1
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Nomura Y, Kim N, Zhu B, Hamzah M, Zhang H, Yokobayashi Y. Optimization of Exon-Skipping Riboswitches and Their Applications to Control Mammalian Cell Fate. ACS Synth Biol 2024. [PMID: 39318128 DOI: 10.1021/acssynbio.4c00295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Mammalian riboswitches that can regulate transgene expression via RNA-small molecule interaction have promising applications in medicine and biotechnology, as they involve no protein factors that can induce immunogenic reactions and are not dependent on specially engineered promoters. However, the lack of cell-permeable and low-toxicity small molecules and cognate aptamers that can be exploited as riboswitches and the modest switching performance of mammalian riboswitches have limited their applications. In this study, we systematically optimized the design of a riboswitch that regulates exon skipping via an RNA aptamer that binds ASP2905. We examined two design strategies to modulate the stability of the aptamer base stem that blocks the 5' splice site to fine-tune the riboswitch characteristics. Furthermore, an optimized riboswitch was used to generate a mouse embryonic stem cell line that can be chemically induced to differentiate into myogenic cells by activating Myod1 expression and a human embryonic kidney cell line that can be induced to trigger apoptosis by activating BAX expression. The results demonstrate the tight chemical regulation of transgenes in mammalian cells to control their phenotype without exogenous protein factors.
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Affiliation(s)
- Yoko Nomura
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 9040495, Japan
| | - Narae Kim
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 9040495, Japan
| | - Bochen Zhu
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 9040495, Japan
| | - Muhammad Hamzah
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 9040495, Japan
| | - Haifeng Zhang
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 9040495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 9040495, Japan
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2
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Schmitt T, Huck C, Oberhof N, Hsu LY, Blasco E, Dreuw A, Tegeder P. Characteristics and long-term kinetics of an azobenzene derivative and a donor-acceptor Stenhouse adduct as orthogonal photoswitches. Phys Chem Chem Phys 2024; 26:7190-7202. [PMID: 38349743 DOI: 10.1039/d3cp05786k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Light-triggered molecular switches are extensively researched for their applications in medicine, chemistry and material science and, if combined, particularly for their use in multifunctional smart materials, for which orthogonally, i.e. individually, addressable photoswitches are needed. In such a multifunctional mixture, the switching properties, efficiencies and the overall performance may be impaired by undesired mutual dependences of the photoswitches on each other. Within this study, we compare the performance of the pure photoswitches, namely an azobenzene derivative (Azo) and a donor-acceptor Stenhouse adduct (DASA), with the switching properties of their mixture using time-resolved temperature-dependent UV/VIS absorption spectroscopy, time-resolved IR absorption spectroscopy at room temperature and quantum mechanical calculations to determine effective cross sections, switching kinetics as well as activation energies of thermally induced steps. We find slightly improved effective cross sections, percentages of switched molecules and no increased activation barriers of the equimolar mixture compared to the single compounds. Thus, the studied mixture Azo + DASA is very promising for future applications in multifunctional smart materials.
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Affiliation(s)
- Tanja Schmitt
- Physikalisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, 69120 Heidelberg, Germany.
| | - Christian Huck
- Physikalisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, 69120 Heidelberg, Germany.
| | - Nils Oberhof
- Interdisziplinäres Zentrum für Wissenschaftliches Rechnen, Ruprecht-Karls-Universität Heidelberg, 69120 Heidelberg, Germany
| | - Li-Yun Hsu
- Institute for Molecular System Engineering and Advanced Materials, Ruprecht-Karls-Universität Heidelberg, 69120 Heidelberg, Germany
| | - Eva Blasco
- Institute for Molecular System Engineering and Advanced Materials, Ruprecht-Karls-Universität Heidelberg, 69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisziplinäres Zentrum für Wissenschaftliches Rechnen, Ruprecht-Karls-Universität Heidelberg, 69120 Heidelberg, Germany
| | - Petra Tegeder
- Physikalisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, 69120 Heidelberg, Germany.
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3
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Fernandes RJ, Remón P, Moro AJ, Seco A, Ferreira ASD, Pischel U, Basílio N. Toward Light-Controlled Supramolecular Peptide Dimerization. J Org Chem 2021; 86:8472-8478. [PMID: 34060851 PMCID: PMC9161448 DOI: 10.1021/acs.joc.1c00464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The selective photodeprotection of the NVoc-modified FGG tripeptide yields the transformation of its 1:1 receptor-ligand complex with cucurbit[8]uril into a homoternary FGG2@CB8 assembly. The resulting light-induced dimerization of the model peptide provides a tool for the implementation of stimuli-responsive supramolecular chemistry in biologically relevant contexts.
