1
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Giltrap A, Yuan Y, Davis BG. Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology. Chem Rev 2024; 124:889-928. [PMID: 38231473 PMCID: PMC10870719 DOI: 10.1021/acs.chemrev.3c00579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024]
Abstract
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.
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Affiliation(s)
- Andrew
M. Giltrap
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Yizhi Yuan
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Benjamin G. Davis
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
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2
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Layden A, Ma X, Johnson CA, He XJ, Buczynski SA, Banghart MR. A Biomimetic C-Terminal Extension Strategy for Photocaging Amidated Neuropeptides. J Am Chem Soc 2023; 145:19611-19621. [PMID: 37649440 PMCID: PMC10510324 DOI: 10.1021/jacs.3c03913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 09/01/2023]
Abstract
Photoactivatable neuropeptides offer a robust stimulus-response relationship that can drive mechanistic studies into the physiological mechanisms of neuropeptidergic transmission. The majority of neuropeptides contain a C-terminal amide, which offers a potentially general site for installation of a C-terminal caging group. Here, we report a biomimetic caging strategy in which the neuropeptide C-terminus is extended via a photocleavable amino acid to mimic the proneuropeptides found in large dense-core vesicles. We explored this approach with four prominent neuropeptides: gastrin-releasing peptide (GRP), oxytocin (OT), substance P (SP), and cholecystokinin (CCK). C-terminus extension greatly reduced the activity of all four peptides at heterologously expressed receptors. In cell type-specific electrophysiological recordings from acute brain slices, subsecond flashes of ultraviolet light produced rapidly activating membrane currents via activation of endogenous G protein-coupled receptors. Subsequent mechanistic studies with caged CCK revealed a role for extracellular proteases in shaping the temporal dynamics of CCK signaling, and a striking switch-like, cell-autonomous anti-opioid effect of transient CCK signaling in hippocampal parvalbumin interneurons. These results suggest that C-terminus extension with a photocleavable linker may be a general strategy for photocaging amidated neuropeptides and demonstrate how photocaged neuropeptides can provide mechanistic insights into neuropeptide signaling that are inaccessible using conventional approaches.
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Affiliation(s)
| | | | - Caroline A. Johnson
- Department of Neurobiology,
School of Biological Sciences, University
of California San Diego, La Jolla, California 92093, United States
| | | | - Stanley A. Buczynski
- Department of Neurobiology,
School of Biological Sciences, University
of California San Diego, La Jolla, California 92093, United States
| | - Matthew R. Banghart
- Department of Neurobiology,
School of Biological Sciences, University
of California San Diego, La Jolla, California 92093, United States
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3
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Bickerton LE, Langton MJ. Controlling transmembrane ion transport via photo-regulated carrier mobility. Chem Sci 2022; 13:9531-9536. [PMID: 36091898 PMCID: PMC9400602 DOI: 10.1039/d2sc03322d] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/07/2022] [Indexed: 11/21/2022] Open
Abstract
Stimuli-responsive transmembrane ion carriers allow for targeted and controllable transport activity, with potential applications as therapeutics for channelopathies and cancer, and in fundamental studies into ion transport phenomena. These applications require OFF-ON activation from a fully inactive state which does not exhibit background activity, but this remains challenging to achieve with synthetic transport systems. Here we introduce a novel mechanism for photo-gating mobile ion carriers, which involves modulating the mobility of the carriers within the lipid bilayer membrane. By appending a membrane-targeting anchor to the carrier using a photo-cleavable linker, the carrier's ion transport activity is fully switched off by suppressing its ability to shuttle between the two aqueous-membrane interfaces of the bilayer. The system can be reactivated rapidly in situ within the membrane by photo-triggered cleavage of the anchor to release the mobile ion carrier. This approach does not involve direct functionalization of the ion binding site of the carrier, and so does not require the de novo design of novel ion binding motifs to implement the photo-caging of activity. This work demonstrates that controlling the mobility of artificial transport systems enables precise control over activity, opening up new avenues for spatio-temporally targeted ionophores.
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Affiliation(s)
- Laura E Bickerton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Matthew J Langton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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4
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Recent Advances in Protein Caging Tools for Protein Photoactivation. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12083750] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In biosciences and biotechnologies, it is recently critical to promote research regarding the regulation of the dynamic functions of proteins of interest. Light-induced control of protein activity is a strong tool for a wide variety of applications because light can be spatiotemporally irradiated in high resolutions. Therefore, synthetic, semi-synthetic, and genetic engineering techniques for photoactivation of proteins have been actively developed. In this review, the conventional approaches will be outlined. As a solution for overcoming barriers in conventional ones, our recent approaches in which proteins were chemically modified with biotinylated caging reagents are introduced to photo-activate a variety of proteins without genetic engineering and elaborate optimization. This review mainly focuses on protein caging and describes the concepts underlying the development of reported approaches that can contribute to the emergence of both novel protein photo-regulating methods and their killer applications.
