101
|
Abstract
Recently developed methods that can photochemically control protein activities and functions in live cells have opened up new opportunities for studying signaling networks at the cellular and subcellular levels. Our laboratory has reported a genetically encoded photoactivatable intein, which allows the direct photocontrol of primary sequences of proteins, and consequently, their activities and functions in live mammalian cells. Herein, we provide details on experimental design and the utilization of this photocaged intein to photoactivate the Src tyrosine kinase in human embryonic kidney (HEK) 293T cells. The described procedures may be adopted to photocontrol other proteins in other types of mammalian cells.
Collapse
|
102
|
Padilla MS, Farley CA, Chatkewitz LE, Young DD. Synthesis and incorporation of a caged tyrosine amino acid possessing a bioorthogonal handle. Tetrahedron Lett 2016; 57:4709-4712. [PMID: 28533567 PMCID: PMC5438197 DOI: 10.1016/j.tetlet.2016.09.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Reversing a bioconjugation in a spatial and temporal fashion has widespread applications, especially toward targeted drug delivery. We report the synthesis and incorporation of an unnatural amino acid with an alkyne modified dimethoxy-ortho-nitrobenzyl caging group. This unnatural amino acid can be utilized in a Glaser-Hay conjugation to generate a bioconjugate, but also is able to disrupt the bioconjugate when irradiated with light. These combined features allow for the preparation of bioconjugates with a high degree of site-specificity and allow for the separation of the two components if necessary.
Collapse
Affiliation(s)
- Marshall S Padilla
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Christopher A Farley
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Lindsay E Chatkewitz
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Douglas D Young
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| |
Collapse
|
103
|
Ross B, Mehta S, Zhang J. Molecular tools for acute spatiotemporal manipulation of signal transduction. Curr Opin Chem Biol 2016; 34:135-142. [PMID: 27639090 DOI: 10.1016/j.cbpa.2016.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 08/15/2016] [Accepted: 08/17/2016] [Indexed: 01/14/2023]
Abstract
The biochemical activities involved in signal transduction in cells are under tight spatiotemporal regulation. To study the effects of the spatial patterning and temporal dynamics of biochemical activities on downstream signaling, researchers require methods to manipulate signaling pathways acutely and rapidly. In this review, we summarize recent developments in the design of three broad classes of molecular tools for perturbing signal transduction, classified by their type of input signal: chemically induced, optically induced, and magnetically induced.
Collapse
Affiliation(s)
- Brian Ross
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
104
|
Xiao H, Schultz PG. At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023945. [PMID: 27413101 DOI: 10.1101/cshperspect.a023945] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ability to site-specifically incorporate noncanonical amino acids (ncAAs) with novel structures into proteins in living cells affords a powerful tool to investigate and manipulate protein structure and function. More than 200 ncAAs with diverse biological, chemical, and physical properties have been genetically encoded in response to nonsense or frameshift codons in both prokaryotic and eukaryotic organisms with high fidelity and efficiency. In this review, recent advances in the technology and its application to problems in protein biochemistry, cellular biology, and medicine are highlighted.
Collapse
Affiliation(s)
- Han Xiao
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Peter G Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037 California Institute for Biomedical Research, La Jolla, California 92037
| |
Collapse
|
105
|
Hu P, Feng T, Yeung CC, Koo CK, Lau KC, Lam MHW. A Photo-Triggered Traceless Staudinger-Bertozzi Ligation Reaction. Chemistry 2016; 22:11537-42. [DOI: 10.1002/chem.201601807] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Peng Hu
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
| | - Tianshi Feng
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
- Advanced Laboratory for Environmental Research & Technology; USTC-CityU Suzhou China
- CAS Key Laboratory of Soft Matter Chemistry; Department of Polymer Science and Engineering; University of Science and Technology of China, Hefei; Anhui 230026 China
| | - Chi-Chung Yeung
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
| | - Chi-Kin Koo
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
| | - Kai-Chung Lau
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
| | - Michael H. W. Lam
- Department of Chemistry and Biology; City University of Hong Kong; 83 Tat Chee Avenue Hong Kong SAR China
| |
Collapse
|
106
|
Abstract
The site-specific incorporation of unnatural amino acids (Uaas) via genetic code expansion provides a powerful method to introduce synthetic moieties into specific positions of a protein directly in the live cell. The technique, first developed in bacteria, is nowadays widely applicable in mammalian cells. In general, different Uaas are incorporated with different efficiency. By comparing the incorporation efficiency of several Uaas recently designed for bioorthogonal chemistry, we present here a facile dual-fluorescence assay to evaluate relative yields of Uaa incorporation. Several biological questions can be addressed using Uaas tools. In recent years, photo-cross-linking Uaas have been extensively applied to map ligand-binding sites on G protein-coupled receptors (GPCRs). We describe a simple and efficient two-plasmid system to incorporate a photoactivatable Uaa into a class B GPCR, and demonstrate cross-linking to its nonmodified natural ligand.
