151
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Abstract
Cell migration is required for many physiological processes, including wound repair and embryogenesis, and relies on precisely orchestrated events that are regulated in a spatially and temporally controlled manner. Most traditional approaches for studying migration, such as genetic methods or the use of chemical inhibitors, do not offer insight into these important components of protein function. However, chemical tools, which respond on a more rapid time scale and in localized regions of the cell, are capable of providing more detailed, real-time information. This Review describes these recent approaches to investigate cell migration and focuses on proteins that are activated by light or small molecules, as well as fluorescent sensors of protein activity.
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Affiliation(s)
- Brenda N. Goguen
- Departments of Biology and Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Barbara Imperiali
- Departments of Biology and Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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152
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Abstract
Genetic code expansion, for the site-specific incorporation of unnatural amino acids into proteins, is currently limited to cultured cells and unicellular organisms. Here we expand the genetic code of a multicellular animal, the nematode Caenorhabditis elegans.
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Affiliation(s)
- Sebastian Greiss
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, U.K
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, U.K
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153
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Toettcher JE, Gong D, Lim WA, Weiner OD. Light control of plasma membrane recruitment using the Phy-PIF system. Methods Enzymol 2011; 497:409-23. [PMID: 21601096 DOI: 10.1016/b978-0-12-385075-1.00017-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The ability to control the activity of intracellular signaling processes in live cells would be an extraordinarily powerful tool. Ideally, such an intracellular input would be (i) genetically encoded, (ii) able to be turned on and off in defined temporal or spatial patterns, (iii) fast to switch between on and off states, and (iv) orthogonal to other cellular processes. The light-gated interaction between fragments of two plant proteins--termed Phy and PIF--satisfies each of these constraints. In this system, Phy can be switched between two conformations using red and infrared light, while PIF only binds one of these states. This chapter describes known constraints for designing genetic constructs using Phy and PIF and provides protocols for expressing these constructs in mammalian cells, purifying the small molecule chromophore required for the system's light responsivity, and measuring light-gated binding by microscopy.
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Affiliation(s)
- Jared E Toettcher
- Cardiovascular Research Institute and Department of Biochemistry, University of California San Francisco, San Francisco, California, USA
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154
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Groff D, Chen PR, Peters FB, Schultz PG. A genetically encoded epsilon-N-methyl lysine in mammalian cells. Chembiochem 2010; 11:1066-8. [PMID: 20422671 DOI: 10.1002/cbic.200900690] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dan Groff
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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155
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156
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Riggsbee CW, Deiters A. Recent advances in the photochemical control of protein function. Trends Biotechnol 2010; 28:468-75. [PMID: 20667607 DOI: 10.1016/j.tibtech.2010.06.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 05/21/2010] [Accepted: 06/01/2010] [Indexed: 12/20/2022]
Abstract
Biological processes are regulated with a high level of spatial and temporal resolution. To understand and manipulate these processes, scientists need to be able to regulate them with Nature's level of precision. In this context, light is a unique regulatory element because it can be precisely controlled in terms of location, timing and amplitude. Moreover, most biological laboratories have a wide range of light sources as standard equipment. This review article summarizes the most recent advances in light-mediated regulation of protein function and its application in a cellular context. Specifically, the photocaging of small-molecule modulators of protein function and of specific amino acid residues in proteins is discussed. In addition, examples of the photochemical control of protein function through the application of genetically engineered natural-light receptors are presented.
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Affiliation(s)
- Chad W Riggsbee
- Department of Chemistry, North Carolina State University, Raleigh, NC 27607, USA
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157
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Gautier A, Nguyen DP, Lusic H, An W, Deiters A, Chin JW. Genetically encoded photocontrol of protein localization in mammalian cells. J Am Chem Soc 2010; 132:4086-8. [PMID: 20218600 DOI: 10.1021/ja910688s] [Citation(s) in RCA: 213] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Precise photochemical control of protein function can be achieved through the site-specific introduction of caging groups. Chemical and enzymatic methods, including in vitro translation and chemical ligation, have been used to photocage proteins in vitro. These methods have been extended to allow the introduction of caged proteins into cells by permeabilization or microinjection, but cellular delivery remains challenging. Since lysine residues are key determinants for nuclear localization sequences, the target of key post-translational modifications (including ubiquitination, methylation, and acetylation), and key residues in many important enzyme active sites, we were interested in photocaging lysine to control protein localization, post-translational modification, and enzymatic activity. Photochemical control of these important functions mediated by lysine residues in proteins has not previously been demonstrated in living cells. Here we synthesized 1 and evolved a pyrrolysyl-tRNA synthetase/tRNA pair to genetically encode the incorporation of this amino acid in response to an amber codon in mammalian cells. To exemplify the utility of this amino acid, we caged the nuclear localization sequences (NLSs) of nucleoplasmin and the tumor suppressor p53 in human cells, thus mislocalizing the proteins in the cytosol. We triggered protein nuclear import with a pulse of light, allowing us to directly quantify the kinetics of nuclear import.