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Affiliation(s)
- Rita J Fernandes
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Patricia Remón
- CIQSO - Centre for Research in Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, E-21071 Huelva, Spain
| | - Artur J Moro
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - André Seco
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana S D Ferreira
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Uwe Pischel
- CIQSO - Centre for Research in Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, E-21071 Huelva, Spain
| | - Nuno Basílio
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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4
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Role of carboxylic group pattern on protein surface in the recognition of iron oxide nanoparticles: A key for protein corona formation. Int J Biol Macromol 2020; 164:1715-1728. [PMID: 32758605 DOI: 10.1016/j.ijbiomac.2020.07.295] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 01/30/2023]
Abstract
The knowledge of protein-nanoparticle interplay is of crucial importance to predict the fate of nanomaterials in biological environments. Indeed, protein corona on nanomaterials is responsible for the physiological response of the organism, influencing cell processes, from transport to accumulation and toxicity. Herein, a comparison using four different proteins reveals the existence of patterned regions of carboxylic groups acting as recognition sites for naked iron oxide nanoparticles. Readily interacting proteins display a distinctive surface distribution of carboxylic groups, recalling the geometric shape of an ellipse. This is morphologically complementary to nanoparticles curvature and compatible with the topography of exposed FeIII sites laying on the nanomaterial surface. The recognition site, absent in non-interacting proteins, promotes the nanoparticle harboring and allows the formation of functional protein coronas. The present work envisages the possibility of predicting the composition and the biological properties of protein corona on metal oxide nanoparticles.
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5
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Chang HJ, Bonnet J. Synthetic receptors to understand and control cellular functions. Methods Enzymol 2020; 633:143-167. [DOI: 10.1016/bs.mie.2019.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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6
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Gangopadhyay SA, Cox KJ, Manna D, Lim D, Maji B, Zhou Q, Choudhary A. Precision Control of CRISPR-Cas9 Using Small Molecules and Light. Biochemistry 2019; 58:234-244. [PMID: 30640437 PMCID: PMC6586488 DOI: 10.1021/acs.biochem.8b01202] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system is an adaptive immune system of bacteria that has furnished several RNA-guided DNA endonucleases (e.g., Cas9) that are revolutionizing the field of genome engineering. Cas9 is being used to effect genomic alterations as well as in gene drives, where a particular trait may be propagated through a targeted species population over several generations. The ease of targeting catalytically impaired Cas9 to any genomic loci has led to development of technologies for base editing, chromatin imaging and modeling, epigenetic editing, and gene regulation. Unsurprisingly, Cas9 is being developed for numerous applications in biotechnology and biomedical research and as a gene therapy agent for multiple pathologies. There is a need for precise control of Cas9 activity over several dimensions, including those of dose, time, and space in these applications. Such precision controls, which are required of therapeutic agents, are particularly important for Cas9 as off-target effects, chromosomal translocations, immunogenic response, genotoxicity, and embryonic mosaicism are observed at elevated levels and with prolonged activity of Cas9. Here, we provide a perspective on advances in the precision control of Cas9 over aforementioned dimensions using external stimuli (e.g., small molecules or light) for controlled activation, inhibition, or degradation of Cas9.
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Affiliation(s)
- Soumyashree A. Gangopadhyay
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Kurt J. Cox
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Debasish Manna
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Donghyun Lim
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Basudeb Maji
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Qingxuan Zhou
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
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7
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Sechi M, Lall RK, Afolabi SO, Singh A, Joshi DC, Chiu SY, Mukhtar H, Syed DN. Fisetin targets YB-1/RSK axis independent of its effect on ERK signaling: insights from in vitro and in vivo melanoma models. Sci Rep 2018; 8:15726. [PMID: 30356079 PMCID: PMC6200766 DOI: 10.1038/s41598-018-33879-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 10/06/2018] [Indexed: 12/14/2022] Open
Abstract
The anti-proliferative activity of dietary flavonoid fisetin has been validated in various cancer models. Establishing its precise mechanism of action has proved somewhat challenging given the multiplicity of its targets. We demonstrated that YB-1 promotes epithelial-to-mesenchymal transition and its inhibition suppressed tumor cell proliferation and invasion. The p90 ribosomal S6 kinase (RSK), an important ERK effector, activates YB-1 to drive melanoma growth. We found that fisetin treatment of monolayer/3-D melanoma cultures resulted in YB-1 dephosphorylation and reduced transcript levels. In parallel, fisetin suppressed mesenchymal markers and matrix-metalloproteinases in melanoma cells. Data from cell-free/cell-based systems indicated that fisetin inhibited RSK activity through binding to the kinase. Affinity studies for RSK isoforms evaluated stronger interaction for RSK2 than RSK1. Competition assays performed to monitor binding responses revealed that YB-1 and RSK2 do not compete, rather binding of fisetin to RSK2 promotes its binding to YB-1. Fisetin suppressed YB-1/RSK signaling independent of its effect on ERK, and reduced MDR1 levels. Comparable efficacy of fisetin and vemurafenib for inhibiting melanoma growth was noted albeit through divergent modulation of ERK. Our studies provide insight into additional modes of regulation through which fisetin interferes with melanoma growth underscoring its potential therapeutic efficacy in disease progression.