Collapse
|
107
|
Incorporation of non-canonical amino acids into proteins in yeast. Fungal Genet Biol 2016; 89:137-156. [DOI: 10.1016/j.fgb.2016.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 12/22/2022]
|
108
|
Kang JY, Kawaguchi D, Wang L. Optical Control of a Neuronal Protein Using a Genetically Encoded Unnatural Amino Acid in Neurons. J Vis Exp 2016:e53818. [PMID: 27078635 DOI: 10.3791/53818] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Photostimulation is a noninvasive way to control biological events with excellent spatial and temporal resolution. New methods are desired to photo-regulate endogenous proteins expressed in their native environment. Here, we present an approach to optically control the function of a neuronal protein directly in neurons using a genetically encoded unnatural amino acid (Uaa). By using an orthogonal tRNA/aminoacyl-tRNA synthetase pair to suppress the amber codon, a photo-reactive Uaa 4,5-dimethoxy-2-nitrobenzyl-cysteine (Cmn) is site-specifically incorporated in the pore of a neuronal protein Kir2.1, an inwardly rectifying potassium channel. The bulky Cmn physically blocks the channel pore, rendering Kir2.1 non-conducting. Light illumination instantaneously converts Cmn into a smaller natural amino acid Cys, activating Kir2.1 channel function. We express these photo-inducible inwardly rectifying potassium (PIRK) channels in rat hippocampal primary neurons, and demonstrate that light-activation of PIRK ceases the neuronal firing due to the outflux of K(+) current through the activated Kir2.1 channels. Using in utero electroporation, we also express PIRK in the embryonic mouse neocortex in vivo, showing the light-activation of PIRK in neocortical neurons. Genetically encoding Uaa imposes no restrictions on target protein type or cellular location, and a family of photoreactive Uaas is available for modulating different natural amino acid residues. This technique thus has the potential to be generally applied to many neuronal proteins to achieve optical regulation of different processes in brains. The current protocol presents an accessible procedure for intricate Uaa incorporation in neurons in vitro and in vivo to achieve photo control of neuronal protein activity on the molecular level.
Collapse
Affiliation(s)
- Ji-Yong Kang
- Department of Neuroscience, School of Medicine, Tufts University
| | - Daichi Kawaguchi
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco;
| |
Collapse
|
109
|
Anion–π interactions in complexes of proteins and halogen-containing amino acids. J Biol Inorg Chem 2016; 21:357-68. [DOI: 10.1007/s00775-016-1346-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 02/08/2016] [Indexed: 10/22/2022]
|
110
|
Walker OS, Elsässer SJ, Mahesh M, Bachman M, Balasubramanian S, Chin JW. Photoactivation of Mutant Isocitrate Dehydrogenase 2 Reveals Rapid Cancer-Associated Metabolic and Epigenetic Changes. J Am Chem Soc 2016; 138:718-21. [PMID: 26761588 PMCID: PMC4821487 DOI: 10.1021/jacs.5b07627] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Isocitrate dehydrogenase is mutated
at a key active site arginine
residue (Arg172 in IDH2) in many cancers, leading to the synthesis
of the oncometabolite (R)-2-hydroxyglutarate (2HG).
To investigate the early events following acquisition of this mutation
in mammalian cells we created a photoactivatable version of IDH2(R172K),
in which K172 is replaced with a photocaged lysine (PCK), via genetic
code expansion. Illumination of cells expressing this mutant protein
led to a rapid increase in the levels of 2HG, with 2HG levels reaching
those measured in patient tumor samples, within 8 h. 2HG accumulation
is closely followed by a global decrease in 5-hydroxymethylcytosine
(5-hmC) in DNA, demonstrating that perturbations in epigenetic DNA
base modifications are an early consequence of mutant IDH2 in cells.
Our results provide a paradigm for rapidly and synchronously uncloaking
diverse oncogenic mutations in live cells to reveal the sequence of
events through which they may ultimately cause transformation.
Collapse
Affiliation(s)
- Olivia S Walker
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.,Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Simon J Elsässer
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.,Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Mohan Mahesh
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Martin Bachman
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Cancer Research U.K. Cambridge Institute , Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Cancer Research U.K. Cambridge Institute , Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.,Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
111
|
Abstract
S-Sulfenylation is a post-translational modification with a crucial role in regulating protein function. However, its analysis has remained challenging due to the lack of facile sulfenic acid models. We report the first photocaged cysteine sulfenic acid with efficient photodeprotection and demonstrate its utility by generating sulfenic acid in a thiol peroxidase after illumination in vitro. These caged sulfoxides should be promising for site-specific incorporation of Cys sulfenic acid in living cells via genetic code expansion.
Collapse
Affiliation(s)
- Jia Pan
- The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458
| | - Kate S. Carroll
- The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458
| |
Collapse
|
112
|
Wong PT, Chen D, Tang S, Yanik S, Payne M, Mukherjee J, Coulter A, Tang K, Tao K, Sun K, Baker JR, Choi SK. Modular Integration of Upconverting Nanocrystal-Dendrimer Composites for Folate Receptor-Specific NIR Imaging and Light-Triggered Drug Release. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:6078-6090. [PMID: 26476917 DOI: 10.1002/smll.201501575] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/13/2015] [Indexed: 06/05/2023]
Abstract
Upconversion nanocrystals (UCNs) display near-infrared (NIR)-responsive photoluminescent properties for NIR imaging and drug delivery. The development of effective strategies for UCN integration with other complementary nanostructures for targeting and drug conjugation is highly desirable. This study reports on a core/shell-based theranostic system designed by UCN integration with a folate (FA)-conjugated dendrimer for tumor targeting and with photocaged doxorubicin as a cytotoxic agent. Two types of UCNs (NaYF4:Yb/Er (or Yb/Tm); diameter = ≈50 to 54 nm) are described, each displaying distinct emission properties upon NIR (980 nm) excitation. The UCNs are surface modified through covalent attachment of photocaged doxorubicin (ONB-Dox) and a multivalent FA-conjugated polyamidoamine (PAMAM) dendrimer G5(FA)6 to prepare UCN@(ONB-Dox)(G5FA). Surface plasmon resonance experiments performed with G5(FA)6 dendrimer alone show nanomolar binding avidity (KD = 5.9 × 10(-9) M) to the folate binding protein. This dendrimer binding corresponds with selective binding and uptake of UCN@(ONB-Dox)(G5FA) by FAR-positive KB carcinoma cells in vitro. Furthermore, UCN@(ONB-Dox)(G5FA) treatment of FAR(+) KB cells inhibits cell growth in a light dependent manner. These results validate the utility of modularly integrated UCN-dendrimer nanocomposites for cell type specific NIR imaging and light-controlled drug release, thus serving as a new theranostic system.