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Affiliation(s)
- Arnaud Gautier
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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158
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Fekner T, Li X, Chan MK. Pyrrolysine Analogs for Translational Incorporation into Proteins. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000204] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tomasz Fekner
- Department of Chemistry, Department of Biochemistry, and Biophysics Graduate Program, The Ohio State University, 484 W 12th Ave., Columbus, OH 43210, USA, Fax: +1‐614‐292 6773
| | - Xin Li
- Department of Chemistry, Department of Biochemistry, and Biophysics Graduate Program, The Ohio State University, 484 W 12th Ave., Columbus, OH 43210, USA, Fax: +1‐614‐292 6773
| | - Michael K. Chan
- Department of Chemistry, Department of Biochemistry, and Biophysics Graduate Program, The Ohio State University, 484 W 12th Ave., Columbus, OH 43210, USA, Fax: +1‐614‐292 6773
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159
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160
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Revilla-López G, Torras J, Curcó D, Casanovas J, Calaza MI, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Grodzinski P, Alemán C. NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids. J Phys Chem B 2010; 114:7413-22. [PMID: 20455555 PMCID: PMC2896893 DOI: 10.1021/jp102092m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peptides and proteins find an ever-increasing number of applications in the biomedical and materials engineering fields. The use of non-proteinogenic amino acids endowed with diverse physicochemical and structural features opens the possibility to design proteins and peptides with novel properties and functions. Moreover, non-proteinogenic residues are particularly useful to control the three-dimensional arrangement of peptidic chains, which is a crucial issue for most applications. However, information regarding such amino acids--also called non-coded, non-canonical, or non-standard--is usually scattered among publications specialized in quite diverse fields as well as in patents. Making all these data useful to the scientific community requires new tools and a framework for their assembly and coherent organization. We have successfully compiled, organized, and built a database (NCAD, Non-Coded Amino acids Database) containing information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, conformational propensities established experimentally, and applications. The architecture of the database is presented in this work together with the first family of non-coded residues included, namely, alpha-tetrasubstituted alpha-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example.
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Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Juan Torras
- Departament d’Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - David Curcó
- Departament d’Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona E-08028, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/ Jaume II n°69, Lleida E-25001, Spain
| | - M. Isabel Calaza
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - David Zanuy
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Piotr Grodzinski
- Alliance for Nanotechnology in Cancer, National Cancer Institute, Bethesda, MD 20892, USA
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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161
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Choi SK, Thomas T, Li MH, Kotlyar A, Desai A, Baker JR. Light-controlled release of caged doxorubicin from folate receptor-targeting PAMAM dendrimer nanoconjugate. Chem Commun (Camb) 2010; 46:2632-4. [PMID: 20449327 PMCID: PMC2901837 DOI: 10.1039/b927215c] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis and in vitro evaluation of folate receptor-targeted nanoconjugate that releases its therapeutic payload via a photochemical mechanism.