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Affiliation(s)
- Mario Sechi
- Department of Chemistry and Pharmacy, University of Sassari, Sassari, Italy
| | - Rahul K Lall
- Department of Dermatology, University of Wisconsin, Madison, USA
| | - Saheed O Afolabi
- Department of Dermatology, University of Wisconsin, Madison, USA
| | - Anant Singh
- Department of Dermatology, University of Wisconsin, Madison, USA
| | - Dinesh C Joshi
- Department of Neuroscience, University of Wisconsin, Madison, USA
| | - Shing-Yan Chiu
- Department of Neuroscience, University of Wisconsin, Madison, USA
| | - Hasan Mukhtar
- Department of Dermatology, University of Wisconsin, Madison, USA
| | - Deeba N Syed
- Department of Dermatology, University of Wisconsin, Madison, USA.
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8
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Sannigrahi A, Chall S, Jawed JJ, Kundu A, Majumdar S, Chattopadhyay K. Nanoparticle Induced Conformational Switch Between α-Helix and β-Sheet Attenuates Immunogenic Response of MPT63. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8807-8817. [PMID: 29986589 DOI: 10.1021/acs.langmuir.8b00354] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Although significant efforts have been devoted to develop nanoparticle-based biopharmaceuticals, it is not understood how protein conformation and nanoparticle surface modulate each other in optimizing the activity and/or toxicity of the biological molecules. This is particularly important for a protein, which can adopt different conformational states separated by a relatively small energy barrier. In this paper, we have studied nanoparticle binding-induced conformational switch from β-sheet to α-helix of MPT63, a small major secreted protein from Mycobacterium tuberculosis and a drug target against Tuberculosis. The binding of magnetite nanoparticles to MPT63 results in a β-sheet to α-helix switch near the sequence stretch between the 19th and 30th amino acids. As a consequence, the immunogenic response of the protein becomes compromised, which could be restored by protein engineering. This study emphasizes that conformational stability toward NP surface binding may require optimization involving genetic engineering for development of a nanoparticle conjugated pharmaceutical.
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Affiliation(s)
- Achinta Sannigrahi
- Structural Biology & Bio-Informatics Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mallick Road , Kolkata 700032 , India
| | - Sayantani Chall
- Structural Biology & Bio-Informatics Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mallick Road , Kolkata 700032 , India
| | | | - Amrita Kundu
- Structural Biology & Bio-Informatics Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mallick Road , Kolkata 700032 , India
| | - Subrata Majumdar
- Department of Molecular Medicine , Bose Institute , Kolkata 700054 , India
| | - Krishnananda Chattopadhyay
- Structural Biology & Bio-Informatics Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mallick Road , Kolkata 700032 , India
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9
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Kaiser CE, Rincon Pabon JP, Khowsathit J, Castaldi MP, Kazmirski SL, Weis DD, Zhang AX, Karanicolas J. Modulating Antibody Structure and Function through Directed Mutations and Chemical Rescue. ACS Synth Biol 2018; 7:1152-1162. [PMID: 29609459 DOI: 10.1021/acssynbio.8b00124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Monoclonal antibody therapeutics have revolutionized the treatment of diseases such as cancer and autoimmune disorders, and also serve as research reagents for diverse and unparalleled applications. To extend their utility in both contexts, we have begun development of tunable antibodies, whose activity can be controlled by addition of a small molecule. Conceptually, we envision that incorporating cavity-forming mutations into an antibody can disrupt its structure, thereby reducing its affinity for antigen; addition of a small molecule may then restore the active structure, and thus rescue antigen binding. As a first proof of concept toward implementing this strategy, we have incorporated individual tryptophan to glycine mutations into FITC-E2, an anti-fluorescein single-chain variable fragment (scFv). We find that these can disrupt the protein structure and diminish antigen binding, and further that both structure and function can be rescued by addition of indole to complement the deleted side chain. While the magnitude of the affinity difference triggered by indole is modest in this first model system, it nonetheless provides a framework for future mutation/ligand pairs that may induce more dramatic responses. Disrupting and subsequently rescuing antibody activity, as exemplified by this first example, may represent a new approach to "design in" fine-tuned control of antibody activity for a variety of future applications.