Collapse
Affiliation(s)
- Pamela T Wong
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Dexin Chen
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Shengzhuang Tang
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sean Yanik
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Michael Payne
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jhindan Mukherjee
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Alexa Coulter
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kenny Tang
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ke Tao
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Kang Sun
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - James R Baker
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Seok Ki Choi
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| |
Collapse
|
113
|
Kim J, Bertozzi CR. A Bioorthogonal Reaction of N-Oxide and Boron Reagents. Angew Chem Int Ed Engl 2015; 54:15777-81. [PMID: 26568479 DOI: 10.1002/anie.201508861] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Indexed: 12/15/2022]
Abstract
The development of bioorthogonal reactions has classically focused on bond-forming ligation reactions. In this report, we seek to expand the functional repertoire of such transformations by introducing a new bond-cleaving reaction between N-oxide and boron reagents. The reaction features a large dynamic range of reactivity, showcasing second-order rate constants as high as 2.3×10(3) M(-1) s(-1) using diboron reaction partners. Diboron reagents display minimal cell toxicity at millimolar concentrations, penetrate cell membranes, and effectively reduce N-oxides inside mammalian cells. This new bioorthogonal process based on miniscule components is thus well-suited for activating molecules within cells under chemical control. Furthermore, we demonstrate that the metabolic diversity of nature enables the use of naturally occurring functional groups that display inherent biocompatibility alongside abiotic components for organism-specific applications.
Collapse
Affiliation(s)
- Justin Kim
- Department of Chemistry and Howard Hughes Medical Institute, Stanford University, 380 Roth Way, Stanford, CA 94305 (USA)
| | - Carolyn R Bertozzi
- Department of Chemistry and Howard Hughes Medical Institute, Stanford University, 380 Roth Way, Stanford, CA 94305 (USA).
| |
Collapse
|
114
|
Affiliation(s)
- Justin Kim
- Department of Chemistry and Howard Hughes Medical Institute, Stanford University, 380 Roth Way, Stanford, CA 94305 (USA)
| | - Carolyn R. Bertozzi
- Department of Chemistry and Howard Hughes Medical Institute, Stanford University, 380 Roth Way, Stanford, CA 94305 (USA)
| |
Collapse
|
115
|
Genetic incorporation of recycled unnatural amino acids. Amino Acids 2015; 48:357-63. [PMID: 26358464 DOI: 10.1007/s00726-015-2087-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/25/2015] [Indexed: 01/24/2023]
Abstract
The genetic incorporation of unnatural amino acids (UAAs) into proteins has been a useful tool for protein engineering. However, most UAAs are expensive, and the method requires a high concentration of UAAs, which has been a drawback of the technology, especially for large-scale applications. To address this problem, a method to recycle cultured UAAs was developed. The method is based on recycling a culture medium containing the UAA, in which some of essential nutrients were resupplemented after each culture cycle, and induction of protein expression was controlled with glucose. Under optimal conditions, five UAAs were recycled for up to seven rounds of expression without a decrease in expression level, cell density, or incorporation fidelity. This method can generally be applied to other UAAs; therefore, it is useful for reducing the cost of UAAs for genetic incorporation and helpful for expanding the use of the technology to industrial applications.
Collapse
|
116
|
Soye BJD, Patel JR, Isaacs FJ, Jewett MC. Repurposing the translation apparatus for synthetic biology. Curr Opin Chem Biol 2015; 28:83-90. [PMID: 26186264 DOI: 10.1016/j.cbpa.2015.06.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022]
Abstract
The translation system (the ribosome and associated factors) is the cell's factory for protein synthesis. The extraordinary catalytic capacity of the protein synthesis machinery has driven extensive efforts to harness it for novel functions. For example, pioneering efforts have demonstrated that it is possible to genetically encode more than the 20 natural amino acids and that this encoding can be a powerful tool to expand the chemical diversity of proteins. Here, we discuss recent advances in efforts to expand the chemistry of living systems, highlighting improvements to the molecular machinery and genomically recoded organisms, applications of cell-free systems, and extensions of these efforts to include eukaryotic systems. The transformative potential of repurposing the translation apparatus has emerged as one of the defining opportunities at the interface of chemical and synthetic biology.
