51
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Salveson PJ, Haerianardakani S, Thuy-Boun A, Kreutzer AG, Nowick JS. Controlling the Oligomerization State of Aβ-Derived Peptides with Light. J Am Chem Soc 2018; 140:5842-5852. [PMID: 29627987 DOI: 10.1021/jacs.8b02658] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A key challenge in studying the biological and biophysical properties of amyloid-forming peptides is that they assemble to form heterogeneous mixtures of soluble oligomers and insoluble fibrils. Photolabile protecting groups have emerged as tools to control the properties of biomolecules with light. Blocking intermolecular hydrogen bonds that stabilize amyloid oligomers provides a general strategy to control the biological and biophysical properties of amyloid-forming peptides. In this paper we describe the design, synthesis, and characterization of macrocyclic β-hairpin peptides that are derived from amyloidogenic peptides and contain the N-2-nitrobenzyl photolabile protecting group. Each peptide contains two heptapeptide segments from Aβ16-36 or Aβ17-36 constrained into β-hairpins. The N-2-nitrobenzyl group is appended to the amide backbone of Gly33 to disrupt the oligomerization of the peptides by disrupting intermolecular hydrogen bonds. X-ray crystallography reveals that N-2-nitrobenzyl groups can either block assembly into discrete oligomers or permit formation of trimers, hexamers, and dodecamers. Photolysis of the N-2-nitrobenzyl groups with long-wave UV light unmasks the amide backbone and alters the assembly and the biological properties of the macrocyclic β-hairpin peptides. SDS-PAGE studies show that removing the N-2-nitrobenzyl groups alters the assembly of the peptides. MTT conversion and LDH release assays show that decaging the peptides induces cytotoxicity. Circular dichroism studies and dye leakage assays with liposomes reveal that decaging modulates interactions of the peptides with lipid bilayers. Collectively, these studies demonstrate that incorporating N-2-nitrobenzyl groups into macrocyclic β-hairpin peptides provides a new strategy to probe the structures and the biological properties of amyloid oligomers.
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Affiliation(s)
- Patrick J Salveson
- Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States
| | - Sepehr Haerianardakani
- Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States
| | - Alexander Thuy-Boun
- Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States
| | - Adam G Kreutzer
- Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States
| | - James S Nowick
- Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States
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52
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Leopold AV, Chernov KG, Verkhusha VV. Optogenetically controlled protein kinases for regulation of cellular signaling. Chem Soc Rev 2018; 47:2454-2484. [PMID: 29498733 DOI: 10.1039/c7cs00404d] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein kinases are involved in the regulation of many cellular processes including cell differentiation, survival, migration, axon guidance and neuronal plasticity. A growing set of optogenetic tools, termed opto-kinases, allows activation and inhibition of different protein kinases with light. The optogenetic regulation enables fast, reversible and non-invasive manipulation of protein kinase activities, complementing traditional methods, such as treatment with growth factors, protein kinase inhibitors or chemical dimerizers. In this review, we summarize the properties of the existing optogenetic tools for controlling tyrosine kinases and serine-threonine kinases. We discuss how the opto-kinases can be applied for studies of spatial and temporal aspects of protein kinase signaling in cells and organisms. We compare approaches for chemical and optogenetic regulation of protein kinase activity and present guidelines for selection of opto-kinases and equipment to control them with light. We also describe strategies to engineer novel opto-kinases on the basis of various photoreceptors.
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Affiliation(s)
- Anna V Leopold
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
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53
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemical Control of Biological Processes in Cells and Animals. Angew Chem Int Ed Engl 2018; 57:2768-2798. [PMID: 28521066 PMCID: PMC6026863 DOI: 10.1002/anie.201700171] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/06/2017] [Indexed: 12/13/2022]
Abstract
Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.
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Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Taylor Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Yuta Naro
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
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54
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Zhang W, Hamouri F, Feng Z, Aujard I, Ducos B, Ye S, Weiss S, Volovitch M, Vriz S, Jullien L, Bensimon D. Control of Protein Activity and Gene Expression by Cyclofen-OH Uncaging. Chembiochem 2018; 19:1232-1238. [PMID: 29341391 DOI: 10.1002/cbic.201700630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 11/06/2022]
Abstract
The use of light to control the expression of genes and the activity of proteins is a rapidly expanding field. Whereas many of these approaches use fusion between a light-activable protein and the protein of interest to control the activity of the latter, it is also possible to control the activity of a protein by uncaging a specific ligand. In that context, controlling the activation of a protein fused to the modified estrogen receptor (ERT) by uncaging its ligand cyclofen-OH has emerged as a generic and versatile method to control the activation of proteins quantitatively, quickly, and locally in a live organism. We present that approach and its uses in a variety of physiological contexts.
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Affiliation(s)
- Weiting Zhang
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University, 24 rue Lhomond, 75005, Paris, France.,IBENS, CNRS-UMR8197, INSERM-U1024, PSL Research University, 46 rue d'Ulm, 75005, Paris, France
| | - Fatima Hamouri
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University, 24 rue Lhomond, 75005, Paris, France.,IBENS, CNRS-UMR8197, INSERM-U1024, PSL Research University, 46 rue d'Ulm, 75005, Paris, France
| | - Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
| | - Isabelle Aujard
- PASTEUR, Département de Chimie, École Normale Supérieure, UPMC Univ Paris 06, CNRS, PSL Research University, 75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, École Normale Supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Bertrand Ducos
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University, 24 rue Lhomond, 75005, Paris, France.,IBENS, CNRS-UMR8197, INSERM-U1024, PSL Research University, 46 rue d'Ulm, 75005, Paris, France
| | - Shixin Ye
- Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, 75005, Paris, France
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA, 90024, USA
| | - Michel Volovitch
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS UMR 7241, INSERM U1050, 11 place Marcellin Berthelot, 75005, Paris, France.,Department of Biology, Ecole Normale Supérieure, PSL Research University, 46 rue d'Ulm, 75005, Paris, France
| | - Sophie Vriz
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS UMR 7241, INSERM U1050, 11 place Marcellin Berthelot, 75005, Paris, France.,Department of Life Sciences, Paris-Diderot University, Sorbonne-Paris-Cité, 5 rue Thomas Mann, 75013, Paris, France
| | - Ludovic Jullien
- PASTEUR, Département de Chimie, École Normale Supérieure, UPMC Univ Paris 06, CNRS, PSL Research University, 75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, École Normale Supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - David Bensimon
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University, 24 rue Lhomond, 75005, Paris, France.,IBENS, CNRS-UMR8197, INSERM-U1024, PSL Research University, 46 rue d'Ulm, 75005, Paris, France.,Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA, 90024, USA
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55
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemische Steuerung biologischer Vorgänge in Zellen und Tieren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201700171] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Taylor Courtney
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Yuta Naro
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Alexander Deiters
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
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56
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Guduru SKR, Arya P. Synthesis and biological evaluation of rapamycin-derived, next generation small molecules. MEDCHEMCOMM 2018; 9:27-43. [PMID: 30108899 PMCID: PMC6072512 DOI: 10.1039/c7md00474e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/21/2017] [Indexed: 12/20/2022]
Abstract
Over the years, rapamycin has attracted serious attention due to its remarkable biological properties and as a potent inhibitor of the mammalian target of rapamycin (mTOR) protein through its binding with FKBP-12. Several efficient strategies that utilize synthetic and biosynthetic approaches have been utilized to develop small molecule rapamycin analogs or for synthesizing hybrid compounds containing a partial rapamycin structure to improve pharmacokinetic properties. Herein, we report selected case studies related to the synthesis of rapamycin-derived compounds and hybrid molecules to explore their biological properties.