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Affiliation(s)
- Christine E. Kaiser
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Juan Pablo Rincon Pabon
- Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Jittasak Khowsathit
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
| | - M. Paola Castaldi
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Steven L. Kazmirski
- Structure and Biophysics, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - David D. Weis
- Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Andrew X. Zhang
- Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
| | - John Karanicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
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10
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Affiliation(s)
- George M. Burslem
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
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11
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Mao J, DeSantis C, Bong D. Small Molecule Recognition Triggers Secondary and Tertiary Interactions in DNA Folding and Hammerhead Ribozyme Catalysis. J Am Chem Soc 2017; 139:9815-9818. [PMID: 28691825 DOI: 10.1021/jacs.7b05448] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have identified tris(2-aminoethyl)amine (tren)-derived scaffolds with two (t2M) or four (t4M) melamine rings that can target oligo T/U domains in DNA/RNA. Unstructured T-rich DNAs cooperatively fold with the tren derivatives to form hairpin-like structures. Both t2M and t4M act as functional switches in a family of hammerhead ribozymes deactivated by stem or loop replacement with a U-rich sequence. Catalysis of bond scission in these hammerhead ribozymes could be restored by putative t2M/t4M refolding of stem secondary structure or tertiary bridging interactions between loop and stem. The simplicity of the t2M/t4M binding site enables programming of allostery in RNAs, recoding oligo-U domains as potential sites for secondary structure or tertiary contact. In combination with a facile and general method for installation of the t2M motif on primary amines, the method described herein streamlines design of synthetic allosteric riboswitches and small molecule-nucleic acid complexes.
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Affiliation(s)
- Jie Mao
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Chris DeSantis
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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12
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Rose JC, Huang PS, Camp ND, Ye J, Leidal AM, Goreshnik I, Trevillian BM, Dickinson MS, Cunningham-Bryant D, Debnath J, Baker D, Wolf-Yadlin A, Maly DJ. A computationally engineered RAS rheostat reveals RAS-ERK signaling dynamics. Nat Chem Biol 2016; 13:119-126. [PMID: 27870838 PMCID: PMC5161653 DOI: 10.1038/nchembio.2244] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 09/08/2016] [Indexed: 01/07/2023]
Abstract
Synthetic protein switches controlled with user-defined inputs are powerful tools for studying and controlling dynamic cellular processes. To date, these approaches have relied primarily on intermolecular regulation. Here, we report a computationally-guided framework for engineering intramolecular regulation of protein function. We utilize this framework to develop Chemically Inducible Activator of RAS (CIAR), a single-component RAS rheostat that directly activates endogenous RAS in response to a small molecule. Using CIAR, we show that direct RAS activation elicits markedly different RAS/ERK signaling dynamics compared to growth factor stimulation, and that these dynamics differ between cell types. We also found that the clinically-approved RAF inhibitor vemurafenib potently primes cells to respond to direct wild-type RAS activation. These results demonstrate the utility of CIAR for quantitatively interrogating RAS signaling. Finally, we demonstrate the general utility of our approach to design intramolecularly-regulated protein tools by applying this methodology to the Rho Family GEFs.
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Affiliation(s)
- John C Rose
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, Washington, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Nathan D Camp
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jordan Ye
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Andrew M Leidal
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Miles S Dickinson
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | | | - Jayanta Debnath
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington, USA.,Institute for Protein Design, University of Washington, Seattle, Washington, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | | | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, Washington, USA.,Department of Biochemistry, University of Washington, Seattle, Washington, USA
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13
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Fonoudi H, Ansari H, Abbasalizadeh S, Blue GM, Aghdami N, Winlaw DS, Harvey RP, Bosman A, Baharvand H. Large-Scale Production of Cardiomyocytes from Human Pluripotent Stem Cells Using a Highly Reproducible Small Molecule-Based Differentiation Protocol. J Vis Exp 2016. [PMID: 27500408 DOI: 10.3791/54276] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Maximizing the benefit of human pluripotent stem cells (hPSCs) for research, disease modeling, pharmaceutical and clinical applications requires robust methods for the large-scale production of functional cell types, including cardiomyocytes. Here we demonstrate that the temporal manipulation of WNT, TGF-β, and SHH signaling pathways leads to highly efficient cardiomyocyte differentiation of single-cell passaged hPSC lines in both static suspension and stirred suspension bioreactor systems. Employing this strategy resulted in ~ 100% beating spheroids, consistently containing > 80% cardiac troponin T-positive cells after 15 days of culture, validated in multiple hPSC lines. We also report on a variation of this protocol for use with cell lines not currently adapted to single-cell passaging, the success of which has been verified in 42 hPSC lines. Cardiomyocytes generated using these protocols express lineage-specific markers and show expected electrophysiological functionalities. Our protocol presents a simple, efficient and robust platform for the large-scale production of human cardiomyocytes.