Collapse
Affiliation(s)
- Benjamin J Des Soye
- Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Northwestern Institute on Complex Systems, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Suite 11-131, Chicago, IL 60611, USA.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Jaymin R Patel
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06510, USA
| | - Farren J Isaacs
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06510, USA
| | - Michael C Jewett
- Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Northwestern Institute on Complex Systems, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Suite 11-131, Chicago, IL 60611, USA.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| |
Collapse
|
117
|
Lim SI, Kwon I. Bioconjugation of therapeutic proteins and enzymes using the expanded set of genetically encoded amino acids. Crit Rev Biotechnol 2015; 36:803-15. [DOI: 10.3109/07388551.2015.1048504] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sung In Lim
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and
| | - Inchan Kwon
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA and
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| |
Collapse
|
118
|
Wong PT, Choi SK. Mechanisms of Drug Release in Nanotherapeutic Delivery Systems. Chem Rev 2015; 115:3388-432. [DOI: 10.1021/cr5004634] [Citation(s) in RCA: 349] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Pamela T. Wong
- Michigan
Nanotechnology Institute
for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Seok Ki Choi
- Michigan
Nanotechnology Institute
for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
119
|
Wang J, Cheng B, Li J, Zhang Z, Hong W, Chen X, Chen PR. Chemical Remodeling of Cell-Surface Sialic Acids through a Palladium-Triggered Bioorthogonal Elimination Reaction. Angew Chem Int Ed Engl 2015; 54:5364-8. [DOI: 10.1002/anie.201409145] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 02/11/2015] [Indexed: 01/01/2023]
|
120
|
Wang J, Cheng B, Li J, Zhang Z, Hong W, Chen X, Chen PR. Chemical Remodeling of Cell-Surface Sialic Acids through a Palladium-Triggered Bioorthogonal Elimination Reaction. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
121
|
Ren W, Ji A, Ai HW. Light Activation of Protein Splicing with a Photocaged Fast Intein. J Am Chem Soc 2015; 137:2155-8. [DOI: 10.1021/ja508597d] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Wei Ren
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| | - Ao Ji
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| | - Hui-wang Ai
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, California 92521, United States
| |
Collapse
|
122
|
Faal T, Wong PT, Tang S, Coulter A, Chen Y, Tu CH, Baker JR, Choi SK, Inlay MA. 4-Hydroxytamoxifen probes for light-dependent spatiotemporal control of Cre-ER mediated reporter gene expression. MOLECULAR BIOSYSTEMS 2015; 11:783-90. [DOI: 10.1039/c4mb00581c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Here, we synthesized and validated a photocaged hydroxytamoxifen molecule to achieve spatiotemporal control of gene expression with light.
Collapse
Affiliation(s)
- Tannaz Faal
- Sue and Bill Gross Stem Cell Research Center
- University of California Irvine
- Irvine
- USA
- Department of Molecular Biology and Biochemistry
| | - Pamela T. Wong
- Department of Internal Medicine
- Michigan Nanotechnology Institute for Medicine and Biological Sciences
- University of Michigan
- Ann Arbor
- USA
| | - Shengzhuang Tang
- Department of Internal Medicine
- Michigan Nanotechnology Institute for Medicine and Biological Sciences
- University of Michigan
- Ann Arbor
- USA
| | - Alexa Coulter
- Department of Internal Medicine
- Michigan Nanotechnology Institute for Medicine and Biological Sciences
- University of Michigan
- Ann Arbor
- USA
| | - Yumay Chen
- Sue and Bill Gross Stem Cell Research Center
- University of California Irvine
- Irvine
- USA
- Department of Medicine
| | - Christina H. Tu
- Sue and Bill Gross Stem Cell Research Center
- University of California Irvine
- Irvine
- USA
| | - James R. Baker
- Department of Internal Medicine
- Michigan Nanotechnology Institute for Medicine and Biological Sciences
- University of Michigan
- Ann Arbor
- USA
| | - Seok Ki Choi
- Department of Internal Medicine
- Michigan Nanotechnology Institute for Medicine and Biological Sciences
- University of Michigan
- Ann Arbor
- USA
| | - Matthew A. Inlay
- Sue and Bill Gross Stem Cell Research Center
- University of California Irvine
- Irvine
- USA
- Department of Molecular Biology and Biochemistry
| |
Collapse
|
123
|
Rakauskaitė R, Urbanavičiūtė G, Rukšėnaitė A, Liutkevičiūtė Z, Juškėnas R, Masevičius V, Klimašauskas S. Biosynthetic selenoproteins with genetically-encoded photocaged selenocysteines. Chem Commun (Camb) 2015; 51:8245-8. [DOI: 10.1039/c4cc07910h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first general approach for the biosynthesis of selenoproteins that contain photocaged selenocysteine residues at genetically-encoded positions is described.
Collapse
Affiliation(s)
- Rasa Rakauskaitė
- Institute of Biotechnology
- Vilnius University
- Vilnius LT-02241
- Lithuania
| | | | | | | | - Robertas Juškėnas
- Institute of Biotechnology
- Vilnius University
- Vilnius LT-02241
- Lithuania
- Faculty of Chemistry
| | - Viktoras Masevičius
- Institute of Biotechnology
- Vilnius University
- Vilnius LT-02241
- Lithuania
- Faculty of Chemistry
| | | |
Collapse
|
124
|
Padilla MS, Young DD. Photosensitive GFP mutants containing an azobenzene unnatural amino acid. Bioorg Med Chem Lett 2014; 25:470-3. [PMID: 25563892 DOI: 10.1016/j.bmcl.2014.12.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 11/19/2022]
Abstract
The incorporation of unnatural amino acids represents a unique mechanism for the modulation of protein function. This approach has been utilized to generate photoswitchable GFP mutants, capable of demonstrating modulated fluorescence upon exposure to UV irradiation. Overall these photosensitive GFP mutants can be employed in various biosensing and diagnostic techniques to better understand protein function and processing.