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Affiliation(s)
- Shiva Krishna Reddy Guduru
- Center for Drug Discovery , Department of Pharmacology and Chemical Biology , Baylor College of Medicine , One Baylor Plaza , Houston , Texas 77030 , USA . ; ; Tel: +1 713 798 8794
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , One Baylor Plaza , Houston , Texas 77030 , USA
| | - Prabhat Arya
- Chemistry and Chemical Biology , Dr. Reddy's Institute of Life Sciences (DRILS) , University of Hyderabad Campus , Hyderabad 500046 , India
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57
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Hörner M, Chatelle C, Mühlhäuser WWD, Stocker DR, Coats M, Weber W, Radziwill G. Optogenetic control of focal adhesion kinase signaling. Cell Signal 2017; 42:176-183. [PMID: 29074139 DOI: 10.1016/j.cellsig.2017.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/06/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
Abstract
Focal adhesion kinase (FAK) integrates signaling from integrins, growth factor receptors and mechanical stress to control cell adhesion, motility, survival and proliferation. Here, we developed a single-component, photo-activatable FAK, termed optoFAK, by using blue light-induced oligomerization of cryptochrome 2 (CRY2) to activate FAK-CRY2 fusion proteins. OptoFAK functions uncoupled from physiological stimuli and activates downstream signaling rapidly and reversibly upon blue light exposure. OptoFAK stimulates SRC creating a positive feedback loop on FAK activation, facilitating phosphorylation of paxillin and p130Cas in adherent cells. In detached cells or in mechanically stressed adherent cells, optoFAK is autophosphorylated upon exposure to blue light, however, downstream signaling is hampered indicating that the accessibility to these substrates is disturbed. OptoFAK may prove to be a useful tool to study the biological function of FAK in growth factor and integrin signaling, tension-mediated focal adhesion maturation or anoikis and could additionally serve as test system for kinase inhibitors.
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Affiliation(s)
- Maximilian Hörner
- Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany.
| | - Claire Chatelle
- Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
| | - Wignand W D Mühlhäuser
- Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany.
| | - David R Stocker
- Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany
| | - Michael Coats
- Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany.
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany.
| | - Gerald Radziwill
- Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany.
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58
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Abstract
To orchestrate the function and development of multicellular organisms, cells integrate intra- and extracellular information. This information is processed via signal networks in space and time, steering dynamic changes in cellular structure and function. Defects in those signal networks can lead to developmental disorders or cancer. However, experimental analysis of signal networks is challenging as their state changes dynamically and differs between individual cells. Thus, causal relationships between network components are blurred if lysates from large cell populations are analyzed. To directly study causal relationships, perturbations that target specific components have to be combined with measurements of cellular responses within individual cells. However, using standard single-cell techniques, the number of signal activities that can be monitored simultaneously is limited. Furthermore, diffusion of signal network components limits the spatial precision of perturbations, which blurs the analysis of spatiotemporal processing in signal networks. Hybrid strategies based on optogenetics, surface patterning, chemical tools, and protein design can overcome those limitations and thereby sharpen our view into the dynamic spatiotemporal state of signal networks and enable unique insights into the mechanisms that control cellular function in space and time.
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Affiliation(s)
- Dominic Kamps
- Department for Systemic Cell Biology, Max
Planck Institute of Molecular Physiology and Fakultät für
Chemie und Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
| | - Leif Dehmelt
- Department for Systemic Cell Biology, Max
Planck Institute of Molecular Physiology and Fakultät für
Chemie und Chemische Biologie, Technische Universität Dortmund, Dortmund, Germany
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59
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Khamo JS, Krishnamurthy VV, Sharum SR, Mondal P, Zhang K. Applications of Optobiology in Intact Cells and Multicellular Organisms. J Mol Biol 2017; 429:2999-3017. [PMID: 28882542 DOI: 10.1016/j.jmb.2017.08.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 08/26/2017] [Accepted: 08/28/2017] [Indexed: 12/25/2022]
Abstract
Temporal kinetics and spatial coordination of signal transduction in cells are vital for cell fate determination. Tools that allow for precise modulation of spatiotemporal regulation of intracellular signaling in intact cells and multicellular organisms remain limited. The emerging optobiological approaches use light to control protein-protein interaction in live cells and multicellular organisms. Optobiology empowers light-mediated control of diverse cellular and organismal functions such as neuronal activity, intracellular signaling, gene expression, cell proliferation, differentiation, migration, and apoptosis. In this review, we highlight recent developments in optobiology, focusing on new features of second-generation optobiological tools. We cover applications of optobiological approaches in the study of cellular and organismal functions, discuss current challenges, and present our outlook. Taking advantage of the high spatial and temporal resolution of light control, optobiology promises to provide new insights into the coordination of signaling circuits in intact cells and multicellular organisms.