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5
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Blum AP, Yin J, Lin HH, Oliver BA, Kammeyer JK, Thompson MP, Gilson MK, Gianneschi NC. Stimuli Induced Uptake of Protein-Like Peptide Brush Polymers. Chemistry 2022; 28:e202103438. [PMID: 34811828 PMCID: PMC8861929 DOI: 10.1002/chem.202103438] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Indexed: 01/26/2023]
Abstract
Recently, we presented a strategy for packaging peptides as side-chains in high-density brush polymers. For this globular protein-like polymer (PLP) formulation, therapeutic peptides were shown to resist proteolytic degradation, enter cells efficiently and maintain biological function. In this paper, we establish the role charge plays in dictating the cellular uptake of these peptide formulations, finding that peptides with a net positive charge will enter cells when polymerized, while those formed from anionic or neutral peptides remain outside of cells. Given these findings, we explored whether cellular uptake could be selectively induced by a stimulus. In our design, a cationic peptide is appended to a sequence of charge-neutralizing anionic amino acids through stimuli-responsive cleavable linkers. As a proof-of-concept study, we tested this strategy with two different classes of stimuli, exogenous UV light and an enzyme (a matrix metalloproteinase) associated with the inflammatory response. The key finding is that these materials enter cells only when acted upon by the stimulus. This approach makes it possible to achieve delivery of the polymers, therapeutic peptides or an appended cargo into cells in response to an appropriate stimulus.
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Affiliation(s)
- Angela P Blum
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, CA, 92093, La Jolla, United States
- Department of Chemistry, Hamilton College, 198 College Hill Road, NY 13323, Clinton, United States
| | - Jian Yin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, CA, 92093, La Jolla, United States
| | - Helen H Lin
- Department of Chemistry, Hamilton College, 198 College Hill Road, NY 13323, Clinton, United States
| | - Blayne A Oliver
- Department of Chemistry, Hamilton College, 198 College Hill Road, NY 13323, Clinton, United States
| | - Jacquelin K Kammeyer
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, CA, 92093, La Jolla, United States
| | - Matthew P Thompson
- Department of Chemistry, Department of Materials Science & Engineering, Department of Biomedical Engineering, Department of Medicine, Department of Pharmacology, International Institute of Nanotechnology, Chemistry of Life Processes Institute, Northwestern University, 633 Clark St., IL, 60208, Evanston, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, CA, 92093, La Jolla, United States
| | - Nathan C Gianneschi
- Department of Chemistry, Department of Materials Science & Engineering, Department of Biomedical Engineering, Department of Medicine, Department of Pharmacology, International Institute of Nanotechnology, Chemistry of Life Processes Institute, Northwestern University, 633 Clark St., IL, 60208, Evanston, United States
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6
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Carlini AS, Touve MA, Fernández-Caro H, Thompson MP, Cassidy MF, Cao W, Gianneschi NC. UV-responsive cyclic peptide progelator bioinks. Faraday Discuss 2019; 219:44-57. [PMID: 31549115 PMCID: PMC7363176 DOI: 10.1039/c9fd00026g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We describe cyclic peptide progelators which cleave in response to UV light to generate linearized peptides which then self-assemble into gel networks. Cyclic peptide progelators were synthesized, where the peptides were sterically constrained, but upon UV irradiation, predictable cleavage products were generated. Amino acid sequences and formulation conditions were altered to tune the mechanical properties of the resulting gels. Characterization of the resulting morphologies and chemistry was achieved through liquid phase and standard TEM methods, combined with matrix assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS).
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Affiliation(s)
- Andrea S Carlini
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
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7
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Richardson D, Itkonen J, Nievas J, Urtti A, Casteleijn MG. Accelerated pharmaceutical protein development with integrated cell free expression, purification, and bioconjugation. Sci Rep 2018; 8:11967. [PMID: 30097621 PMCID: PMC6086869 DOI: 10.1038/s41598-018-30435-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/30/2018] [Indexed: 12/02/2022] Open
Abstract
The use of living cells for the synthesis of pharmaceutical proteins, though state-of-the-art, is hindered by its lengthy process comprising of many steps that may affect the protein’s stability and activity. We aimed to integrate protein expression, purification, and bioconjugation in small volumes coupled with cell free protein synthesis for the target protein, ciliary neurotrophic factor. Split-intein mediated capture by use of capture peptides onto a solid surface was efficient at 89–93%. Proof-of-principle of light triggered release was compared to affinity chromatography (His6 fusion tag coupled with Ni-NTA). The latter was more efficient, but more time consuming. Light triggered release was clearly demonstrated. Moreover, we transferred biotin from the capture peptide to the target protein without further purification steps. Finally, the target protein was released in a buffer-volume and composition of our choice, omitting the need for protein concentration or changing the buffer. Split-intein mediated capture, protein trans splicing followed by light triggered release, and bioconjugation for proteins synthesized in cell free systems might be performed in an integrated workflow resulting in the fast production of the target protein.
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Affiliation(s)
- Dominique Richardson
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Jaakko Itkonen
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Julia Nievas
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Arto Urtti
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.,Institute of Chemistry, St Petersburg State University, Petergoff, St Petersburg, Russian Federation
| | - Marco G Casteleijn
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
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8
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Klippenstein V, Mony L, Paoletti P. Probing Ion Channel Structure and Function Using Light-Sensitive Amino Acids. Trends Biochem Sci 2018; 43:436-451. [PMID: 29650383 DOI: 10.1016/j.tibs.2018.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 02/25/2018] [Accepted: 02/27/2018] [Indexed: 12/13/2022]
Abstract
Approaches to remotely control and monitor ion channel operation with light are expanding rapidly in the biophysics and neuroscience fields. A recent development directly introduces light sensitivity into proteins by utilizing photosensitive unnatural amino acids (UAAs) incorporated using the genetic code expansion technique. The introduction of UAAs results in unique molecular level control and, when combined with the maximal spatiotemporal resolution and poor invasiveness of light, enables direct manipulation and interrogation of ion channel functionality. Here, we review the diverse applications of light-sensitive UAAs in two superfamilies of ion channels (voltage- and ligand-gated ion channels; VGICs and LGICs) and summarize existing UAA tools, their mode of action, potential, caveats, and technical considerations to their use in illuminating ion channel structure and function.