Collapse
Affiliation(s)
- Marshall S Padilla
- Department of Chemistry, College of William & Mary, Williamsburg, VA 23187, USA
| | - Douglas D Young
- Department of Chemistry, College of William & Mary, Williamsburg, VA 23187, USA
| |
Collapse
|
125
|
Luo J, Uprety R, Naro Y, Chou C, Nguyen DP, Chin JW, Deiters A. Genetically encoded optochemical probes for simultaneous fluorescence reporting and light activation of protein function with two-photon excitation. J Am Chem Soc 2014; 136:15551-8. [PMID: 25341086 PMCID: PMC4333581 DOI: 10.1021/ja5055862] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
![]()
The site-specific
incorporation of three new coumarin lysine analogues
into proteins was achieved in bacterial and mammalian cells using
an engineered pyrrolysyl-tRNA synthetase system. The genetically encoded
coumarin lysines were successfully applied as fluorescent cellular
probes for protein localization and for the optical activation of
protein function. As a proof-of-principle, photoregulation of firefly
luciferase was achieved in live cells by caging a key lysine residue,
and excellent OFF to ON light-switching ratios were observed. Furthermore,
two-photon and single-photon optochemical control of EGFP maturation
was demonstrated, enabling the use of different, potentially orthogonal
excitation wavelengths (365, 405, and 760 nm) for the sequential activation
of protein function in live cells. These results demonstrate that
coumarin lysines are a new and valuable class of optical probes that
can be used for the investigation and regulation of protein structure,
dynamics, function, and localization in live cells. The small size
of coumarin, the site-specific incorporation, the application as both
a light-activated caging group and as a fluorescent probe, and the
broad range of excitation wavelengths are advantageous over other
genetically encoded photocontrol systems and provide a precise and
multifunctional tool for cellular biology.
Collapse
Affiliation(s)
- Ji Luo
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | | | | | | | | | | | | |
Collapse
|
126
|
Engelke H, Chou C, Uprety R, Jess P, Deiters A. Control of protein function through optochemical translocation. ACS Synth Biol 2014; 3:731-6. [PMID: 24933258 PMCID: PMC4210160 DOI: 10.1021/sb400192a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Controlled manipulation of proteins
and their function is important
in almost all biological disciplines. Here, we demonstrate control
of protein activity with light. We present two different applications—light-triggered
transcription and light-triggered protease cleavage—both based
on the same concept of protein mislocation, followed by optochemically
triggered translocation to an active cellular compartment. In our
approach, we genetically encode a photocaged lysine into the nuclear
localization signal (NLS) of the transcription factor SATB1. This
blocks nuclear import of the protein until illumination induces caging
group removal and release of the protein into the nucleus. In the
first application, prepending this NLS to the transcription factor
FOXO3 allows us to optochemically switch on its transcription activity.
The second application uses the developed light-activated NLS to control
nuclear import of TEV protease and subsequent cleavage of nuclear
proteins containing TEV cleavage sites. The small size of the light-controlled
NLS (only 20 amino acids) minimizes impact of its insertion on protein
function and promises a general approach to a wide range of optochemical
applications. Since the light-activated NLS is genetically encoded
and optically triggered, it will prove useful to address a variety
of problems requiring spatial and temporal control of protein function,
for example, in stem-cell, developmental, and cancer biology.
Collapse
Affiliation(s)
- Hanna Engelke
- Department
of Chemistry and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstraße 11, 81377 München, Germany
| | - Chungjung Chou
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Rajendra Uprety
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Phillip Jess
- Department
of Physics and MCB, University of California, Berkeley, California 94720, United States
| | - Alexander Deiters
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
127
|
Abstract
Substantial efforts in the past decade have resulted in the systematic expansion of genetic codes, allowing for the direct ribosomal incorporation of ∼100 unnatural amino acids into bacteria, yeast, mammalian cells, and animals. Here, we illustrate the versatility of expanded genetic codes in biology and bioengineering, focusing on the application of expanded genetic codes to problems in protein, cell, synthetic, and experimental evolutionary biology. As the expanded genetic code field continues to develop, its place as a foundational technology in the whole of biological sciences will solidify.
Collapse
Affiliation(s)
- Xiang Li
- Department of Biomedical Engineering, University of California at Irvine, 3120 Natural Sciences II, Irvine, CA 92697 (USA)
| | | |
Collapse
|
128
|
Genetic code expansion and bioorthogonal labelling enables cell specific proteomics in an animal. Curr Opin Chem Biol 2014; 21:154-60. [DOI: 10.1016/j.cbpa.2014.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/02/2014] [Accepted: 07/04/2014] [Indexed: 11/20/2022]
|
129
|
Baker AS, Deiters A. Optical control of protein function through unnatural amino acid mutagenesis and other optogenetic approaches. ACS Chem Biol 2014; 9:1398-407. [PMID: 24819585 DOI: 10.1021/cb500176x] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Biological processes are naturally regulated with high spatial and temporal resolution at the molecular, cellular, and systems level. To control and study processes with the same resolution, light-sensitive groups and domains have been employed to optically activate and deactivate protein function. Optical control is a noninvasive technique in which the amplitude, wavelength, spatial location, and timing of the light illumination can be easily controlled. This review focuses on applications of genetically encoded unnatural amino acids containing light-removable protecting groups to optically trigger protein function, while also discussing select optogenetic approaches using natural light-sensitive domains to engineer optical control of biological processes.