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Affiliation(s)
- Seok Ki Choi
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Medical School, Ann Arbor, MI 48109, USA
| | - Thommey Thomas
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Medical School, Ann Arbor, MI 48109, USA
| | - Ming-Hsin Li
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Medical School, Ann Arbor, MI 48109, USA
| | - Alina Kotlyar
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Medical School, Ann Arbor, MI 48109, USA
| | - Ankur Desai
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Medical School, Ann Arbor, MI 48109, USA
| | - James R. Baker
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Medical School, Ann Arbor, MI 48109, USA
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162
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Young TS, Schultz PG. Beyond the canonical 20 amino acids: expanding the genetic lexicon. J Biol Chem 2010; 285:11039-44. [PMID: 20147747 DOI: 10.1074/jbc.r109.091306] [Citation(s) in RCA: 257] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ability to genetically encode unnatural amino acids beyond the common 20 has allowed unprecedented control over the chemical structures of recombinantly expressed proteins. Orthogonal aminoacyl-tRNA synthetase/tRNA pairs have been used together with nonsense, rare, or 4-bp codons to incorporate >50 unnatural amino acids into proteins in Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, and mammalian cell lines. This has allowed the expression of proteins containing amino acids with novel side chains, including fluorophores, post-translational modifications, metal ion chelators, photocaged and photocross-linking moieties, uniquely reactive functional groups, and NMR, IR, and x-ray crystallographic probes.
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Affiliation(s)
- Travis S Young
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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163
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Guo J, Melançon CE, Lee HS, Groff D, Schultz PG. Evolution of amber suppressor tRNAs for efficient bacterial production of proteins containing nonnatural amino acids. Angew Chem Int Ed Engl 2010; 48:9148-51. [PMID: 19856359 DOI: 10.1002/anie.200904035] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jiantao Guo
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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164
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Deiters A. Principles and applications of the photochemical control of cellular processes. Chembiochem 2010; 11:47-53. [PMID: 19911402 PMCID: PMC3768145 DOI: 10.1002/cbic.200900529] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander Deiters
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695-8204, USA.
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165
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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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166
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Jones DH, Cellitti SE, Hao X, Zhang Q, Jahnz M, Summerer D, Schultz PG, Uno T, Geierstanger BH. Site-specific labeling of proteins with NMR-active unnatural amino acids. JOURNAL OF BIOMOLECULAR NMR 2010; 46:89-100. [PMID: 19669620 DOI: 10.1007/s10858-009-9365-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 07/17/2009] [Indexed: 05/19/2023]
Abstract
A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame shift codon specifies the incorporation site in the protein to be studied. These unnatural amino acids can be isotopically labeled and provide unique opportunities for site-specific labeling of proteins for NMR studies. In this perspective, we discuss these opportunities including new photocaged unnatural amino acids, outline usage of metal chelating and spin-labeled unnatural amino acids and expand the approach to in-cell NMR experiments.
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Affiliation(s)
- David H Jones
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121-1125, USA
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167
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Deiters A. Light activation as a method of regulating and studying gene expression. Curr Opin Chem Biol 2009; 13:678-86. [PMID: 19857985 DOI: 10.1016/j.cbpa.2009.09.026] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 09/18/2009] [Accepted: 09/25/2009] [Indexed: 12/14/2022]
Abstract
Recently, several advances have been made in the activation and deactivation of gene expression using light. These developments are based on the application of small molecule inducers of gene expression, antisense- or RNA interference-mediated gene silencing, and the photochemical control of proteins regulating gene function. The majority of the examples employ a classical 'caging technology', through the chemical installation of a light-removable protecting group on the biological molecule (small molecule, oligonucleotide, or protein) of interest and rendering it inactive. UV light irradiation then removes the caging group and activates the molecule, enabling control over gene activity with high spatial and temporal resolution.
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Affiliation(s)
- Alexander Deiters
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695-8204, USA.
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168
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Guo J, Melançon C, Lee HS, Groff D, Schultz P. Evolution of Amber Suppressor tRNAs for Efficient Bacterial Production of Proteins Containing Nonnatural Amino Acids. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904035] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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169
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Abstract
As the focus of synthesis increasingly shifts from its historical emphasis on molecular structure to function, improved strategies are clearly required for the generation of molecules with defined physical, chemical, and biological properties. In contrast, living organisms are remarkably adept at producing molecules and molecular assemblies with an impressive array of functions - from enzymes and antibodies to the photosynthetic center. Thus, the marriage of Nature's synthetic strategies, molecules, and biosynthetic machinery with more traditional synthetic approaches might enable the generation of molecules with properties difficult to achieve by chemical strategies alone. Here we illustrate the potential of this approach and overview some opportunities and challenges in the coming years.