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Affiliation(s)
- Viktoria Klippenstein
- Institut de Biologie de I'ENS (IBENS), CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, Université PSL, 46 rue d'Ulm, 75005 Paris, France; These authors contributed equally to this work
| | - Laetitia Mony
- Institut de Biologie de I'ENS (IBENS), CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, Université PSL, 46 rue d'Ulm, 75005 Paris, France; These authors contributed equally to this work
| | - Pierre Paoletti
- Institut de Biologie de I'ENS (IBENS), CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, Université PSL, 46 rue d'Ulm, 75005 Paris, France.
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9
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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.
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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;
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10
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Kim Y, Miyashita M, Miyagawa H. Photocontrol of Elicitor Activity of PIP-1 to Investigate Temporal Factors Involved in Phytoalexin Biosynthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:5894-901. [PMID: 26047371 DOI: 10.1021/acs.jafc.5b01910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The peptide elicitor PIP-1 can induce various immune responses in tobacco cells. Previously, we showed that types of responses induced by PIP-1 are different depending on its stimulation periods; short-term stimulation induces weak responses, whereas long-term stimulation leads to strong responses including production of the phytoalexin capsidiol. However, key components that directly regulate the initiation of capsidiol biosynthesis in response to continuous stimulation with PIP-1 remain unclear. In this study, we designed a photocleavable PIP-1 analog containing 3-amino-3-(2-nitrophenyl)propionic acid as a photocleavable residue. The activity of the analog can be "switched off" using ultraviolet (UV) irradiation without undesired side effects. This analog induced a significant level of capsidiol production unless UV-irradiated, whereas no capsidiol production was observed when tobacco cells were UV-irradiated 1 h after treatment. Using this analog, we found that the elicitor-inducible 3-hydroxy-3-methylglutaryl-CoA reductase activity is regulated based on the duration of the stimulation with PIP-1, which could be associated with the initiation of capsidiol biosynthesis.
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Affiliation(s)
- Yonghyun Kim
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masahiro Miyashita
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Hisashi Miyagawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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11
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Bao C, Ma M, Meng F, Lin Q, Zhu L. Efficient synthetic supramolecular channels and their light-deactivated ion transport in bilayer lipid membranes. NEW J CHEM 2015. [DOI: 10.1039/c5nj00937e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient ion transport and photo-deactivation was achieved from the self-assembled channel of o-nitrobenzyl-based amphiphilic small molecules.
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Affiliation(s)
- Chunyan Bao
- Key Laboratory for Advanced Materials
- Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Meixin Ma
- Key Laboratory for Advanced Materials
- Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Funa Meng
- Key Laboratory for Advanced Materials
- Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Qiuning Lin
- Key Laboratory for Advanced Materials
- Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Linyong Zhu
- Key Laboratory for Advanced Materials
- Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai
- P. R. China
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12
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Dougherty DA, Van Arnam EB. In vivo incorporation of non-canonical amino acids by using the chemical aminoacylation strategy: a broadly applicable mechanistic tool. Chembiochem 2014; 15:1710-20. [PMID: 24990307 DOI: 10.1002/cbic.201402080] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Indexed: 01/05/2023]
Abstract
We describe a strategy for incorporating non-canonical amino acids site-specifically into proteins expressed in living cells, involving organic synthesis to chemically aminoacylate a suppressor tRNA, protein expression in Xenopus oocytes, and monitoring protein function, primarily by electrophysiology. With this protocol, a very wide range of non-canonical amino acids can be employed, allowing both systematic structure-function studies and the incorporation of reactive functionalities. Here, we present an overview of the methodology and examples meant to illustrate the versatility and power of the method as a tool for investigating protein structure and function.
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Affiliation(s)
- Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 (USA).
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13
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Genetically encoding a light switch in an ionotropic glutamate receptor reveals subunit-specific interfaces. Proc Natl Acad Sci U S A 2014; 111:6081-6. [PMID: 24715733 DOI: 10.1073/pnas.1318808111] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Reprogramming receptors to artificially respond to light has strong potential for molecular studies and interrogation of biological functions. Here, we design a light-controlled ionotropic glutamate receptor by genetically encoding a photoreactive unnatural amino acid (UAA). The photo-cross-linker p-azido-L-phenylalanine (AzF) was encoded in NMDA receptors (NMDARs), a class of glutamate-gated ion channels that play key roles in neuronal development and plasticity. AzF incorporation in the obligatory GluN1 subunit at the GluN1/GluN2B N-terminal domain (NTD) upper lobe dimer interface leads to an irreversible allosteric inhibition of channel activity upon UV illumination. In contrast, when pairing the UAA-containing GluN1 subunit with the GluN2A subunit, light-dependent inactivation is completely absent. By combining electrophysiological and biochemical analyses, we identify subunit-specific structural determinants at the GluN1/GluN2 NTD dimer interfaces that critically dictate UV-controlled inactivation. Our work reveals that the two major NMDAR subtypes differ in their ectodomain-subunit interactions, in particular their electrostatic contacts, resulting in GluN1 NTD coupling more tightly to the GluN2B NTD than to the GluN2A NTD. It also paves the way for engineering light-sensitive ligand-gated ion channels with subtype specificity through the genetic code expansion.
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14
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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.