Collapse
Affiliation(s)
- Austin S. Baker
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
130
|
Uprety R, Luo J, Liu J, Naro Y, Samanta S, Deiters A. Genetic Encoding of Caged Cysteine and Caged Homocysteine in Bacterial and Mammalian Cells. Chembiochem 2014; 15:1793-9. [DOI: 10.1002/cbic.201400073] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Indexed: 12/19/2022]
|
131
|
Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 801] [Impact Index Per Article: 80.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | | |
Collapse
|
132
|
An in vivo photo-cross-linking approach reveals a homodimerization domain of Aha1 in S. cerevisiae. PLoS One 2014; 9:e89436. [PMID: 24614167 PMCID: PMC3948627 DOI: 10.1371/journal.pone.0089436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 01/23/2014] [Indexed: 11/19/2022] Open
Abstract
Protein-protein interactions play an essential role in almost any biological processes. Therefore, there is a particular need for methods which describe the interactions of a defined target protein in its physiological context. Here we report a method to photo-cross-link interacting proteins in S. cerevisiae by using the non-canonical amino acid p-azido-L-phenylalanine (pAzpa). Based on the expanded genetic code the photoreactive non-canonical amino acid pAzpa was site-specifically incorporated at eight positions into a domain of Aha1 that was previously described to bind Hsp90 in vitro to function as a cochaperone of Hsp90 and activates its ATPase activity. In vivo photo-cross-linking to the cognate binding partner of Aha1 was carried out by irradiation of mutant strains with UV light (365 nm) to induce covalent intermolecular bonds. Surprisingly, an interaction between Aha1 and Hsp90 was not detected, although, we could confirm binding of suppressed pAzpa containing Aha1 to Hsp90 by native co-immunoprecipitation. However, a homodimer consisting of two covalently crosslinked Aha1 monomers was identified by mass spectrometry. This homodimer could also be confirmed using p-benzoyl-L-phenylalanine, another photoreactive non-canonical amino acid. Crosslinking was highly specific as it was dependent on irradiation using UV light, the exact position of the non-canonical amino acid in the protein sequence as well as on the addition of the non-canonical amino acid to the growth medium. Therefore it seems possible that an interaction of Aha1 with Hsp90 takes place at different positions than previously described in vitro highlighting the importance of in vivo techniques to study protein-protein interactions. Accordingly, the expanded genetic code can easily be applied to other S. cerevisiae proteins to study their interaction under physiological relevant conditions in vivo.
Collapse
|
133
|
Camacho-Soto K, Castillo-Montoya J, Tye B, Ghosh I. Ligand-Gated Split-Kinases. J Am Chem Soc 2014; 136:3995-4002. [DOI: 10.1021/ja4130803] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Karla Camacho-Soto
- Department of Chemistry and
Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Javier Castillo-Montoya
- Department of Chemistry and
Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Blake Tye
- Department of Chemistry and
Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Indraneel Ghosh
- Department of Chemistry and
Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| |
Collapse
|
134
|
Schmidt MJ, Summerer D. Genetic code expansion as a tool to study regulatory processes of transcription. Front Chem 2014; 2:7. [PMID: 24790976 PMCID: PMC3982524 DOI: 10.3389/fchem.2014.00007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/07/2014] [Indexed: 12/19/2022] Open
Abstract
The expansion of the genetic code with non-canonical amino acids (ncAA) enables the chemical and biophysical properties of proteins to be tailored, inside cells, with a previously unattainable level of precision. A wide range of ncAA with functions not found in canonical amino acids have been genetically encoded in recent years and have delivered insights into biological processes that would be difficult to access with traditional approaches of molecular biology. A major field for the development and application of novel ncAA-functions has been transcription and its regulation. This is particularly attractive, since advanced DNA sequencing- and proteomics-techniques continue to deliver vast information on these processes on a global level, but complementing methodologies to study them on a detailed, molecular level and in living cells have been comparably scarce. In a growing number of studies, genetic code expansion has now been applied to precisely control the chemical properties of transcription factors, RNA polymerases and histones, and this has enabled new insights into their interactions, conformational changes, cellular localizations and the functional roles of posttranslational modifications.
Collapse
Affiliation(s)
- Moritz J Schmidt
- Department of Chemistry, Zukunftskolleg and Konstanz Research School Chemical Biology, University of Konstanz Konstanz, Germany
| | - Daniel Summerer
- Department of Chemistry, Zukunftskolleg and Konstanz Research School Chemical Biology, University of Konstanz Konstanz, Germany
| |
Collapse
|
135
|
Abstract
Genetic code expansion and reprogramming enable the site-specific incorporation of diverse designer amino acids into proteins produced in cells and animals. Recent advances are enhancing the efficiency of unnatural amino acid incorporation by creating and evolving orthogonal ribosomes and manipulating the genome. Increasing the number of distinct amino acids that can be site-specifically encoded has been facilitated by the evolution of orthogonal quadruplet decoding ribosomes and the discovery of mutually orthogonal synthetase/tRNA pairs. Rapid progress in moving genetic code expansion from bacteria to eukaryotic cells and animals (C. elegans and D. melanogaster) and the incorporation of useful unnatural amino acids has been aided by the development and application of the pyrrolysyl-transfer RNA (tRNA) synthetase/tRNA pair for unnatural amino acid incorporation. Combining chemoselective reactions with encoded amino acids has facilitated the installation of posttranslational modifications, as well as rapid derivatization with diverse fluorophores for imaging.
Collapse
Affiliation(s)
- Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 OQH, United Kingdom;
| |
Collapse
|
136
|
Nguyen DP, Mahesh M, Elsässer SJ, Hancock SM, Uttamapinant C, Chin JW. Genetic encoding of photocaged cysteine allows photoactivation of TEV protease in live mammalian cells. J Am Chem Soc 2014; 136:2240-3. [PMID: 24479649 PMCID: PMC4333589 DOI: 10.1021/ja412191m] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
We demonstrate the evolution of the
PylRS/tRNACUA pair
for genetically encoding photocaged cysteine. By characterizing the
incorporation in Escherichia coli and
mammalian cells, and the photodeprotection process in vitro and in mammalian cells, we establish conditions for rapid efficient
photodeprotection to reveal native proteins in live cells. We demonstrate
the utility of this approach by rapidly activating TEV protease following
illumination of single cells.