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Affiliation(s)
- Hananeh Fonoudi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR; Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute; St. Vincent´s Clinical School, Faculty of Medicine, University of New South Wales; Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Hassan Ansari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR; Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Saeed Abbasalizadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR
| | - Gillian M Blue
- Heart Centre for Children, The Children´s Hospital at Westmead; Sydney Medical School, University of Sydney
| | - Nasser Aghdami
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR
| | - David S Winlaw
- Heart Centre for Children, The Children´s Hospital at Westmead; Sydney Medical School, University of Sydney
| | - Richard P Harvey
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute; St. Vincent´s Clinical School, Faculty of Medicine, University of New South Wales; School of Biotechnology and Biomolecular Sciences, University of New South Wales
| | - Alexis Bosman
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute; St. Vincent´s Clinical School, Faculty of Medicine, University of New South Wales;
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR; Department of Developmental Biology, University of Science and Culture
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14
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Luo J, Liu Q, Morihiro K, Deiters A. Small-molecule control of protein function through Staudinger reduction. Nat Chem 2016; 8:1027-1034. [PMID: 27768095 PMCID: PMC5119652 DOI: 10.1038/nchem.2573] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/13/2016] [Indexed: 01/08/2023]
Abstract
Using small molecules to control the function of proteins in live cells with complete specificity is highly desirable, but challenging. Here we report a small molecule switch that can be used to control protein activity. The approach uses a phosphine-mediated Staudinger reduction to activate protein function. Genetic encoding of an ortho-azidobenzyloxycarbonyl amino acid using a pyrrolysyl tRNA synthetase/tRNACUA pair in mammalian cells enables the site-specific introduction of a small molecule-removable protecting group into the protein of interest. Strategic placement of this group renders the protein inactive until deprotection through a bioorthogonal Staudinger reduction delivers the active, wild-type protein. This developed methodology was applied to the conditional control of several cellular processes, including bioluminescence (luciferase), fluorescence (EGFP), protein translocation (nuclear localization sequence), DNA recombination (Cre), and gene editing (Cas9).
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Affiliation(s)
- Ji Luo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Qingyang Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Kunihiko Morihiro
- 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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15
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Zhou W, Deiters A. Conditional Control of CRISPR/Cas9 Function. Angew Chem Int Ed Engl 2016; 55:5394-9. [PMID: 26996256 DOI: 10.1002/anie.201511441] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/21/2016] [Indexed: 12/26/2022]
Abstract
The recently discovered CRISPR/Cas9 endonuclease system, comprised of a guide RNA for the recognition of a DNA target and the Cas9 nuclease protein for binding and processing the target, has been extensively studied and has been widely applied in genome editing, synthetic biology, and transcriptional modulation in cells and animals. Toward more precise genomic modification and further expansion of the CRISPR/Cas9 system as a spatiotemporally controlled gene regulatory system, several approaches of conditional activation of Cas9 function using small molecules and light have recently been developed. These methods have led to improvements in the genome editing specificity of the CRISPR/Cas9 system and enabled its activation with temporal and spatial precision.
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Affiliation(s)
- Wenyuan Zhou
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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16
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Long MC, Poganik JR, Aye Y. On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry. J Am Chem Soc 2016; 138:3610-22. [PMID: 26907082 PMCID: PMC4805449 DOI: 10.1021/jacs.5b12608] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 11/28/2022]
Abstract
Proximity enhancement is a central chemical tenet underpinning an exciting suite of small-molecule toolsets that have allowed us to unravel many biological complexities. The leitmotif of this opus is "tethering"-a strategy in which a multifunctional small molecule serves as a template to bring proteins/biomolecules together. Scaffolding approaches have been powerfully applied to control diverse biological outcomes such as protein-protein association, protein stability, activity, and improve imaging capabilities. A new twist on this strategy has recently appeared, in which the small-molecule probe is engineered to unleash controlled amounts of reactive chemical signals within the microenvironment of a target protein. Modification of a specific target elicits a precisely timed and spatially controlled gain-of-function (or dominant loss-of-function) signaling response. Presented herein is a unique personal outlook conceptualizing the powerful proximity-enhanced chemical biology toolsets into two paradigms: "multifunctional scaffolding" versus "on-demand targeting". By addressing the latest advances and challenges in the established yet constantly evolving multifunctional scaffolding strategies as well as in the emerging on-demand precision targeting (and related) systems, this Perspective is aimed at choosing when it is best to employ each of the two strategies, with an emphasis toward further promoting novel applications and discoveries stemming from these innovative chemical biology platforms.
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Affiliation(s)
- Marcus
J. C. Long
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Jesse R. Poganik
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
| | - Yimon Aye
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United
States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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17
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Affiliation(s)
- Wenyuan Zhou
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Alexander Deiters
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
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18
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Schena A, Griss R, Johnsson K. Modulating protein activity using tethered ligands with mutually exclusive binding sites. Nat Commun 2015. [PMID: 26198003 PMCID: PMC4525150 DOI: 10.1038/ncomms8830] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The possibility to design proteins whose activities can be switched on and off by unrelated effector molecules would enable applications in various research areas, ranging from biosensing to synthetic biology. We describe here a general method to modulate the activity of a protein in response to the concentration of a specific effector. The approach is based on synthetic ligands that possess two mutually exclusive binding sites, one for the protein of interest and one for the effector. Tethering such a ligand to the protein of interest results in an intramolecular ligand–protein interaction that can be disrupted through the presence of the effector. Specifically, we introduce a luciferase controlled by another protein, a human carbonic anhydrase whose activity can be controlled by proteins or small molecules in vitro and on living cells, and novel fluorescent and bioluminescent biosensors. Designing proteins whose activities can be switched on and off by effector molecules is a central challenge in protein engineering. Here, the authors use tethered chemical ligands with two mutually exclusive binding sites as a general method to modulate protein activity in response to specific effectors.