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Affiliation(s)
- John S Khamo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Savanna R Sharum
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Payel Mondal
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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60
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Marter K, Wetzel J, Eichhorst J, Eremina N, Leboulle G, Barth A, Wiesner B, Eisenhardt D. Inhibition of Protein Synthesis with Highly Soluble Caged Compounds. ChemistrySelect 2017. [DOI: 10.1002/slct.201701175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kathrin Marter
- FB Biologie, Chemie, Pharmazie, Institut für Biologie, Neurobiologie; Freie Universität Berlin; Königin-Luise-Straße 28/30 14195 Berlin Germany
- Neuralomics; Leibniz-Institut für Neurobiologie; Brenneckestraße 6 39118 Magdeburg Germany
- Center for Behavioral Brain Sciences; Magdeburg Germany
- Neurale Plastizität und Kommunikation, Institut für Pharmakologie und Toxikologie; Medizinische Fakultät; Otto-von-Guericke-Universität Magdeburg; Leipziger Str. 44 39120 Magdeburg Germany
| | - Janina Wetzel
- FB Biologie, Chemie, Pharmazie, Institut für Biologie, Neurobiologie; Freie Universität Berlin; Königin-Luise-Straße 28/30 14195 Berlin Germany
- Leibniz-Institut für Molekulare Pharmakologie; Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Jenny Eichhorst
- Leibniz-Institut für Molekulare Pharmakologie; Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Nadja Eremina
- Department of Biochemistry and Biophysics; Stockholm University; Svante Arrhenius väg 16C 10691 Stockholm Sweden
| | - Gérard Leboulle
- FB Biologie, Chemie, Pharmazie, Institut für Biologie, Neurobiologie; Freie Universität Berlin; Königin-Luise-Straße 28/30 14195 Berlin Germany
| | - Andreas Barth
- Department of Biochemistry and Biophysics; Stockholm University; Svante Arrhenius väg 16C 10691 Stockholm Sweden
| | - Burkhard Wiesner
- Leibniz-Institut für Molekulare Pharmakologie; Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Dorothea Eisenhardt
- FB Biologie, Chemie, Pharmazie, Institut für Biologie, Neurobiologie; Freie Universität Berlin; Königin-Luise-Straße 28/30 14195 Berlin Germany
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61
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Identification of postsynaptic phosphatidylinositol-4,5-bisphosphate (PIP 2) roles for synaptic plasticity using chemically induced dimerization. Sci Rep 2017; 7:3351. [PMID: 28611378 PMCID: PMC5469801 DOI: 10.1038/s41598-017-03520-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 05/02/2017] [Indexed: 11/16/2022] Open
Abstract
Phosphatidylinositol-4,5-bisphosphate (PIP2), one of the key phospholipids, directly interacts with several membrane and cytosolic proteins at neuronal plasma membranes, leading to changes in neuronal properties including the feature and surface expression of ionotropic receptors. Although PIP2 is also concentrated at the dendritic spines, little is known about the direct physiological functions of PIP2 at postsynaptic as opposed to presynaptic sites. Most previous studies used genetic and pharmacological methods to modulate enzymes that alter PIP2 levels, making it difficult to delineate time- or region-specific roles of PIP2. We used chemically-induced dimerization to translocate inositol polyphosphate 5-phosphatase (Inp54p) to plasma membranes in the presence of rapamycin. Upon redistribution of Inp54p, long-term depression (LTD) induced by low-frequency stimulation was blocked in the mouse hippocampal CA3-CA1 pathway, but the catalytically-dead mutant did not affect LTD induction. Collectively, PIP2 is critically required for induction of LTD whereas translocation of Inp54p to plasma membranes has no effect on the intrinsic properties of the neurons, basal synaptic transmission, long-term potentiation or expression of LTD.
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62
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Wong PT, Roberts EW, Tang S, Mukherjee J, Cannon J, Nip AJ, Corbin K, Krummel MF, Choi SK. Control of an Unusual Photo-Claisen Rearrangement in Coumarin Caged Tamoxifen through an Extended Spacer. ACS Chem Biol 2017; 12:1001-1010. [PMID: 28191924 PMCID: PMC5404426 DOI: 10.1021/acschembio.6b00999] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The use of coumarin
caged molecules has been well documented in
numerous photocaging applications including for the spatiotemporal
control of Cre-estrogen receptor (Cre-ERT2) recombinase activity.
In this article, we report that 4-hydroxytamoxifen (4OHT) caged with
coumarin via a conventional ether linkage led to
an unexpected photo-Claisen rearrangement which significantly competed
with the release of free 4OHT. The basis for this unwanted reaction
appears to be related to the coumarin structure and its radical-based
mechanism of uncaging, as it did not occur in ortho-nitrobenzyl (ONB) caged 4OHT that was otherwise linked in the same
manner. In an effort to perform design optimization, we introduced
a self-immolative linker longer than the ether linkage and identified
an optimal linker which allowed rapid 4OHT release by both single-photon
and two-photon absorption mechanisms. The ability of this construct
to actively control Cre-ERT2 mediated gene modifications was investigated
in mouse embryonic fibroblasts (MEFs) in which the expression of a
green fluorescent protein (GFP) reporter dependent gene recombination
was controlled by 4OHT release and measured by confocal fluorescence
microscopy and flow cytometry. In summary, we report the implications
of this photo-Claisen rearrangement in coumarin caged compounds and
demonstrate a rational linker strategy for addressing this unwanted
side reaction.
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Affiliation(s)
| | - Edward W. Roberts
- Department
of Pathology, University of California, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, California 94143, United States
| | | | | | | | - Alyssa J. Nip
- Department
of Pathology, University of California, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, California 94143, United States
| | - Kaitlin Corbin
- Department
of Pathology, University of California, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, California 94143, United States
| | - Matthew F. Krummel
- Department
of Pathology, University of California, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, California 94143, United States
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63
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Chen X, Venkatachalapathy M, Kamps D, Weigel S, Kumar R, Orlich M, Garrecht R, Hirtz M, Niemeyer CM, Wu YW, Dehmelt L. “Molecular Activity Painting”: Switch-like, Light-Controlled Perturbations inside Living Cells. Angew Chem Int Ed Engl 2017; 56:5916-5920. [DOI: 10.1002/anie.201611432] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/10/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max-Planck Society; Dortmund Germany
| | - Muthukumaran Venkatachalapathy
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Dominic Kamps
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Simone Weigel
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Ravi Kumar
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF); Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Michael Orlich
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Ruben Garrecht
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Michael Hirtz
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF); Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max-Planck Society; Dortmund Germany
| | - Leif Dehmelt
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
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64
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Chen X, Venkatachalapathy M, Kamps D, Weigel S, Kumar R, Orlich M, Garrecht R, Hirtz M, Niemeyer CM, Wu YW, Dehmelt L. “Molecular Activity Painting”: schaltbare, lichtgesteuerte Manipulation in lebenden Zellen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611432] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
| | - Muthukumaran Venkatachalapathy
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Dominic Kamps
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Simone Weigel
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Ravi Kumar
- Institut für Nanotechnologie (INT) und Karlsruhe Nano Micro Facility (KNMF); Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Michael Orlich
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Ruben Garrecht
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Michael Hirtz
- Institut für Nanotechnologie (INT) und Karlsruhe Nano Micro Facility (KNMF); Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Christof M. Niemeyer
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Yao-Wen Wu
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
| | - Leif Dehmelt
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
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65
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Mondal P, Khamo JS, Krishnamurthy VV, Cai Q, Zhang K. Drive the Car(go)s-New Modalities to Control Cargo Trafficking in Live Cells. Front Mol Neurosci 2017; 10:4. [PMID: 28163671 PMCID: PMC5247435 DOI: 10.3389/fnmol.2017.00004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/05/2017] [Indexed: 11/13/2022] Open
Abstract
Synaptic transmission is a fundamental molecular process underlying learning and memory. Successful synaptic transmission involves coupled interaction between electrical signals (action potentials) and chemical signals (neurotransmitters). Defective synaptic transmission has been reported in a variety of neurological disorders such as Autism and Alzheimer’s disease. A large variety of macromolecules and organelles are enriched near functional synapses. Although a portion of macromolecules can be produced locally at the synapse, a large number of synaptic components especially the membrane-bound receptors and peptide neurotransmitters require active transport machinery to reach their sites of action. This spatial relocation is mediated by energy-consuming, motor protein-driven cargo trafficking. Properly regulated cargo trafficking is of fundamental importance to neuronal functions, including synaptic transmission. In this review, we discuss the molecular machinery of cargo trafficking with emphasis on new experimental strategies that enable direct modulation of cargo trafficking in live cells. These strategies promise to provide insights into a quantitative understanding of cargo trafficking, which could lead to new intervention strategies for the treatment of neurological diseases.