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Affiliation(s)
- Xu Wu
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA
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170
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Sletten E, Bertozzi C. Bioorthogonale Chemie - oder: in einem Meer aus Funktionalität nach Selektivität fischen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900942] [Citation(s) in RCA: 522] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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171
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Affiliation(s)
- Albert Isidro-Llobet
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
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172
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Melançon CE, Schultz PG. One plasmid selection system for the rapid evolution of aminoacyl-tRNA synthetases. Bioorg Med Chem Lett 2009; 19:3845-7. [PMID: 19398201 PMCID: PMC2714362 DOI: 10.1016/j.bmcl.2009.04.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 04/02/2009] [Accepted: 04/03/2009] [Indexed: 11/18/2022]
Abstract
We have developed a rapid, straightforward, one plasmid dual positive/negative selection system for the evolution of aminoacyl-tRNA synthetases with altered specificities in Escherichia coli. This system utilizes an amber stop codon containing chloramphenicol acetyltransferase/uracil phosphoribosyltransferase fusion gene. We demonstrate the utility of the system by identifying a variant of the Methanococcus jannaschii tyrosyl synthetase from a library of 10(9) variants that selectively incorporates para-iodophenylalanine in response to an amber stop codon.
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Affiliation(s)
- Charles E Melançon
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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173
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Peters FB, Brock A, Wang J, Schultz PG. Photocleavage of the polypeptide backbone by 2-nitrophenylalanine. ACTA ACUST UNITED AC 2009; 16:148-52. [PMID: 19246005 DOI: 10.1016/j.chembiol.2009.01.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 01/16/2009] [Accepted: 01/30/2009] [Indexed: 10/21/2022]
Abstract
Photocleavage of the polypeptide backbone is potentially a powerful and general method to activate or deactivate functional peptides and proteins with high spatial and temporal resolution. Here we show that 2-nitrophenylalanine is able to photochemically cleave the polypeptide backbone by an unusual cinnoline-forming reaction. This unnatural amino acid was genetically encoded in E. coli, and protein containing 2-nitrophenylalanine was expressed and site-specifically photocleaved.
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Affiliation(s)
- Francis B Peters
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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174
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Chen P, Groff D, Guo J, Ou W, Cellitti S, Geierstanger B, Schultz P. A Facile System for Encoding Unnatural Amino Acids in Mammalian Cells. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900683] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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175
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Richards NGJ. Shining a light on post-translational modification. HFSP JOURNAL 2009; 2:57-60. [PMID: 19404471 DOI: 10.2976/1.2889161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Indexed: 11/19/2022]
Abstract
Post-translational modification, such as phosphorylation or glycosylation, provides a mechanism for increasing the diversity of protein structures in the cell and regulating biological activity. In addition, such modifications may result in the localization of proteins to specific cellular organelles, with incorrect targeting being associated with a number of diseases. The simplest strategy to identify the functional importance of post-translational modifications is to use mutagenesis methods to replace the residue that is post-translationally modified by one that cannot undergo the relevant chemical transformation. Merely causing "loss of function" does not, however, address questions concerning how cellular function depends on the timing of post-translational changes andor the movement of modified proteins between organelles. The recent demonstration that genetically encoded "photocaged" proteins can be employed to resolve such issues therefore represents an exciting advance in this research area, and is an elegant illustration of the power of combining the power of chemical synthesis and methods for manipulating the biological machinery of protein synthesis.
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Affiliation(s)
- Nigel G J Richards
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, FL 32611-7200, USA
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176
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Wang Q, Parrish AR, Wang L. Expanding the genetic code for biological studies. CHEMISTRY & BIOLOGY 2009; 16:323-36. [PMID: 19318213 PMCID: PMC2696486 DOI: 10.1016/j.chembiol.2009.03.001] [Citation(s) in RCA: 172] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 02/25/2009] [Accepted: 03/03/2009] [Indexed: 11/15/2022]
Abstract
Using an orthogonal tRNA-synthetase pair, unnatural amino acids can be genetically encoded with high efficiency and fidelity, and over 40 unnatural amino acids have been site-specifically incorporated into proteins in Escherichia coli, yeast, or mammalian cells. Novel chemical or physical properties embodied in these amino acids enable new means for tailored manipulation of proteins. This review summarizes the methodology and recent progress in expanding this technology to eukaryotic cells. Applications of genetically encoded unnatural amino acids are highlighted with reports on labeling and modifying proteins, probing protein structure and function, identifying and regulating protein activity, and generating proteins with new properties. Genetic incorporation of unnatural amino acids provides a powerful method for investigating a wide variety of biological processes both in vitro and in vivo.