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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
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15
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Pless SA, Ahern CA. Unnatural Amino Acids as Probes of Ligand-Receptor Interactions and Their Conformational Consequences. Annu Rev Pharmacol Toxicol 2013; 53:211-29. [DOI: 10.1146/annurev-pharmtox-011112-140343] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stephan A. Pless
- Department of Anesthesiology, Pharmacology and Therapeutics and Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Christopher A. Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242;
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16
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Shigenaga A. [Development of stimulus-responsive amino acids and their application to chemical biology use]. YAKUGAKU ZASSHI 2012; 132:1075-82. [PMID: 23023427 DOI: 10.1248/yakushi.132.1075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An understanding of the physiological significance of peptides and proteins is indispensable in the fields of life sciences and drug development. Recently, methods for controlling peptide and protein activities using stimuli such as UV irradiation have been attracting much attention because of their potential for clarifying the physiological roles of the peptides/proteins. In this context, we have developed a stimulus-responsive amino acid that induces peptide-bond cleavage after exposure to a stimulus. Although it has previously been reported that stimulus-responsive units can respond to a specific stimulus, our stimulus-responsive amino acid is potentially applicable to any stimulus simply by changing the protective group. In this review, the design and synthesis of stimulus-responsive amino acids are described. Their applications in chemical biology, including their use for spatiotemporal control of the activity of peptides in living cells, are also reported.
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Affiliation(s)
- Akira Shigenaga
- Institute of Health Biosciences and Graduate School of Pharmaceutical Sciences, The University of Tokushima, Tokushima, Japan.
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17
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Butterfield S, Hejjaoui M, Fauvet B, Awad L, Lashuel HA. Chemical strategies for controlling protein folding and elucidating the molecular mechanisms of amyloid formation and toxicity. J Mol Biol 2012; 421:204-36. [PMID: 22342932 DOI: 10.1016/j.jmb.2012.01.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 01/30/2012] [Accepted: 01/31/2012] [Indexed: 12/12/2022]
Abstract
It has been more than a century since the first evidence linking the process of amyloid formation to the pathogenesis of Alzheimer's disease. During the last three decades in particular, increasing evidence from various sources (pathology, genetics, cell culture studies, biochemistry, and biophysics) continues to point to a central role for the pathogenesis of several incurable neurodegenerative and systemic diseases. This is in part driven by our improved understanding of the molecular mechanisms of protein misfolding and aggregation and the structural properties of the different aggregates in the amyloid pathway and the emergence of new tools and experimental approaches that permit better characterization of amyloid formation in vivo. Despite these advances, detailed mechanistic understanding of protein aggregation and amyloid formation in vitro and in vivo presents several challenges that remain to be addressed and several fundamental questions about the molecular and structural determinants of amyloid formation and toxicity and the mechanisms of amyloid-induced toxicity remain unanswered. To address this knowledge gap and technical challenges, there is a critical need for developing novel tools and experimental approaches that will not only permit the detection and monitoring of molecular events that underlie this process but also allow for the manipulation of these events in a spatial and temporal fashion both in and out of the cell. This review is primarily dedicated in highlighting recent results that illustrate how advances in chemistry and chemical biology have been and can be used to address some of the questions and technical challenges mentioned above. We believe that combining recent advances in the development of new fluorescent probes, imaging tools that enabled the visualization and tracking of molecular events with advances in organic synthesis, and novel approaches for protein synthesis and engineering provide unique opportunities to gain a molecular-level understanding of the process of amyloid formation. We hope that this review will stimulate further research in this area and catalyze increased collaboration at the interface of chemistry and biology to decipher the mechanisms and roles of protein folding, misfolding, and aggregation in health and disease.
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Affiliation(s)
- Sara Butterfield
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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18
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Bindman N, Merkx R, Koehler R, Herrman N, van der Donk WA. Photochemical cleavage of leader peptides. Chem Commun (Camb) 2010; 46:8935-7. [PMID: 21046030 PMCID: PMC3100556 DOI: 10.1039/c0cc02945a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a photolabile linker compatible with Fmoc solid phase peptide synthesis and Cu(I)-catalyzed alkyne-azide cycloaddition that allows photochemical cleavage to afford a C-terminal peptide fragment with a native amino terminus.
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Affiliation(s)
- Noah Bindman
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Remco Merkx
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Robert Koehler
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Nicholas Herrman
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, USA
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Shigenaga A, Yamamoto J, Nishioka N, Otaka A. Enantioselective synthesis of stimulus-responsive amino acid via asymmetric α-amination of aldehyde. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.07.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Zhu J. Bioactive modification of poly(ethylene glycol) hydrogels for tissue engineering. Biomaterials 2010; 31:4639-56. [PMID: 20303169 PMCID: PMC2907908 DOI: 10.1016/j.biomaterials.2010.02.044] [Citation(s) in RCA: 835] [Impact Index Per Article: 59.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 02/16/2010] [Indexed: 12/12/2022]
Abstract
In this review, we explore different approaches for introducing bioactivity into poly(ethylene glycol) (PEG) hydrogels. Hydrogels are excellent scaffolding materials for repairing and regenerating a variety of tissues because they can provide a highly swollen three-dimensional (3D) environment similar to soft tissues. Synthetic hydrogels like PEG-based hydrogels have advantages over natural hydrogels, such as the ability for photopolymerization, adjustable mechanical properties, and easy control of scaffold architecture and chemical compositions. However, PEG hydrogels alone cannot provide an ideal environment to support cell adhesion and tissue formation due to their bio-inert nature. The natural extracellular matrix (ECM) has been an attractive model for the design and fabrication of bioactive scaffolds for tissue engineering. ECM-mimetic modification of PEG hydrogels has emerged as an important strategy to modulate specific cellular responses. To tether ECM-derived bioactive molecules (BMs) to PEG hydrogels, various strategies have been developed for the incorporation of key ECM biofunctions, such as specific cell adhesion, proteolytic degradation, and signal molecule-binding. A number of cell types have been immobilized on bioactive PEG hydrogels to provide fundamental knowledge of cell/scaffold interactions. This review addresses the recent progress in material designs and fabrication approaches leading to the development of bioactive hydrogels as tissue engineering scaffolds.