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Affiliation(s)
- Payel Mondal
- Department of Biochemistry, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - John S Khamo
- Department of Biochemistry, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | | | - Qi Cai
- Department of Biochemistry, University of Illinois at Urbana-Champaign Urbana, IL, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-ChampaignUrbana, IL, USA; Neuroscience Program, University of Illinois at Urbana-ChampaignUrbana, IL, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbana, IL, USA
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66
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Abstract
An optimal tool to unravel the role of a specific player within a cellular network or process requires its spatiotemporally resolved perturbation. Chemically induced dimerization (CID) by the rapamycin system has proven useful to induce protein dimerization or translocation with high spatiotemporal precision. Recently, we and others have added reversibility of the dimerization event as a novel feature to CID approaches. Among those, our reversible chemical dimerizer (rCD1) shows the fastest release kinetics observed, comparable to optogenetic methods. Induction and termination of enzyme activities, including phosphatidylinositol 3-kinase (PI3K) and 5-phosphatase (5Ptase), therefore allowed us to monitor the relaxation of the downstream effectors within living cells by imaging and traditional biochemical methods. Because switching off the rCD1-induced enzyme activity is sufficiently fast, it is possible to estimate kinetic parameters for enzyme activity and metabolism. Fast reversible CIDs are therefore unique tools for performing semiquantitative biochemistry in intact cells. In this chapter, we discuss advantages and constraints for the design of reversible CID applications. We provide detailed protocols for rCD1 synthesis, CID component expression in and delivery to mammalian cells and the determination of enzyme kinetics inside intact cells by a specially designed image acquisition and data analysis method.
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Affiliation(s)
- M Schifferer
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - S Feng
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - F Stein
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - C Schultz
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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67
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Beck JR, Truong T, Stains CI. Temporal Analysis of PP2A Phosphatase Activity During Insulin Stimulation Using a Direct Activity Probe. ACS Chem Biol 2016; 11:3284-3288. [PMID: 27805358 DOI: 10.1021/acschembio.6b00697] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein serine/threonine phosphatases (PSPs) are ubiquitously expressed in mammalian cells. In particular, PP2A accounts for up to 1% of the total protein within cells. Despite clear evidence for the role of PP2A in cellular signaling, there is a lack of information concerning the magnitude and temporal dynamics of PP2A catalytic activity during insulin stimulation. Herein, we describe the development of a direct, fluorescent activity probe capable of reporting on global changes in PP2A enzymatic activity in unfractionated cell lysates. Utilizing this new probe, we profiled the magnitude as well as temporal dynamics of PP2A activity during insulin stimulation of liver hepatocytes. These results provide direct evidence for the rapid response of PP2A catalytic activity to extracellular stimulation, as well as insight into the complex regulation of phosphorylation levels by opposing kinase and phosphatase activities within the cell. This study provides a new tool for investigating the chemical biology of PSPs.
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Affiliation(s)
- Jon R. Beck
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Tiffany Truong
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Cliff I. Stains
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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68
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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.
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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.
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69
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Lee SY, Lee H, Lee HK, Lee SW, Ha SC, Kwon T, Seo JK, Lee C, Rhee HW. Proximity-Directed Labeling Reveals a New Rapamycin-Induced Heterodimer of FKBP25 and FRB in Live Cells. ACS CENTRAL SCIENCE 2016; 2:506-16. [PMID: 27610411 PMCID: PMC4999972 DOI: 10.1021/acscentsci.6b00137] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Indexed: 05/23/2023]
Abstract
Mammalian target of rapamycin (mTOR) signaling is a core pathway in cellular metabolism, and control of the mTOR pathway by rapamycin shows potential for the treatment of metabolic diseases. In this study, we employed a new proximity biotin-labeling method using promiscuous biotin ligase (pBirA) to identify unknown elements in the rapamycin-induced interactome on the FK506-rapamycin binding (FRB) domain in living cells. FKBP25 showed the strongest biotin labeling by FRB-pBirA in the presence of rapamycin. Immunoprecipitation and immunofluorescence experiments confirmed that endogenous FKBP25 has a rapamycin-induced physical interaction with the FRB domain. Furthermore, the crystal structure of the ternary complex of FRB-rapamycin-FKBP25 was determined at 1.67-Å resolution. In this crystal structure we found that the conformational changes of FRB generate a hole where there is a methionine-rich space, and covalent metalloid coordination was observed at C2085 of FRB located at the bottom of the hole. Our results imply that FKBP25 might have a unique physiological role related to metallomics in mTOR signaling.