Collapse
Affiliation(s)
- Duy P Nguyen
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | | | | | | | | | | |
Collapse
|
137
|
Kang JY, Kawaguchi D, Coin I, Xiang Z, O'Leary DDM, Slesinger PA, Wang L. In vivo expression of a light-activatable potassium channel using unnatural amino acids. Neuron 2014; 80:358-70. [PMID: 24139041 DOI: 10.1016/j.neuron.2013.08.016] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2013] [Indexed: 01/28/2023]
Abstract
Optical control of protein function provides excellent spatial-temporal resolution for studying proteins in situ. Although light-sensitive exogenous proteins and ligands have been used to manipulate neuronal activity, a method for optical control of neuronal proteins using unnatural amino acids (Uaa) in vivo is lacking. Here, we describe the genetic incorporation of a photoreactive Uaa into the pore of an inwardly rectifying potassium channel Kir2.1. The Uaa occluded the pore, rendering the channel nonconducting, and, on brief light illumination, was released to permit outward K(+) current. Expression of this photoinducible inwardly rectifying potassium (PIRK) channel in rat hippocampal neurons created a light-activatable PIRK switch for suppressing neuronal firing. We also expanded the genetic code of mammals to express PIRK channels in embryonic mouse neocortex in vivo and demonstrated a light-activated PIRK current in cortical neurons. These principles could be generally expanded to other proteins expressed in the brain to enable optical regulation.
Collapse
Affiliation(s)
- Ji-Yong Kang
- The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | | | | | | | | | | |
Collapse
|
138
|
Borozan SZ, Stojanović SĐ. Halogen bonding in complexes of proteins and non-natural amino acids. Comput Biol Chem 2013; 47:231-9. [DOI: 10.1016/j.compbiolchem.2013.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/10/2013] [Accepted: 10/10/2013] [Indexed: 12/15/2022]
|
139
|
Rohrbach F, Schäfer F, Fichte MAH, Pfeiffer F, Müller J, Pötzsch B, Heckel A, Mayer G. Aptamerbasiertes Caging zur selektiven Maskierung von Proteindomänen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
140
|
Rohrbach F, Schäfer F, Fichte MAH, Pfeiffer F, Müller J, Pötzsch B, Heckel A, Mayer G. Aptamer-guided caging for selective masking of protein domains. Angew Chem Int Ed Engl 2013; 52:11912-5. [PMID: 24127310 DOI: 10.1002/anie.201306686] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/30/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Falk Rohrbach
- Life and Medical Sciences Institute, Gerhard Domagk-Strasse 1, 53121 Bonn (Germany) http://www.mayerlab.de
| | | | | | | | | | | | | | | |
Collapse
|
141
|
Hemphill J, Chou C, Chin JW, Deiters A. Genetically encoded light-activated transcription for spatiotemporal control of gene expression and gene silencing in mammalian cells. J Am Chem Soc 2013; 135:13433-9. [PMID: 23931657 DOI: 10.1021/ja4051026] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photocaging provides a method to spatially and temporally control biological function and gene expression with high resolution. Proteins can be photochemically controlled through the site-specific installation of caging groups on amino acid side chains that are essential for protein function. The photocaging of a synthetic gene network using unnatural amino acid mutagenesis in mammalian cells was demonstrated with an engineered bacteriophage RNA polymerase. A caged T7 RNA polymerase was expressed in cells with an expanded genetic code and used in the photochemical activation of genes under control of an orthogonal T7 promoter, demonstrating tight spatial and temporal control. The synthetic gene expression system was validated with two reporter genes (luciferase and EGFP) and applied to the light-triggered transcription of short hairpin RNA constructs for the induction of RNA interference.
Collapse
Affiliation(s)
- James Hemphill
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | | | | | | |
Collapse
|
142
|
Inlay MA, Choe V, Bharathi S, Fernhoff NB, Baker JR, Weissman IL, Choi SK. Synthesis of a photocaged tamoxifen for light-dependent activation of Cre-ER recombinase-driven gene modification. Chem Commun (Camb) 2013; 49:4971-3. [PMID: 23612712 PMCID: PMC3926663 DOI: 10.1039/c3cc42179a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We report the design of a water-soluble, quaternized tamoxifen photoprobe and demonstrate its application in light-controlled induction of green fluorescent protein expression via a Cre-ER recombinase system.
Collapse
Affiliation(s)
- Matthew A. Inlay
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Veronica Choe
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sophia Bharathi
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nathaniel B. Fernhoff
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James R. Baker
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seok Ki Choi
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
143
|
Martić S, Kraatz HB. Chemical biology toolkit for exploring protein kinase catalyzed phosphorylation reactions. Chem Sci 2013. [DOI: 10.1039/c2sc20846f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
144
|
Ahmed I, Fruk L. The power of light: photosensitive tools for chemical biology. ACTA ACUST UNITED AC 2013; 9:565-70. [DOI: 10.1039/c2mb25407g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
145
|
Venancio-Marques A, Liu YJ, Diguet A, di Maio T, Gautier A, Baigl D. Modification-free photocontrol of β-lactam conversion with spatiotemporal resolution. ACS Synth Biol 2012; 1:526-31. [PMID: 23656229 DOI: 10.1021/sb300010a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
β-Lactams can be converted into β-amino acids by β-lactamase, a bacterial enzyme, leading to significant change in the biological function of the substrate molecules. Here we describe a method for photocontrol of β-lactam conversion without gene nor enzyme modification. This is achieved by the addition of a cationic photosensitive surfactant, AzoTAB, to a gene expression medium containing DNA coding for β-lactamase, the enzyme capable of the desired conversion. In the absence of UV (365 nm) or after illumination by blue light (480 nm) for 4 min, conversion of β-lactam is strongly reduced while the application of UV for 4 min results in a strong enhancement of substrate conversion. Several cycles of activation/inhibition are obtained upon successive UV/blue light illuminations. When both reconstituted photoresponsive gene expression medium and β-lactamase substrate are encapsulated in independent microfluidic chambers, selective UV illumination results in spatially resolved activation of substrate conversion.