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Affiliation(s)
- Junmin Zhu
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA.
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21
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Shigenaga A, Yamamoto J, Sumikawa Y, Furuta T, Otaka A. Development and photo-responsive peptide bond cleavage reaction of two-photon near-infrared excitation-responsive peptide. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.03.079] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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22
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Hanek AP, Lester HA, Dougherty DA. Photochemical proteolysis of an unstructured linker of the GABAAR extracellular domain prevents GABA but not pentobarbital activation. Mol Pharmacol 2010; 78:29-35. [PMID: 20363860 DOI: 10.1124/mol.109.059832] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The GABA type A receptor (GABA(A)R) is the major inhibitory receptor in the mammalian central nervous system and the target of numerous pharmaceuticals. The alpha-subunit of these pentameric Cys-loop neurotransmitter-gated ion channels contributes to the binding of both GABA and allosteric modulators such as the benzodiazepines, suggesting a role for this subunit in the conformational changes associated with activation of the receptor. Herein we use the nonsense suppression methodology to incorporate a photoactivatable unnatural amino acid and photochemically cleave the backbone of the alpha subunit of the alpha(1)beta(2) GABA(A)R in a linker region that is believed to span the subunit. Proteolytic cleavage impairs GABA but not pentobarbital activation, strongly suggesting that conformational changes involving this linker region are critical to the GABA activation pathway.
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Affiliation(s)
- Ariele P Hanek
- Division of Chemistry and Chemical Engineering, Division of Biology, California Institute of Technology, Pasadena, California, USA
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23
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Eastwood AL, Blum AP, Zacharias NM, Dougherty DA. A selenide-based approach to photochemical cleavage of peptide and protein backbones at engineered backbone esters. J Org Chem 2010; 74:9241-4. [PMID: 19902952 DOI: 10.1021/jo901368g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A strategy for photochemical cleavage of peptide and protein backbones is described, which is based on a selenide-mediated cleavage of a backbone ester moiety. Studies in model systems establish the viability of the chemistry and suggest the method could be a valuable tool for chemical biology studies of proteins.
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Affiliation(s)
- Amy L Eastwood
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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Floyd N, Oldham NJ, Eyles CJ, Taylor S, Filatov DA, Brouard M, Davis BG. Photoinduced, Family-Specific, Site-Selective Cleavage of TIM-Barrel Proteins. J Am Chem Soc 2009; 131:12518-9. [DOI: 10.1021/ja9026105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicola Floyd
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, U.K., Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, OX1 3QZ, U.K., The School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, U.K., Computational Biology Research Group, University of Oxford, Oxford, OX1 3RE, U.K., and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1
| | - Neil J. Oldham
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, U.K., Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, OX1 3QZ, U.K., The School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, U.K., Computational Biology Research Group, University of Oxford, Oxford, OX1 3RE, U.K., and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1
| | - Christopher J. Eyles
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, U.K., Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, OX1 3QZ, U.K., The School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, U.K., Computational Biology Research Group, University of Oxford, Oxford, OX1 3RE, U.K., and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1
| | - Stephen Taylor
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, U.K., Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, OX1 3QZ, U.K., The School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, U.K., Computational Biology Research Group, University of Oxford, Oxford, OX1 3RE, U.K., and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1
| | - Dmitry A. Filatov
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, U.K., Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, OX1 3QZ, U.K., The School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, U.K., Computational Biology Research Group, University of Oxford, Oxford, OX1 3RE, U.K., and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1
| | - Mark Brouard
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, U.K., Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, OX1 3QZ, U.K., The School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, U.K., Computational Biology Research Group, University of Oxford, Oxford, OX1 3RE, U.K., and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1
| | - Benjamin G. Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, U.K., Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, OX1 3QZ, U.K., The School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, U.K., Computational Biology Research Group, University of Oxford, Oxford, OX1 3RE, U.K., and Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1
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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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27
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FRET-based assay of the processing reaction kinetics of stimulus-responsive peptides: influence of amino acid sequence on reaction kinetics. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.01.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Abstract
K(+) channels are revered for their universal action of suppressing electrical activity in nerve and muscle, as well as regulating salt and water transport in epithelial tissues involved in metabolism and digestion. These multisubunit membrane-embedded proteins carry out their physiological chore, selectively allowing the passage of potassium across the membrane, in response to changes in membrane voltage and ligand concentration. Elucidating the diverse gating properties of K(+) channels is of great biological interest since their molecular motions provide insight into how these structurally similar proteins function in a wide variety of tissues. Armed with patch clamps, chart recorders, and now high-resolution structures, electrophysiologists have been dipping into the top tray of the chemist's tool box: synthesizing cysteine-modifying agents and organic cations and grinding up insects, spiders, and other vermin to isolate natural products to poke, probe, and prod K(+) channels. Recently, there has been further cross-fertilization between chemists and K(+) channelologists, resulting in greater accessibility to more elaborate synthetic methodologies and screening approaches. In this review, we catalogue the evolution of chemical tools and approaches that have been utilized to elucidate the mechanistic underpinnings of K(+) channel biology.
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Affiliation(s)
- Christopher A Ahern
- Department of Anesthesiology, University of British Columbia, 2350 Health Science Mall, Vancouver, BC V6T 1Z3, Canada.