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Affiliation(s)
- Song-Yi Lee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Hakbong Lee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Hye-Kyeong Lee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Seung-Won Lee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Sung Chul Ha
- Pohang
Accelerator Laboratory, Pohang University
of Science and Technology, Pohang, Kyungbuk 37673, Korea
| | - Taejoon Kwon
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Jeong Kon Seo
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Changwook Lee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Department of Biological
Sciences, UNIST Central Research Facilities
(UCRF), and Deparment of Biomedical Engineering, Ulsan
National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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70
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Hughes JH, Kumar S. Synthetic mechanobiology: engineering cellular force generation and signaling. Curr Opin Biotechnol 2016; 40:82-89. [PMID: 27023733 DOI: 10.1016/j.copbio.2016.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 10/24/2022]
Abstract
Mechanobiology seeks to understand and control mechanical and related biophysical communication between cells and their surroundings. While experimental efforts in this field have traditionally emphasized manipulation of the extracellular force environment, a new suite of approaches has recently emerged in which cell phenotype and signaling are controlled by directly engineering the cell itself. One route is to control cell behavior by modulating gene expression using conditional promoters. Alternatively, protein activity can be actuated directly using synthetic protein ligands, chemically induced protein dimerization, optogenetic strategies, or functionalized magnetic nanoparticles. Proof-of-principle studies are already demonstrating the translational potential of these approaches, and future technological development will permit increasingly precise control over cell mechanobiology and improve our understanding of the underlying signaling events.
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Affiliation(s)
- Jasmine Hannah Hughes
- Department of Bioengineering, University of California, Berkeley, United States; UC Berkeley - UCSF Graduate Program in Bioengineering, United States
| | - Sanjay Kumar
- Department of Bioengineering, University of California, Berkeley, United States.
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71
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Abstract
Allosteric transition, defined as conformational changes induced by ligand binding, is one of the fundamental properties of proteins. Allostery has been observed and characterized in many proteins, and has been recently utilized to control protein function via regulation of protein activity. Here, we review the physical and evolutionary origin of protein allostery, as well as its importance to protein regulation, drug discovery, and biological processes in living systems. We describe recently developed approaches to identify allosteric pathways, connected sets of pairwise interactions that are responsible for propagation of conformational change from the ligand-binding site to a distal functional site. We then present experimental and computational protein engineering approaches for control of protein function by modulation of allosteric sites. As an example of application of these approaches, we describe a synergistic computational and experimental approach to rescue the cystic-fibrosis-associated protein cystic fibrosis transmembrane conductance regulator, which upon deletion of a single residue misfolds and causes disease. This example demonstrates the power of allosteric manipulation in proteins to both elucidate mechanisms of molecular function and to develop therapeutic strategies that rescue those functions. Allosteric control of proteins provides a tool to shine a light on the complex cascades of cellular processes and facilitate unprecedented interrogation of biological systems.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
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72
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Xu B, Zhou X, Stains CI. An improved miniprotein host for fluorogenic supramolecular assembly on the surface of living cells. RSC Adv 2016. [DOI: 10.1039/c6ra01215a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A new host–guest pair produces a significant increase in the brightness of supramolecular complexes on the surface of living cells.
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Affiliation(s)
- Bi Xu
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - Xinqi Zhou
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - Cliff I. Stains
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
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73
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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.
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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
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74
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Xu B, Zhou X, Stains CI. Supramolecular Assembly of an Evolved Miniprotein Host and Fluorogenic Guest Pair. J Am Chem Soc 2015; 137:14252-5. [DOI: 10.1021/jacs.5b09494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bi Xu
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Xinqi Zhou
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Cliff I. Stains
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
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75
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van Bergeijk P, Hoogenraad CC, Kapitein LC. Right Time, Right Place: Probing the Functions of Organelle Positioning. Trends Cell Biol 2015; 26:121-134. [PMID: 26541125 DOI: 10.1016/j.tcb.2015.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
Abstract
The proper spatial arrangement of organelles underlies many cellular processes including signaling, polarization, and growth. Despite the importance of local positioning, the precise connection between subcellular localization and organelle function is often not fully understood. To address this, recent studies have developed and employed different strategies to directly manipulate organelle distributions, such as the use of (light-sensitive) heterodimerization to control the interaction between selected organelles and specific motor proteins, adaptor molecules, or anchoring factors. We review here the importance of subcellular localization as well as tools to control local organelle positioning. Because these approaches allow spatiotemporal control of organelle distribution, they will be invaluable tools to unravel local functioning and the mechanisms that control positioning.
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Affiliation(s)
- Petra van Bergeijk
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Lukas C Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands.
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76
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Chemically induced dimerization: reversible and spatiotemporal control of protein function in cells. Curr Opin Chem Biol 2015; 28:194-201. [DOI: 10.1016/j.cbpa.2015.09.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/21/2015] [Accepted: 09/07/2015] [Indexed: 12/21/2022]
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77
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Wang J, Wei Y, Hu X, Fang YY, Li X, Liu J, Wang S, Yuan Q. Protein Activity Regulation: Inhibition by Closed-Loop Aptamer-Based Structures and Restoration by Near-IR Stimulation. J Am Chem Soc 2015; 137:10576-84. [PMID: 26258907 DOI: 10.1021/jacs.5b04894] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Regulation of protein activity is vital for understanding the molecular mechanism of biological activities. In this work, protein activity is suppressed by proximity-dependent surface hybridization and subsequently restored by near-infrared (NIR) light stimulation. Specifically, by constructing closed-loop structures with two aptamer-based affinity ligands, significantly enhanced inhibition of thrombin activity is achieved compared to traditional single affinity ligand based inhibitors. Furthermore, the activity of inhibited thrombin is efficiently recovered under NIR light stimulation by using gold nanorods (AuNRs) as photothermal agents to disrupt the closed-loop structures. Real-time and in situ monitoring of the conversion of fibrinogen into fibrin catalyzed by both inhibited and recovered thrombin was performed with light scattering spectroscopy and laser scanning confocal microscopy (LSCM). Thrombin trapped in the closed-loop structures shows slow reaction kinetics, while the photothermally liberated thrombin displays largely recovered catalytic activity. Human plasma was further employed to demonstrate that both the inhibited and restored thrombin can be applied to clotting reaction in reality. This strategy provides protein activity regulation for studying the molecular basis of biological activities and can be further applied to potential areas such as metabolic pathway regulation and the development of protein-inhibitor pharmaceuticals.
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Affiliation(s)
- Jie Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China
| | - Yurong Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China.,Ministry of Education, Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University , Wuhan 430062, China
| | - Xiaoxia Hu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China
| | - Yu-Yan Fang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China
| | - Xinyang Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China
| | - Jian Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China
| | - Shengfu Wang
- Ministry of Education, Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University , Wuhan 430062, China
| | - Quan Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University , Wuhan 430072, China
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78
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Wright CW, Guo ZF, Liang FS. Light control of cellular processes by using photocaged abscisic acid. Chembiochem 2015; 16:254-61. [PMID: 25530501 PMCID: PMC4849874 DOI: 10.1002/cbic.201402576] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Indexed: 11/08/2022]
Abstract
Abscisic acid (ABA) was chemically modified with a photocaging group to promote photo-induced protein dimerization. This photocontrolled chemically induced dimerization (CID) method based on caged ABA enables dose-dependent light regulation of cellular processes, including transcription, protein translocation, signal transduction, and cytoskeletal remodeling, without the need to perform extensive protein engineering. Caged ABA can be easily modified to respond to different wavelengths of light. Consequently, this strategy should be applicable to the design of light-regulated protein dimerization systems and potentially be used orthogonally with other light-controlled CID systems.