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Affiliation(s)
- Qian Wang
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Angela R. Parrish
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lei Wang
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
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177
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Nöll G, Trawöger S, von Sanden-Flohe M, Dick B, Grininger M. Blue-Light-Triggered Photorelease of Active Chemicals Captured by the Flavoprotein Dodecin. Chembiochem 2009; 10:834-7. [DOI: 10.1002/cbic.200900014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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178
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Young TS, Ahmad I, Brock A, Schultz PG. Expanding the Genetic Repertoire of the Methylotrophic Yeast Pichia pastoris. Biochemistry 2009; 48:2643-53. [DOI: 10.1021/bi802178k] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Travis S. Young
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, and Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121
| | - Insha Ahmad
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, and Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121
| | - Ansgar Brock
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, and Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121
| | - Peter G. Schultz
- Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, and Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121
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179
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Sletten EM, Bertozzi CR. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 2009; 48:6974-98. [PMID: 19714693 PMCID: PMC2864149 DOI: 10.1002/anie.200900942] [Citation(s) in RCA: 2333] [Impact Index Per Article: 155.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.
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Affiliation(s)
- Ellen M. Sletten
- Department of Chemistry, University of California, Berkeley, CA 94720 (USA)
| | - Carolyn R. Bertozzi
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (USA), Fax: (+1)510-643-2628
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180
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Chen PR, Groff D, Guo J, Ou W, Cellitti S, Geierstanger BH, Schultz PG. A facile system for encoding unnatural amino acids in mammalian cells. Angew Chem Int Ed Engl 2009; 48:4052-5. [PMID: 19378306 PMCID: PMC2873846 DOI: 10.1002/anie.200900683] [Citation(s) in RCA: 225] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A shuttle system has been developed to genetically encode unnatural amino acids in mammalian cells using aminoacyl-tRNA synthetases (aaRSs) evolved in E. coli. A pyrrolysyl-tRNA synthetase (PylRS) mutant was evolved in E. coli that selectively aminoacylates a cognate nonsense suppressor tRNA with a photocaged lysine derivative. Transfer of this orthogonal tRNA-aaRS pair into mammalian cells made possible the selective incorporation of this unnatural amino acid into proteins.
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Affiliation(s)
- Peng R. Chen
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute 10550 Torry Pines Road, La Jolla, CA 92037 (USA)
| | - Dan Groff
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute 10550 Torry Pines Road, La Jolla, CA 92037 (USA)
| | - Jiantao Guo
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute 10550 Torry Pines Road, La Jolla, CA 92037 (USA)
| | - Weijia Ou
- Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive, San Diego, CA 92121 (USA)
| | - Susan Cellitti
- Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive, San Diego, CA 92121 (USA)
| | - Bernhard H. Geierstanger
- Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive, San Diego, CA 92121 (USA)
| | - Peter G. Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute 10550 Torry Pines Road, La Jolla, CA 92037 (USA)
- Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive, San Diego, CA 92121 (USA)
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181
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Yi H, Maisonneuve S, Xie J. Synthesis, glycosylation and photolysis of photolabile 2-(2-nitrophenyl)propyloxycarbonyl (NPPOC) protected glycopyranosides. Org Biomol Chem 2009; 7:3847-54. [DOI: 10.1039/b908404e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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182
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Lee KK, Kim E, Joo C, Song J, Han H, Cho M. Site-selective Intramolecular Hydrogen-Bonding Interactions in Phosphorylated Serine and Threonine Dipeptides. J Phys Chem B 2008; 112:16782-7. [DOI: 10.1021/jp803285x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kyung-Koo Lee
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Eunmyung Kim
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Cheonik Joo
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Jaewook Song
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Hogyu Han
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Minhaeng Cho
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea and Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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183