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Katayama K, Tsukiji S, Furuta T, Nagamune T. A bromocoumarin-based linker for synthesis of photocleavable peptidoconjugates with high photosensitivity. Chem Commun (Camb) 2008:5399-401. [PMID: 18985223 DOI: 10.1039/b812058g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new bromocoumarin-based bi-functional linker was developed for preparing photocleavable peptides and proteins with high photolytic efficiency, which have many potential applications in the study and engineering of biological systems.
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Affiliation(s)
- Kentaro Katayama
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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31
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Duca M, Chen S, Hecht SM. Aminoacylation of transfer RNAs with one and two amino acids. Methods 2008; 44:87-99. [PMID: 18241791 DOI: 10.1016/j.ymeth.2007.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 10/20/2007] [Accepted: 10/22/2007] [Indexed: 11/18/2022] Open
Abstract
The detailed synthesis of (bis)aminoacyl-pdCpAs and the corresponding singly and tandemly activated tRNAs is reported. The synthetic pathway leading to these compounds has been validated for simple amino acid residues as well as for amino acids bearing more complex side chains. Protection/deprotection strategies are described. For the bisaminoacylated tRNAs, both the synthesis of tRNAs bearing the same amino acid residue at the 2' and 3' positions and tRNAs bearing two different aminoacyl moieties are reported. Further, it is shown that the tandemly activated tRNAs are able to participate in protein synthesis.
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Affiliation(s)
- Maria Duca
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, USA.
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32
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Rhee H, Lee JS, Lee J, Joo C, Han H, Cho M. Photolytic control and infrared probing of amide I mode in the dipeptide backbone-caged with the 4,5-dimethoxy-2-nitrobenzyl group. J Phys Chem B 2008; 112:2128-35. [PMID: 18211054 DOI: 10.1021/jp074776z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alanine dipeptide analog 1 backbone-caged with a photolabile linker, 4,5-dimethoxy-2-nitrobenzyl (DmNb), was synthesized. UV-pulse-induced photochemical reaction of 1 was monitored by Fourier transform IR absorption spectroscopy under a steady-state condition or in a fast-scan mode. Upon photolysis of 1, the amide I band is changed from a doublet to a singlet with concomitant line shape changes of several IR bands. The change of the amide I band is directly associated with the photocleavage of the covalent N-C bond connecting the backbone amide of 2 to DmNb. Therefore, IR spectroscopy is useful for directly probing the photocleavage of backbone-caged peptide 1 and the concurrent release of native peptide 2. In contrast, UV-vis spectroscopy probing the irradiation-induced structural change of the 2-nitrobenzyl moiety itself may not provide a clue directly relevant to the photocleavage of such N-C bond. Time-resolved IR spectra recorded in a fast-scan mode after pulsed UV irradiation of 1 reveal that such photocleavage occurs at least faster than a few seconds of our instrumental time resolution.
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Affiliation(s)
- Hanju Rhee
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea
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33
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Shigenaga A, Tsuji D, Nishioka N, Tsuda S, Itoh K, Otaka A. Synthesis of a stimulus-responsive processing device and its application to a nucleocytoplasmic shuttle Peptide. Chembiochem 2008; 8:1929-31. [PMID: 17899557 DOI: 10.1002/cbic.200700442] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Akira Shigenaga
- Institute of Health Biosciences and Graduate School of Pharmaceutical Sciences, The University of Tokushima, Shomachi, Tokushima 770-8505, Japan
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Lemke EA, Summerer D, Geierstanger BH, Brittain SM, Schultz PG. Control of protein phosphorylation with a genetically encoded photocaged amino acid. Nat Chem Biol 2007; 3:769-72. [PMID: 17965709 DOI: 10.1038/nchembio.2007.44] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 09/20/2007] [Indexed: 01/15/2023]
Abstract
We genetically encoded the photocaged amino acid 4,5-dimethoxy-2-nitrobenzylserine (DMNB-Ser) in Saccharomyces cerevisiae in response to the amber nonsense codon TAG. This amino acid was converted to serine in living cells by irradiation with relatively low-energy blue light and was used to noninvasively photoactivate phosphorylation of the transcription factor Pho4, which controls the cellular response to inorganic phosphate. When substituted at phosphoserine sites that control nuclear export of Pho4, blocks phosphorylation and subsequent export by the receptor Msn5 (ref. 2). We triggered phosphorylation of individual serine residues with a visible laser pulse and monitored nuclear export of Pho4-GFP fusion constructs in real time. We observed distinct export kinetics for differentially phosphorylated Pho4 mutants, which demonstrates dynamic regulation of Pho4 function. This methodology should also facilitate the analysis of other cellular processes involving free serine residues, including catalysis, biomolecular recognition and ion transport.
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Affiliation(s)
- Edward A Lemke
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road SR202, La Jolla, California 92037, USA
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35
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Gorostiza P, Isacoff E. Optical switches and triggers for the manipulation of ion channels and pores. MOLECULAR BIOSYSTEMS 2007; 3:686-704. [PMID: 17882331 DOI: 10.1039/b710287a] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Like fluorescence sensing techniques, methods to manipulate proteins with light have produced great advances in recent years. Ion channels have been one of the principal protein targets of photoswitched manipulation. In combination with fluorescence detection of cell signaling, this has enabled non-invasive, all-optical experiments on cell and tissue function, both in vitro and in vivo. Optical manipulation of channels has also provided insights into the mechanism of channel function. Optical control elements can be classified according to their molecular reversibility as non-reversible phototriggers where light breaks a chemical bond (e.g. caged ligands) and as photoswitches that reversibly photoisomerize. Synthetic photoswitches constitute nanoscale actuators that can alter channel function using three different strategies. These include (1) nanotoggles, which are tethered photoswitchable ligands that either activate channels (agonists) or inhibit them (blockers or antagonists), (2) nanokeys, which are untethered (freely diffusing) photoswitchable ligands, and (3) nanotweezers, which are photoswitchable crosslinkers. The properties of such photoswitches are discussed here, with a focus on tethered photoswitchable ligands. The recent literature on optical manipulation of ion channels is reviewed for the different channel families, with special emphasis on the understanding of ligand binding and gating processes, applications in nanobiotechnology, and with attention to future prospects in the field.