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Affiliation(s)
- Catherine W Wright
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, NM 87131 (USA)
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79
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Schelkle KM, Griesbaum T, Ollech D, Becht S, Buckup T, Hamburger M, Wombacher R. Lichtinduzierte Proteindimerisierung in lebenden Zellen durch Ein- und Zweiphotonenaktivierung von Gibberellinsäurederivaten. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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80
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Schelkle KM, Griesbaum T, Ollech D, Becht S, Buckup T, Hamburger M, Wombacher R. Light-Induced Protein Dimerization by One- and Two-Photon Activation of Gibberellic Acid Derivatives in Living Cells. Angew Chem Int Ed Engl 2015; 54:2825-9. [DOI: 10.1002/anie.201409196] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/28/2014] [Indexed: 01/02/2023]
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81
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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.
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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
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82
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Brown KA, Zou Y, Shirvanyants D, Zhang J, Samanta S, Mantravadi PK, Dokholyan NV, Deiters A. Light-cleavable rapamycin dimer as an optical trigger for protein dimerization. Chem Commun (Camb) 2015; 51:5702-5. [DOI: 10.1039/c4cc09442e] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein heterodimerization of FKBP12 and FRB can be optically controlled with a photocleavable rapamycin dimer.
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Affiliation(s)
- Kalyn A. Brown
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
- Department of Chemistry
| | - Yan Zou
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - David Shirvanyants
- Department of Biochemistry and Biophysics
- University of North Carolina
- Chapel Hill
- USA
| | - Jie Zhang
- Department of Chemistry
- North Carolina State University
- Raleigh
- USA
| | - Subhas Samanta
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
| | | | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics
- University of North Carolina
- Chapel Hill
- USA
| | - Alexander Deiters
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
- Department of Chemistry
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83
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MacDonald IA, Hathaway NA. Epigenetic roots of immunologic disease and new methods for examining chromatin regulatory pathways. Immunol Cell Biol 2014; 93:261-70. [PMID: 25533290 DOI: 10.1038/icb.2014.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 10/31/2014] [Indexed: 12/19/2022]
Abstract
The ability to accurately quantitate and experimentally examine epigenetic modifications across the human genome has exploded in the past decade. This has given rise to a wealth of new information concerning the contributions of epigenetic regulatory networks to the pathogenesis of human disease. In particular, immunological disorders have strong developmental roots in chromatin regulatory pathways. In this review, we focus on the epigenetic signatures and new discoveries revealing the epigenetic compositions of specific immunological cancers and autoimmune diseases. We also comment on the conserved epigenetic roots among diverse immunological disorders and suggest inhibition strategies that may be relevant for future treatment. Finally, we highlight emerging experimental tools with the capability to examine the mechanisms of chromatin regulatory enzymes with a high level of temporal control. The knowledge of genetic and epigenetic defects in immunological disease combined with new experimental approaches will elucidate the contribution of individual enzymes in complex epigenetic regulatory networks. This could lead to new diagnostic and therapeutic approaches for some very diverse and difficult to treat human diseases.
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Affiliation(s)
- Ian A MacDonald
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Nathaniel A Hathaway
- 1] Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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84
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Zhang K, Cui B. Optogenetic control of intracellular signaling pathways. Trends Biotechnol 2014; 33:92-100. [PMID: 25529484 DOI: 10.1016/j.tibtech.2014.11.007] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 10/29/2014] [Accepted: 11/19/2014] [Indexed: 10/24/2022]
Abstract
Cells employ a plethora of signaling pathways to make their life-and-death decisions. Extensive genetic, biochemical, and physiological studies have led to the accumulation of knowledge about signaling components and their interactions within signaling networks. These conventional approaches, although useful, lack the ability to control the spatial and temporal aspects of signaling processes. The recently emerged optogenetic tools open exciting opportunities by enabling signaling regulation with superior temporal and spatial resolution, easy delivery, rapid reversibility, fewer off-target side effects, and the ability to dissect complex signaling networks. Here we review recent achievements in using light to control intracellular signaling pathways and discuss future prospects for the field, including integration of new genetic approaches into optogenetics.
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Affiliation(s)
- Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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85
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Camacho-Soto K, Castillo-Montoya J, Tye B, Ogunleye LO, Ghosh I. Small molecule gated split-tyrosine phosphatases and orthogonal split-tyrosine kinases. J Am Chem Soc 2014; 136:17078-86. [PMID: 25409264 DOI: 10.1021/ja5080745] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein kinases phosphorylate client proteins, while protein phosphatases catalyze their dephosphorylation and thereby in concert exert reversible control over numerous signal transduction pathways. We have recently reported the design and validation of split-protein kinases that can be conditionally activated by an added small molecule chemical inducer of dimerization (CID), rapamycin. Herein, we provide the rational design and validation of three split-tyrosine phosphatases (PTPs) attached to FKBP and FRB, where catalytic activity can be modulated with rapamycin. We further demonstrate that the orthogonal CIDs, abscisic acid and gibberellic acid, can be used to impart control over the activity of split-tyrosine kinases (PTKs). Finally, we demonstrate that designed split-phosphatases and split-kinases can be activated by orthogonal CIDs in mammalian cells. In sum, we provide a methodology that allows for post-translational orthogonal small molecule control over the activity of user defined split-PTKs and split-PTPs. This methodology has the long-term potential for both interrogating and redesigning phosphorylation dependent signaling pathways.
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Affiliation(s)
- Karla Camacho-Soto
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
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86
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Ballister ER, Aonbangkhen C, Mayo AM, Lampson MA, Chenoweth DM. Localized light-induced protein dimerization in living cells using a photocaged dimerizer. Nat Commun 2014; 5:5475. [PMID: 25400104 PMCID: PMC4308733 DOI: 10.1038/ncomms6475] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/06/2014] [Indexed: 12/17/2022] Open
Abstract
Regulated protein localization is critical for many cellular processes. Several techniques have been developed for experimental control over protein localization, including chemically induced and light-induced dimerization, which both provide temporal control. Light-induced dimerization offers the distinct advantage of spatial precision within subcellular length scales. A number of elegant systems have been reported that utilize natural light-sensitive proteins to induce dimerization via direct protein-protein binding interactions, but the application of these systems at cellular locations beyond the plasma membrane has been limited. Here we present a new technique to rapidly and reversibly control protein localization in living cells with subcellular spatial resolution using a cell-permeable, photoactivatable chemical inducer of dimerization. We demonstrate light-induced recruitment of a cytosolic protein to individual centromeres, kinetochores, mitochondria and centrosomes in human cells, indicating that our system is widely applicable to many cellular locations.