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Affiliation(s)
- Alberto Schena
- 1] École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Avenue Forel 2, EPFL SB ISIC LIP BCH-4303, CH-1015 Lausanne, Switzerland [2] École Polytechnique Fédérale de Lausanne, Institute of Bioengineering, CH-1015 Lausanne, Switzerland [3] National Centre of Competence in Research in Chemical Biology, CH-1015 Lausanne, Switzerland
| | - Rudolf Griss
- 1] École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Avenue Forel 2, EPFL SB ISIC LIP BCH-4303, CH-1015 Lausanne, Switzerland [2] École Polytechnique Fédérale de Lausanne, Institute of Bioengineering, CH-1015 Lausanne, Switzerland [3] National Centre of Competence in Research in Chemical Biology, CH-1015 Lausanne, Switzerland
| | - Kai Johnsson
- 1] École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Avenue Forel 2, EPFL SB ISIC LIP BCH-4303, CH-1015 Lausanne, Switzerland [2] École Polytechnique Fédérale de Lausanne, Institute of Bioengineering, CH-1015 Lausanne, Switzerland [3] National Centre of Competence in Research in Chemical Biology, CH-1015 Lausanne, Switzerland
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19
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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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20
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An optimized optogenetic clustering tool for probing protein interaction and function. Nat Commun 2014; 5:4925. [PMID: 25233328 PMCID: PMC4170572 DOI: 10.1038/ncomms5925] [Citation(s) in RCA: 264] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 08/06/2014] [Indexed: 12/24/2022] Open
Abstract
The Arabidopsis photoreceptor cryptochrome 2 (CRY2) was previously used as an optogenetic module, allowing spatiotemporal control of cellular processes with light. Here we report the development of a new CRY2-derived optogenetic module, 'CRY2olig', which induces rapid, robust, and reversible protein oligomerization in response to light. Using this module, we developed a novel protein interaction assay, Light-Induced Co-clustering, that can be used to interrogate protein interaction dynamics in live cells. In addition to use probing protein interactions, CRY2olig can also be used to induce and reversibly control diverse cellular processes with spatial and temporal resolution. Here we demonstrate disrupting clathrin-mediated endocytosis and promoting Arp2/3-mediated actin polymerization with light. These new CRY2-based approaches expand the growing arsenal of optogenetic strategies to probe cellular function.
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21
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Iyer S, Doktycz MJ. Thrombin-mediated transcriptional regulation using DNA aptamers in DNA-based cell-free protein synthesis. ACS Synth Biol 2014; 3:340-6. [PMID: 24059754 DOI: 10.1021/sb4000756] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Realizing the potential of cell-free systems will require development of ligand-sensitive gene promoters that control gene expression in response to a ligand of interest. Here, we describe an approach to designing ligand-sensitive transcriptional control in cell-free systems that is based on the combination of a DNA aptamer that binds thrombin and the T7 bacteriophage promoter. Placement of the aptamer near the T7 promoter, and using a primarily single-stranded template, results in up to a 6-fold change in gene expression in a ligand concentration-dependent manner. We further demonstrate that the sensitivity to thrombin concentration and the fold change in expression can be tuned by altering the position of the aptamer. The results described here pave the way for the use of DNA aptamers to achieve modular regulation of transcription in response to a wide variety of ligands in cell-free systems.
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Affiliation(s)
- Sukanya Iyer
- Graduate
Program
in Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Mitchel J. Doktycz
- Graduate
Program
in Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center for
Nanophase
Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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22
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Xia X, Piao X, Bong D. Bifacial peptide nucleic acid as an allosteric switch for aptamer and ribozyme function. J Am Chem Soc 2014; 136:7265-8. [PMID: 24796374 DOI: 10.1021/ja5032584] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We demonstrate herein that bifacial peptide nucleic acid (bPNA) hybrid triplexes functionally substitute for duplex DNA or RNA. Structure-function loss in three non-coding nucleic acids was inflicted by replacement of a duplex stem with unstructured oligo-T/U strands, which are bPNA binding sites. Functional rescue was observed on refolding of the oligo-T/U strands into bPNA triplex hybrid stems. Bifacial PNA binding was thus used to allosterically switch-on protein and small-molecule binding in DNA and RNA aptamers, as well as catalytic bond scission in a ribozyme. Duplex stems that support the catalytic site of a minimal type I hammerhead ribozyme were replaced with oligo-U loops, severely crippling or ablating the native RNA splicing function. Refolding of the U-loops into bPNA triplex stems completely restored splicing function in the hybrid system. These studies indicate that bPNA may have general utility as an allosteric trigger for a wide range of functions in non-coding nucleic acids.