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Affiliation(s)
- Pau Gorostiza
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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36
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Fahmi NE, Dedkova L, Wang B, Golovine S, Hecht SM. Site-Specific Incorporation of Glycosylated Serine and Tyrosine Derivatives into Proteins. J Am Chem Soc 2007; 129:3586-97. [PMID: 17338522 DOI: 10.1021/ja067466n] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycosylation of proteins can have a dramatic effect on their physical, chemical, and biological properties. Analogues of dihydrofolate reductase and firefly luciferase containing glycosylated amino acids at single, predetermined sites have been elaborated. Misacylated suppressor tRNAs activated with glycosylated serine and tyrosine derivatives were used for suppression of the nonsense codons in a cell-free protein biosynthesizing system, thereby permitting the preparation of the desired glycosylated proteins. In this fashion, it was possible to obtain proteins containing both mono- and diglycosylated amino acids, including glycosylated serine and tyrosine moieties. For the modified firefly luciferases, the effect of these substitutions on the wavelength of the light emitted by firefly luciferase was investigated. The maximum wavelength for mutants containing peracetylated glycosylated serine derivatives at position 284 showed a red shift in the emission spectra. For mutants containing glycosylated tyrosines, the red shift was observed only when the carbohydrate moiety was fully deacetylated.
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Affiliation(s)
- Nour Eddine Fahmi
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, USA
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37
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Maloney DJ, Ghanem N, Zhou J, Hecht SM. Positional assignment of differentially substituted bisaminoacylated pdCpAs. Org Biomol Chem 2007; 5:3135-8. [PMID: 17878972 DOI: 10.1039/b708786a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The synthesis and NMR analysis of a 2'-O-alanyl, 3'-O-[1-(13)C]valyl-pdCpA derivative has permitted the definitive assignment of the positions of acylation of tandemly activated pdCpAs, and the bisaminoacylated transfer RNAs derived therefrom.
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Affiliation(s)
- David J Maloney
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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Abstract
Photochemical regulation of biological processes offers a high level of control to study intracellular mechanisms with unprecedented spatial and temporal resolution. This report summarizes the advances made in recent years, focusing predominantly on the in vivo regulation of gene function using irradiation with UV light. The majority of the described applications entail the utilization of photocaging groups installed either on a small molecule modulator of biomolecular function or directly on a biological macromolecule itself.
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Affiliation(s)
- Douglas D Young
- North Carolina State University, Department of Chemistry, Campus Box 8204, Raleigh, NC 27695, USA
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39
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Ahn JH, Hwang MY, Oh IS, Park KM, Hahn GH, Choi CY, Kim DM. Preparation method forEscherichia coli S30 extracts completely dependent upon tRNA addition to catalyze cell-free protein synthesis. BIOTECHNOL BIOPROC E 2006. [DOI: 10.1007/bf02932309] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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40
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Parker LL, Kurutz JW, Kent SBH, Kron SJ. Control of the Yeast Cell Cycle with a Photocleavable α-Factor Analogue. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602439] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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41
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Parker LL, Kurutz JW, Kent SBH, Kron SJ. Control of the yeast cell cycle with a photocleavable alpha-factor analogue. Angew Chem Int Ed Engl 2006; 45:6322-5. [PMID: 16937420 PMCID: PMC2788609 DOI: 10.1002/anie.200602439] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Laurie L. Parker
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E. 57th Street, CIS W201A, Chicago, IL 60637 (USA)
| | - Josh W. Kurutz
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E. 57th Street, CIS W201A, Chicago, IL 60637 (USA)
| | - Stephen B. H. Kent
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E. 57th Street, CIS W201A, Chicago, IL 60637 (USA)
| | - Stephen J. Kron
- Department of Molecular Genetics and Cellular Biology, University of Chicago, 924 East 57th Street, Knapp R322, Chicago, IL 60637 (USA)
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42
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Ahn JH, Kim NY, Kim TW, Son JM, Kang TJ, Park CG, Choi CY, Kim DM. Effect of temperature and ATP supply on the efficiency of programmed nonsense suppression. Anal Biochem 2005; 345:110-5. [PMID: 16137633 DOI: 10.1016/j.ab.2005.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Revised: 07/01/2005] [Accepted: 07/12/2005] [Indexed: 11/19/2022]
Abstract
Chemical diversity of protein molecules can be expanded through in vitro incorporation of unnatural amino acids in response to a nonsense codon. Chemically misacylated tRNAs are used for tethering unnatural amino acids to a nonsense-mutated target codon (nonsense suppression). In the course of experiments to introduce S-(2-nitrobenzyl)cysteine (NBC) into a targeted location of human erythropoietin, we found that NBC incorporates more efficiently at lower temperatures. In addition, at a fixed reaction temperature, more NBC was incorporated with a reduced supply of ATP. Since the rate of peptide elongation was remarkably higher at the elevated temperature or with enhanced supply of ATP, these results indicate that the efficiency of nonsense suppression is inversely correlated to the peptide elongation rate. Therefore, maximal yield of nonsense-suppressed proteins is obtained at a compromised elongation rate. The present result will offer a primary guideline to optimize the reaction conditions for in vitro production of protein molecules containing unnatural amino acids.