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Affiliation(s)
- Edward R Ballister
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Chanat Aonbangkhen
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alyssa M Mayo
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael A Lampson
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - David M Chenoweth
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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87
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Adjobo-Hermans MJW. Fast reversibility of dimeriser system enables quantification of signal molecule turnover. Chembiochem 2014; 15:2037-9. [PMID: 25145328 DOI: 10.1002/cbic.201402294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Indexed: 11/10/2022]
Abstract
The design of a brake: Chemical induced dimerisation systems have revolutionised signal transduction research by allowing fast activation of specific proteins. A recent report describes the design of tools that enable the rapid switching off of the induced signal, thereby enabling quantification of signal molecule turnover.
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Affiliation(s)
- Merel J W Adjobo-Hermans
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen (The Netherlands).
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88
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How to control proteins with light in living systems. Nat Chem Biol 2014; 10:533-41. [DOI: 10.1038/nchembio.1534] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 04/21/2014] [Indexed: 11/08/2022]
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89
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Hemphill J, Govan J, Uprety R, Tsang M, Deiters A. Site-specific promoter caging enables optochemical gene activation in cells and animals. J Am Chem Soc 2014; 136:7152-8. [PMID: 24802207 PMCID: PMC4333597 DOI: 10.1021/ja500327g] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
In
cell and molecular biology, double-stranded circular DNA constructs,
known as plasmids, are extensively used to express a gene of interest.
These gene expression systems rely on a specific promoter region to
drive the transcription of genes either constitutively (i.e., in a
continually “ON” state) or conditionally (i.e., in response
to a specific transcription initiator). However, controlling plasmid-based
expression with high spatial and temporal resolution in cellular environments
and in multicellular organisms remains challenging. To overcome this
limitation, we have site-specifically installed nucleobase-caging
groups within a plasmid promoter region to enable optochemical control
of transcription and, thus, gene expression, via photolysis of the
caging groups. Through the light-responsive modification of plasmid-based
gene expression systems, we have demonstrated optochemical activation
of an exogenous fluorescent reporter gene in both tissue culture and
a live animal model, as well as light-induced overexpression of an
endogenous signaling protein.
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Affiliation(s)
- James Hemphill
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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90
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Zimmermann M, Cal R, Janett E, Hoffmann V, Bochet CG, Constable E, Beaufils F, Wymann MP. Cell-permeant and photocleavable chemical inducer of dimerization. Angew Chem Int Ed Engl 2014; 53:4717-20. [PMID: 24677313 PMCID: PMC4499241 DOI: 10.1002/anie.201310969] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Indexed: 11/30/2022]
Abstract
Chemical inducers of dimerization (CIDs) have been developed to orchestrate protein dimerization and translocation. Here we present a novel photocleavable HaloTag- and SNAP-tag-reactive CID (MeNV-HaXS) with excellent selectivity and intracellular reactivity. Excitation at 360 nm cleaves the methyl-6-nitroveratryl core of MeNV-HaXS. MeNV-HaXS covalently links HaloTag- and SNAP-tag fusion proteins, and enables targeting of selected membranes and intracellular organelles. MeNV-HaXS-mediated translocation has been validated for plasma membrane, late endosomes, lysosomes, Golgi, mitochondria, and the actin cytoskeleton. Photocleavage of MeNV-HaXS liberates target proteins and provides access to optical manipulation of protein relocation with high spatiotemporal and subcellular precision. MeNV-HaXS supports kinetic studies of protein dynamics and the manipulation of subcellular enzyme activities, which is exemplified for Golgi-targeted cargo and the assessment of nuclear import kinetics.
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Affiliation(s)
- Mirjam Zimmermann
- University of Basel, Department of BiomedicineMattenstrasse 28, Basel (Switzerland)
| | - Ruben Cal
- University of Basel, Department of BiomedicineMattenstrasse 28, Basel (Switzerland)
| | - Elia Janett
- University of Fribourg, Department of ChemistryChemin du Musée 9, Fribourg (Switzerland)
| | - Viktor Hoffmann
- University of Basel, Department of BiomedicineMattenstrasse 28, Basel (Switzerland)
| | - Christian G Bochet
- University of Fribourg, Department of ChemistryChemin du Musée 9, Fribourg (Switzerland)
| | - Edwin Constable
- University of Basel, Department of ChemistrySpitalstrasse 51, Basel (Switzerland)
| | - Florent Beaufils
- University of Basel, Department of BiomedicineMattenstrasse 28, Basel (Switzerland)
| | - Matthias P Wymann
- University of Basel, Department of BiomedicineMattenstrasse 28, Basel (Switzerland)
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91
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Zimmermann M, Cal R, Janett E, Hoffmann V, Bochet CG, Constable E, Beaufils F, Wymann MP. Ein zellpermeables und photospaltbares Reagens für die selektive intrazelluläre Protein-Protein-Dimerisierung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310969] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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92
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Zhang K, Duan L, Ong Q, Lin Z, Varman PM, Sung K, Cui B. Light-mediated kinetic control reveals the temporal effect of the Raf/MEK/ERK pathway in PC12 cell neurite outgrowth. PLoS One 2014; 9:e92917. [PMID: 24667437 PMCID: PMC3965503 DOI: 10.1371/journal.pone.0092917] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 02/26/2014] [Indexed: 11/29/2022] Open
Abstract
It has been proposed that differential activation kinetics allows cells to use a common set of signaling pathways to specify distinct cellular outcomes. For example, nerve growth factor (NGF) and epidermal growth factor (EGF) induce different activation kinetics of the Raf/MEK/ERK signaling pathway and result in differentiation and proliferation, respectively. However, a direct and quantitative linkage between the temporal profile of Raf/MEK/ERK activation and the cellular outputs has not been established due to a lack of means to precisely perturb its signaling kinetics. Here, we construct a light-gated protein-protein interaction system to regulate the activation pattern of the Raf/MEK/ERK signaling pathway. Light-induced activation of the Raf/MEK/ERK cascade leads to significant neurite outgrowth in rat PC12 pheochromocytoma cell lines in the absence of growth factors. Compared with NGF stimulation, light stimulation induces longer but fewer neurites. Intermittent on/off illumination reveals that cells achieve maximum neurite outgrowth if the off-time duration per cycle is shorter than 45 min. Overall, light-mediated kinetic control enables precise dissection of the temporal dimension within the intracellular signal transduction network.