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Affiliation(s)
- Xin Xia
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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23
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Battle C, Chu X, Jayawickramarajah J. Oligonucleotide-Based Systems for Input-Controlled and Non-Covalently Regulated Protein-Binding. Supramol Chem 2013; 25. [PMID: 24187478 DOI: 10.1080/10610278.2013.810337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Supramolecular chemists continuously take inspiration from complex biological systems to develop functional molecules involved in molecular recognition and self-assembly. In this regard, "smart" synthetic molecules that emulate allosteric proteins are both exciting and challenging, since many allosteric proteins can be considered as molecular switches that bind to other protein targets in a non-covalent fashion, and importantly, are capable of having their output activity controlled by prior binding to input molecules. This review discusses the foundations and passage toward the development of non-covalently operated oligonucleotide-based systems with protein-binding capacity that can be precisely regulated in an input-controlled manner.
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Affiliation(s)
- Cooper Battle
- Department of Chemistry, Tulane University, New Orleans, LA, USA
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24
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Orthogonal control of endogenous gene expression in mammalian cells using synthetic ligands. Biotechnol Bioeng 2013; 110:1419-29. [DOI: 10.1002/bit.24807] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 11/16/2012] [Accepted: 12/03/2012] [Indexed: 12/14/2022]
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25
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Gardner L, Deiters A. Light-controlled synthetic gene circuits. Curr Opin Chem Biol 2012; 16:292-9. [PMID: 22633822 DOI: 10.1016/j.cbpa.2012.04.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 04/10/2012] [Accepted: 04/15/2012] [Indexed: 01/09/2023]
Abstract
Highly complex synthetic gene circuits have been engineered in living organisms to develop systems with new biological properties. A precise trigger to activate or deactivate these complex systems is desired in order to tightly control different parts of a synthetic or natural network. Light represents an excellent tool to achieve this goal as it can be regulated in timing, location, intensity, and wavelength, which allows for precise spatiotemporal control over genetic circuits. Recently, light has been used as a trigger to control the biological function of small molecules, oligonucleotides, and proteins involved as parts in gene circuits. Light activation has enabled the construction of unique systems in living organisms such as band-pass filters and edge-detectors in bacterial cells. Additionally, light also allows for the regulation of intermediate steps of complex dynamic pathways in mammalian cells such as those involved in kinase networks. Herein we describe recent advancements in the area of light-controlled synthetic networks.
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Affiliation(s)
- Laura Gardner
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695, United States
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26
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Peck SH, Chen I, Liu DR. Directed evolution of a small-molecule-triggered intein with improved splicing properties in mammalian cells. ACTA ACUST UNITED AC 2011; 18:619-30. [PMID: 21609843 DOI: 10.1016/j.chembiol.2011.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Revised: 02/16/2011] [Accepted: 02/28/2011] [Indexed: 10/18/2022]
Abstract
Laboratory-created small-molecule-dependent inteins enable protein structure and function to be controlled posttranslationally in living cells. Previously we evolved inteins that splice efficiently in Saccharomyces cerevisiae only in the presence of the cell-permeable small molecule 4-hydroxytamoxifen (4-HT). In mammalian cells, however, these inteins exhibited lower splicing efficiencies and slower splicing in the presence of 4-HT, as well as higher background splicing in the absence of 4-HT. Here we further evolved ligand-dependent inteins in yeast at 30°C and 37°C. The resulting second-generation evolved inteins exhibit substantially improved splicing yields and kinetics. The improvements carried over to mammalian cells, in which the newly evolved inteins spliced with substantially greater (∼2- to 8-fold) efficiency while maintaining low background splicing levels. These second-generation inteins augment the promise of ligand-dependent protein splicing for probing protein function in mammalian cells.
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Affiliation(s)
- Sun H Peck
- Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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27
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Murtaugh ML, Fanning SW, Sharma TM, Terry AM, Horn JR. A combinatorial histidine scanning library approach to engineer highly pH-dependent protein switches. Protein Sci 2011; 20:1619-31. [PMID: 21766385 DOI: 10.1002/pro.696] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 07/07/2011] [Indexed: 12/17/2022]
Abstract
There is growing interest in the development of protein switches, which are proteins whose function, such as binding a target molecule, can be modulated through environmental triggers. Efforts to engineer highly pH sensitive protein-protein interactions typically rely on the rational introduction of ionizable groups in the protein interface. Such experiments are typically time intensive and often sacrifice the protein's affinity at the permissive pH. The underlying thermodynamics of proton-linkage dictate that the presence of multiple ionizable groups, which undergo a pK(a) change on protein binding, are necessary to result in highly pH-dependent binding. To test this hypothesis, a novel combinatorial histidine library was developed where every possible combination of histidine and wild-type residue is sampled throughout the interface of a model anti-RNase A single domain VHH antibody. Antibodies were coselected for high-affinity binding and pH-sensitivity using an in vitro, dual-function selection strategy. The resulting antibodies retained near wild-type affinity yet became highly sensitive to small decreases in pH, drastically decreasing their binding affinity, due to the incorporation of multiple histidine groups. Several trends were observed, such as histidine "hot-spots," which will help enhance the development of pH switch proteins as well as increase our understanding of the role of ionizable residues in protein interfaces. Overall, the combinatorial approach is rapid, general, and robust and should be capable of producing highly pH-sensitive protein affinity reagents for a number of different applications.
