomes more widely utilized, we have composed this review to facilitate its application for the production of peptides and proteins.
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Affiliation(s)
- Youhei Sohma
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, 21st Century COE Program, Kyoto Pharmaceutical University, Kyoto, Japan
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Hahn ME, Muir TW. Photocontrol of Smad2, a multiphosphorylated cell-signaling protein, through caging of activating phosphoserines. Angew Chem Int Ed Engl 2005; 43:5800-3. [PMID: 15523718 DOI: 10.1002/anie.200461141] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michael E Hahn
- The Laboratory of Synthetic Protein Chemistry, The Rockefeller University, Box 223, 1230 York Avenue, New York, NY 10021, USA
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49
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Lawrence DS. The preparation and in vivo applications of caged peptides and proteins. Curr Opin Chem Biol 2005; 9:570-5. [PMID: 16182597 DOI: 10.1016/j.cbpa.2005.09.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 09/08/2005] [Indexed: 11/21/2022]
Abstract
Cellular behavior, such as mitosis and motility, are controlled by both when and where specific intracellular signaling pathways are activated in response to environmental cues. Analogous temporally and spatially controlled events occur throughout the lifetime of an organism (e.g. embryogenesis). Consequently, reagents that can be switched on (or off) at any time or at any place in a cell, a tissue, or a living animal, represent the means by which the biochemical basis of spatially and temporally sensitive biological behavior can be evaluated. This review summarizes recent advances in the design and synthesis of light-activated ('caged') peptides and proteins as well as the application of these caged reagents to unanswered questions in biology.
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Affiliation(s)
- David S Lawrence
- Department of Biochemistry, The Albert Einstein College of Medicine, Bronx, New York, New York 10461, USA.
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Xie H, Braha O, Gu LQ, Cheley S, Bayley H. Single-molecule observation of the catalytic subunit of cAMP-dependent protein kinase binding to an inhibitor peptide. ACTA ACUST UNITED AC 2005; 12:109-20. [PMID: 15664520 DOI: 10.1016/j.chembiol.2004.11.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2004] [Revised: 11/04/2004] [Accepted: 11/05/2004] [Indexed: 11/17/2022]
Abstract
An engineered version of the staphylococcal alpha-hemolysin protein pore, bearing a peptide inhibitor near the entrance to the beta barrel, interacts with the catalytic (C) subunit of cAMP-dependent protein kinase. By monitoring the ionic current through the pore, binding events are detected at the single-molecule level. The kinetic and thermodynamic constants governing the binding interaction and the synergistic effect of MgATP are comparable but not identical to the values in bulk solution. Further, the values are strongly dependent on the applied membrane potential. Additional exploration of these findings may lead to a better understanding of the properties of enzymes at the lipid/water interface. Despite the complications, we suggest that the engineered pore might be used as a sensor element to screen inhibitors that act at either the substrate or ATP binding sites of the C subunit.
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Affiliation(s)
- Hongzhi Xie
- Department of Medical Biochemistry and Genetics, Texas A&M University System Health Science Center, 440 Reynolds Medical Building, College Station, TX 77843-1114, USA
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