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Affiliation(s)
- Kai Zhang
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Liting Duan
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Qunxiang Ong
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Ziliang Lin
- Department of Applied Physics, Stanford University, Stanford, California, United States of America
| | - Pooja Mahendra Varman
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Kijung Sung
- Biophysics Program, Stanford University, Stanford, California, United States of America
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- * E-mail:
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93
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Sample V, Mehta S, Zhang J. Genetically encoded molecular probes to visualize and perturb signaling dynamics in living biological systems. J Cell Sci 2014; 127:1151-60. [PMID: 24634506 PMCID: PMC3953811 DOI: 10.1242/jcs.099994] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/22/2013] [Indexed: 01/05/2023] Open
Abstract
In this Commentary, we discuss two sets of genetically encoded molecular tools that have significantly enhanced our ability to observe and manipulate complex biochemical processes in their native context and that have been essential in deepening our molecular understanding of how intracellular signaling networks function. In particular, genetically encoded biosensors are widely used to directly visualize signaling events in living cells, and we highlight several examples of basic biosensor designs that have enabled researchers to capture the spatial and temporal dynamics of numerous signaling molecules, including second messengers and signaling enzymes, with remarkable detail. Similarly, we discuss a number of genetically encoded biochemical perturbation techniques that are being used to manipulate the activity of various signaling molecules with far greater spatial and temporal selectivity than can be achieved using standard pharmacological or genetic techniques, focusing specifically on examples of chemically driven and light-inducible perturbation strategies. We then describe recent efforts to combine these diverse and powerful molecular tools into a unified platform that can be used to elucidate the molecular details of biological processes that may potentially extend well beyond the realm of signal transduction.
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Affiliation(s)
- Vedangi Sample
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| | - Sohum Mehta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
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94
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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
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95
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Abstract
Manipulation of protein kinase activity is widely used to dissect signaling pathways controlling physiological and pathological processes. Common methods often cannot provide the desired spatial and temporal resolution in control of kinase activity. Regulation of kinase activity by photocaged kinase inhibitors has been successfully used to achieve tight temporal and local control, but inhibitors are limited to inactivation of kinases and often do not provide the desired specificity. Here we report detailed methods for light-mediated activation of kinases in living cells using engineered rapamycin-regulated kinases in conjunction with a photocaged analog of rapamycin.
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96
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97
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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: 30] [Impact Index Per Article: 2.7] [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.
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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
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98
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Rational design of a ligand-controlled protein conformational switch. Proc Natl Acad Sci U S A 2013; 110:6800-4. [PMID: 23569285 DOI: 10.1073/pnas.1218319110] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Design of a regulatable multistate protein is a challenge for protein engineering. Here we design a protein with a unique topology, called uniRapR, whose conformation is controlled by the binding of a small molecule. We confirm switching and control ability of uniRapR in silico, in vitro, and in vivo. As a proof of concept, uniRapR is used as an artificial regulatory domain to control activity of kinases. By activating Src kinase using uniRapR in single cells and whole organism, we observe two unique phenotypes consistent with its role in metastasis. Activation of Src kinase leads to rapid induction of protrusion with polarized spreading in HeLa cells, and morphological changes with loss of cell-cell contacts in the epidermal tissue of zebrafish. The rational creation of uniRapR exemplifies the strength of computational protein design, and offers a powerful means for targeted activation of many pathways to study signaling in living organisms.
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99
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Sample V, Ni Q, Mehta S, Inoue T, Zhang J. Controlling enzymatic action in living cells with a kinase-inducible bimolecular switch. ACS Chem Biol 2013; 8:116-21. [PMID: 23072367 DOI: 10.1021/cb300393w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular probes designed to monitor or perturb signaling events in living cells rely on engineered molecular switches. Here, we show that a kinase-inducible bimolecular switch comprising a kinase-specific substrate and a phosphoamino acid binding domain can be used for acute regulation of cellular events. As a proof of concept, we employed a Protein Kinase A (PKA)-dependent switch and coupled it to a lipid phosphatase to manipulate the level of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P(2)) in living cells. PKA activation results in rapid degradation of PI(4,5)P(2). Conversely, when PKA is inhibited, dephosphorylation of the switch leads to the replenishment of PI(4,5)P(2). Thus, this strategy can be used for reversibly controlling enzymatic action in living cells. Furthermore, its genetic encodability and modular design should facilitate the adaptation of this approach to control different cellular activities as a function of phosphorylation-dependent input signals, thereby providing versatile tools for potentially perturbing or rewiring signaling pathways.
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Affiliation(s)
- Vedangi Sample
- Department
of Pharmacology and Molecular Sciences, ‡Department of Cell Biology, and §The Solomon H.
Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States
| | - Qiang Ni
- Department
of Pharmacology and Molecular Sciences, ‡Department of Cell Biology, and §The Solomon H.
Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States
| | - Sohum Mehta
- Department
of Pharmacology and Molecular Sciences, ‡Department of Cell Biology, and §The Solomon H.
Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States
| | - Takanari Inoue
- Department
of Pharmacology and Molecular Sciences, ‡Department of Cell Biology, and §The Solomon H.
Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States
| | - Jin Zhang
- Department
of Pharmacology and Molecular Sciences, ‡Department of Cell Biology, and §The Solomon H.
Snyder Department of Neuroscience and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States
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100
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DeRose R, Miyamoto T, Inoue T. Manipulating signaling at will: chemically-inducible dimerization (CID) techniques resolve problems in cell biology. Pflugers Arch 2013; 465:409-17. [PMID: 23299847 DOI: 10.1007/s00424-012-1208-6] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 12/12/2012] [Accepted: 12/13/2012] [Indexed: 11/27/2022]
Abstract
Chemically-inducible dimerization (CID) is a powerful tool that has proved useful in solving numerous problems in cell biology and related fields. In this review, we focus on case studies where CID was able to provide insight into otherwise refractory problems. Of particular interest are the cases of lipid second messengers and small GTPases, where the "signaling paradox" (how a small pool of signaling molecules can generate a large range of responses) can be at least partly explained through results gleaned from CID experiments. We also discuss several recent technical advances that provide improved specificity in CID action, novel CID substrates that allow simultaneous orthogonal manipulation of multiple systems in one cell, and several applications that move beyond the traditional CID technique of moving a protein of interest to a specific spatiotemporal location.
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Affiliation(s)
- Robert DeRose
- Department of Cell Biology, Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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