Collapse
Affiliation(s)
- Anna Venancio-Marques
- Department of Chemistry, Ecole Normale Supérieure, 75005 Paris, France
- Université Pierre et Marie Curie Paris 6, 75005 Paris, France
- UMR 8640, CNRS, France
| | - Yan-Jun Liu
- Department of Chemistry, Ecole Normale Supérieure, 75005 Paris, France
- Université Pierre et Marie Curie Paris 6, 75005 Paris, France
- UMR 8640, CNRS, France
| | - Antoine Diguet
- Department of Chemistry, Ecole Normale Supérieure, 75005 Paris, France
- Université Pierre et Marie Curie Paris 6, 75005 Paris, France
- UMR 8640, CNRS, France
| | - Thomas di Maio
- Department of Chemistry, Ecole Normale Supérieure, 75005 Paris, France
- Université Pierre et Marie Curie Paris 6, 75005 Paris, France
- UMR 8640, CNRS, France
| | - Arnaud Gautier
- Department of Chemistry, Ecole Normale Supérieure, 75005 Paris, France
- Université Pierre et Marie Curie Paris 6, 75005 Paris, France
- UMR 8640, CNRS, France
| | - Damien Baigl
- Department of Chemistry, Ecole Normale Supérieure, 75005 Paris, France
- Université Pierre et Marie Curie Paris 6, 75005 Paris, France
- UMR 8640, CNRS, France
| |
Collapse
|
146
|
Gfeller D, Michielin O, Zoete V. SwissSidechain: a molecular and structural database of non-natural sidechains. Nucleic Acids Res 2012; 41:D327-32. [PMID: 23104376 PMCID: PMC3531096 DOI: 10.1093/nar/gks991] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Amino acids form the building blocks of all proteins. Naturally occurring amino acids are restricted to a few tens of sidechains, even when considering post-translational modifications and rare amino acids such as selenocysteine and pyrrolysine. However, the potential chemical diversity of amino acid sidechains is nearly infinite. Exploiting this diversity by using non-natural sidechains to expand the building blocks of proteins and peptides has recently found widespread applications in biochemistry, protein engineering and drug design. Despite these applications, there is currently no unified online bioinformatics resource for non-natural sidechains. With the SwissSidechain database (http://www.swisssidechain.ch), we offer a central and curated platform about non-natural sidechains for researchers in biochemistry, medicinal chemistry, protein engineering and molecular modeling. SwissSidechain provides biophysical, structural and molecular data for hundreds of commercially available non-natural amino acid sidechains, both in l- and d-configurations. The database can be easily browsed by sidechain names, families or physico-chemical properties. We also provide plugins to seamlessly insert non-natural sidechains into peptides and proteins using molecular visualization software, as well as topologies and parameters compatible with molecular mechanics software.
Collapse
Affiliation(s)
- David Gfeller
- Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland
| | | | | |
Collapse
|
147
|
Genetically encoded libraries of nonstandard peptides. J Nucleic Acids 2012; 2012:713510. [PMID: 23097693 PMCID: PMC3477784 DOI: 10.1155/2012/713510] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/12/2012] [Indexed: 11/17/2022] Open
Abstract
The presence of a nonproteinogenic moiety in a nonstandard peptide often improves the biological properties of the peptide. Non-standard peptide libraries are therefore used to obtain valuable molecules for biological, therapeutic, and diagnostic applications. Highly diverse non-standard peptide libraries can be generated by chemically or enzymatically modifying standard peptide libraries synthesized by the ribosomal machinery, using posttranslational modifications. Alternatively, strategies for encoding non-proteinogenic amino acids into the genetic code have been developed for the direct ribosomal synthesis of non-standard peptide libraries. In the strategies for genetic code expansion, non-proteinogenic amino acids are assigned to the nonsense codons or 4-base codons in order to add these amino acids to the universal genetic code. In contrast, in the strategies for genetic code reprogramming, some proteinogenic amino acids are erased from the genetic code and non-proteinogenic amino acids are reassigned to the blank codons. Here, we discuss the generation of genetically encoded non-standard peptide libraries using these strategies and also review recent applications of these libraries to the selection of functional non-standard peptides.
Collapse
|
148
|
Expanding the genetic code of Drosophila melanogaster. Nat Chem Biol 2012; 8:748-50. [DOI: 10.1038/nchembio.1043] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 06/22/2012] [Indexed: 02/01/2023]
|
149
|
Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Light-controlled tools. Angew Chem Int Ed Engl 2012; 51:8446-76. [PMID: 22829531 DOI: 10.1002/anie.201202134] [Citation(s) in RCA: 738] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Indexed: 12/21/2022]
Abstract
Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems--from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.
Collapse
Affiliation(s)
- Clara Brieke
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438 Frankfurt/Main, Germany
| | | | | | | | | |
Collapse
|
150
|
Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Lichtgesteuerte Werkzeuge. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202134] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clara Brieke
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
| | - Falk Rohrbach
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Gottschalk
- Buchmann‐Institut für Molekulare Lebenswissenschaften, Institut für Biochemie, Max‐von‐Laue‐Straße 15, 60438 Frankfurt/Main (Deutschland)
| | - Günter Mayer
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Heckel
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
| |
Collapse
|