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Affiliation(s)
- Douglas D Young
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695-8204, USA
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184
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Cellitti SE, Jones DH, Lagpacan L, Hao X, Zhang Q, Hu H, Brittain SM, Brinker A, Caldwell J, Bursulaya B, Spraggon G, Brock A, Ryu Y, Uno T, Schultz PG, Geierstanger BH. In vivo incorporation of unnatural amino acids to probe structure, dynamics, and ligand binding in a large protein by nuclear magnetic resonance spectroscopy. J Am Chem Soc 2008; 130:9268-81. [PMID: 18576636 DOI: 10.1021/ja801602q] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In vivo incorporation of isotopically labeled unnatural amino acids into large proteins drastically reduces the complexity of nuclear magnetic resonance (NMR) spectra. Incorporation is accomplished by coexpressing an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid added to the media and the protein of interest with a TAG amber codon at the desired incorporation site. To demonstrate the utility of this approach for NMR studies, 2-amino-3-(4-(trifluoromethoxy)phenyl)propanoic acid (OCF 3Phe), (13)C/(15)N-labeled p-methoxyphenylalanine (OMePhe), and (15)N-labeled o-nitrobenzyl-tyrosine (oNBTyr) were incorporated individually into 11 positions around the active site of the 33 kDa thioesterase domain of human fatty acid synthase (FAS-TE). In the process, a novel tRNA synthetase was evolved for OCF 3Phe. Incorporation efficiencies and FAS-TE yields were improved by including an inducible copy of the respective aminoacyl-tRNA synthetase gene on each incorporation plasmid. Using only between 8 and 25 mg of unnatural amino acid, typically 2 mg of FAS-TE, sufficient for one 0.1 mM NMR sample, were produced from 50 mL of Escherichia coli culture grown in rich media. Singly labeled protein samples were then used to study the binding of a tool compound. Chemical shift changes in (1)H-(15)N HSQC, (1)H-(13)C HSQC, and (19)F NMR spectra of the different single site mutants consistently identified the binding site and the effect of ligand binding on conformational exchange of some of the residues. OMePhe or OCF 3Phe mutants of an active site tyrosine inhibited binding; incorporating (15)N-Tyr at this site through UV-cleavage of the nitrobenzyl-photocage from oNBTyr re-established binding. These data suggest not only robust methods for using unnatural amino acids to study large proteins by NMR but also establish a new avenue for the site-specific labeling of proteins at individual residues without altering the protein sequence, a feat that can currently not be accomplished with any other method.
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Affiliation(s)
- Susan E Cellitti
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121-1125, USA
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185
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Lin MZ, Wang L. Selective Labeling of Proteins with Chemical Probes in Living Cells. Physiology (Bethesda) 2008; 23:131-41. [DOI: 10.1152/physiol.00007.2008] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Selective labeling of proteins with small molecules introduces novel chemical and physical properties into proteins, enabling the target protein to be investigated or manipulated with various techniques. Different methods for labeling proteins in living cells have been developed by using protein domains, small peptides, or single amino acids. Their application in cells and in vivo has yielded novel insights into diverse biological processes.
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Affiliation(s)
- Michael Z. Lin
- Department of Pharmacology, University of California at San Diego, La Jolla; and
| | - Lei Wang
- The Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, La Jolla, California
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186
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Caged agonist of P2Y1 and P2Y12 receptors for light-directed facilitation of platelet aggregation. Biochem Pharmacol 2007; 75:1341-7. [PMID: 18199424 DOI: 10.1016/j.bcp.2007.10.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 10/25/2007] [Accepted: 10/27/2007] [Indexed: 11/21/2022]
Abstract
We have prepared a caged form (MRS2703) of a potent dual agonist of the P2Y(1) and P2Y(12) nucleotide receptors, 2-MeSADP, by blocking the beta-phosphate group with a 1-(3,4-dimethyloxyphenyl)eth-1-yl phosphoester. Although MRS2703 is itself inactive at human P2Y(1) and P2Y(12) receptors expressed heterologously in 1321N1 astrocytoma cells or in washed human platelets, this derivative readily regenerates the parent agonist upon mild irradiation with long-wave UV light (360 nm). The functional effect of the regenerated agonist was demonstrated by a rise in intracellular calcium mediated by either P2Y(1) or P2Y(12) receptors in transfected cells. Washed human platelets exposed to a solution of MRS2703 were induced to aggregate upon UV irradiation. At 1.0 microM MRS2703, full aggregation was achieved within 1 min of irradiation. Thus, this caged nucleotide promises to be a useful probe for potent P2Y receptor activation with light-directed spatial and temporal control.
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