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Affiliation(s)
- Jin-Ho Ahn
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, College of Engineering, Seoul National University, Seoul 151-742, Korea
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43
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Pellois JP, Muir TW. A Ligation and Photorelease Strategy for the Temporal and Spatial Control of Protein Function in Living Cells. Angew Chem Int Ed Engl 2005; 44:5713-7. [PMID: 16059958 DOI: 10.1002/anie.200501244] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jean-Philippe Pellois
- The Laboratory of Synthetic Protein Chemistry, The Rockefeller University, Box 223, 1230 York Avenue, New York, NY 10021, USA
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44
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Pellois JP, Muir TW. A Ligation and Photorelease Strategy for the Temporal and Spatial Control of Protein Function in Living Cells. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501244] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Endo M, Nakayama K, Kaida Y, Majima T. Design and Synthesis of Photochemically Controllable Caspase-3. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200460889] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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46
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Endo M, Nakayama K, Kaida Y, Majima T. Design and Synthesis of Photochemically Controllable Caspase-3. Angew Chem Int Ed Engl 2004; 43:5643-5. [PMID: 15495205 DOI: 10.1002/anie.200460889] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Masayuki Endo
- Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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47
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Luo Y, Shoichet MS. Light-Activated Immobilization of Biomolecules to Agarose Hydrogels for Controlled Cellular Response. Biomacromolecules 2004; 5:2315-23. [PMID: 15530047 DOI: 10.1021/bm0495811] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a new method of synthesizing photolabile hydrogel materials for convenient photoimmobilization of biomolecules on surfaces or in 3-D matrixes. Dissolved agarose was modified with photolabile S-(2-nitrobenzyl)cysteine (S-NBC) via 1,1'-carbonyldiimidazole (CDI) activation of primary hydroxyl groups. S-NBC-modified agarose remained soluble and gelable with up to 5% S-NBC substitution, yet gelation was slower and the elastic modulus of the resulting gel was lower than those of unmodified agarose. Irradiating S-NBC-grafted agarose resulted in the loss of the protecting 2-nitrobenzyl groups, thereby exposing free sulfhydryl groups for biomolecular coupling. When appropriately activated with sulfhydryl-reactive groups, either peptides or proteins were effectively immobilized to the photoirradiated hydrogel matrixes, with the irradiation energy dose (i.e., irradiation time) used to control the amount of biomolecule immobilization. When the GRGDS peptide was immobilized on agarose, it was shown to be cell-adhesive and to promote neurite outgrowth from primary, embryonic chick dorsal root ganglion neurons. The immobilized GRGDS surface ligand concentration affected the cellular response: neurite length and density increased with GRGDS surface concentration at low adhesion ligand concentration and then plateaued at higher GRGDS concentration. Grafting 2-nitrobenzyl-protected compounds to hydrogel materials is useful for creating new photolabile hydrogel substrates for light-activated functional group generation and biomolecular immobilization.
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Affiliation(s)
- Ying Luo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
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48
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Strømgaard A, Jensen AA, Strømgaard K. Site-Specific Incorporation of Unnatural Amino Acids into Proteins. Chembiochem 2004; 5:909-16. [PMID: 15239046 DOI: 10.1002/cbic.200400060] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Anne Strømgaard
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
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49
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Monahan SL, Lester HA, Dougherty DA. Site-specific incorporation of unnatural amino acids into receptors expressed in Mammalian cells. CHEMISTRY & BIOLOGY 2003; 10:573-80. [PMID: 12837390 DOI: 10.1016/s1074-5521(03)00124-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe an approach to achieve unnatural amino acid incorporation into channels and receptors expressed in mammalian cells. We show that microelectroporation provides a general method to deliver DNA, mRNA, and tRNA simultaneously. In both CHO cells and cultured neurons, microelectroporation efficiently delivers an in vitro transcribed, serine amber suppressor tRNA, leading to nonsense suppression in a mutant EGFP gene. In CHO cells, both natural and unnatural amino acids chemically appended to a suppressor tRNA are site specifically incorporated into the nicotinic acetylcholine receptor (nAChR). Electrophysiology confirms the expected functional consequences of the unnatural residue. The microelectroporation strategy described here is more general, less tedious, and less damaging to mammalian neuronal and nonneuronal cells than previous approaches to nonsense suppression in small cells and provides the first example of unnatural amino acid incorporation in mammalian cells using chemically aminoacylated tRNA.
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MESH Headings
- Acetylcholine/metabolism
- Amino Acids/chemistry
- Amino Acids/genetics
- Animals
- CHO Cells
- Cells, Cultured
- Codon, Nonsense
- Cricetinae
- Electroporation/methods
- Gene Expression
- Genes, Suppressor
- Green Fluorescent Proteins
- Luminescent Proteins/metabolism
- Neurons
- RNA, Transfer, Amino Acyl/metabolism
- Receptors, Cell Surface/biosynthesis
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/genetics
- Receptors, Nicotinic/genetics
- Receptors, Nicotinic/metabolism
- Transfection
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Affiliation(s)
- Sarah L Monahan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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50
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Beene DL, Dougherty DA, Lester HA. Unnatural amino acid mutagenesis in mapping ion channel function. Curr Opin Neurobiol 2003; 13:264-70. [PMID: 12850209 DOI: 10.1016/s0959-4388(03)00068-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unnatural amino acid mutagenesis makes possible the site-specific incorporation of synthetic amino acids, enabling detailed structure-function studies as well as the incorporation of biophysical probes. This method has been adapted for use with heterologous expression in Xenopus oocytes, allowing experiments on ion channels.
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Affiliation(s)
- Darren L Beene
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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