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Affiliation(s)
- Megan L Murtaugh
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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28
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Gardner L, Zou Y, Mara A, Cropp TA, Deiters A. Photochemical control of bacterial signal processing using a light-activated erythromycin. MOLECULAR BIOSYSTEMS 2011; 7:2554-7. [PMID: 21785768 DOI: 10.1039/c1mb05166k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial cells control resistance to the macrolide antibiotic erythromycin using the MphR(A) repressor protein. Erythromycin binds to MphR(A), causing release of the PmphR promoter, activating expression of the 2'-phosphotransferase Mph(A). We engineered the MphR(A)/promoter system to, in conjunction with a light-activatable derivative of erythromycin, enable photochemical activation of gene expression in E. coli. We applied this photochemical gene switch to the construction of a light-triggered logic gate, a light-controlled band-pass filter, as well as spatial and temporal control of gene expression.
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Affiliation(s)
- Laura Gardner
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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29
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Ud-Dean SMM. Kinetics of optical control of enzyme activity with photoswitchable inhibitors. Interdiscip Sci 2011; 3:79-90. [PMID: 21541838 DOI: 10.1007/s12539-011-0063-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 09/08/2010] [Accepted: 09/15/2010] [Indexed: 05/30/2023]
Abstract
This paper presents theoretical and simulation studies on controlling enzymatic reactions with photoswitchable inhibitors. It is found that the maximum attainable switching ratio (ratio of the steady state rates of product formation in the "on" and the "off" state) of a photoswitchable inhibitor is dependent on its photoswitching factor (ratio of the equilibrium constants of the photostationary states under the "off" and the "on" illuminations). Attachment of multiple photoswitchable groups to an inhibitor molecule increases the theoretically attainable switching ratio. The affinity of the enzyme for the substrate and the inhibitor is the rate-limiting factor of the switching between active and inactive states. Use of inhibitors with high enzyme affinity and photoswitchable groups with high photoswitching factor would provide high switching ratio. These results may help to design better systems for optical control of biochemical processes.
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Affiliation(s)
- S M Minhaz Ud-Dean
- Optics Research Group, Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ, Delft, The Netherlands.
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30
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Eberhard H, Diezmann F, Seitz O. DNA as a molecular ruler: interrogation of a tandem SH2 domain with self-assembled, bivalent DNA-peptide complexes. Angew Chem Int Ed Engl 2011; 50:4146-50. [PMID: 21455916 DOI: 10.1002/anie.201007593] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 01/18/2011] [Indexed: 01/01/2023]
Affiliation(s)
- Hendrik Eberhard
- Department of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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31
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Eberhard H, Diezmann F, Seitz O. DNA as a Molecular Ruler: Interrogation of a Tandem SH2 Domain with Self-Assembled, Bivalent DNA-Peptide Complexes. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007593] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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32
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Peterson-Kaufman KJ, Carlson CD, Rodríguez-Martínez JA, Ansari AZ. Nucleating the assembly of macromolecular complexes. Chembiochem 2010; 11:1955-62. [PMID: 20812316 PMCID: PMC4176617 DOI: 10.1002/cbic.201000255] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Indexed: 12/23/2022]
Abstract
Nature constructs intricate complexes containing numerous binding partners in order to direct a variety of cellular processes. Researchers have taken a cue from these events to develop synthetic molecules that can nucleate natural and unnatural interactions for a diverse set of applications. These molecules can be designed to drive protein dimerization or to modulate the interactions between proteins, lipids, DNA, or RNA and thereby alter cellular pathways. A variety of components within the cellular machinery can be recruited with or replaced by synthetic compounds. Directing the formation of multicomponent complexes with new synthetic molecules can allow unprecedented control over the cellular machinery.
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Affiliation(s)
| | - Clayton D. Carlson
- Department of Biochemistry and the Genome Center, University of Wisconsin, 433 Babcock Drive. Madison, WI 53706
| | - José A. Rodríguez-Martínez
- Department of Biochemistry and the Genome Center, University of Wisconsin, 433 Babcock Drive. Madison, WI 53706
| | - Aseem Z. Ansari
- Department of Biochemistry and the Genome Center, University of Wisconsin, 433 Babcock Drive. Madison, WI 53706
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33
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34
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Young DD, Lively MO, Deiters A. Activation and deactivation of DNAzyme and antisense function with light for the photochemical regulation of gene expression in mammalian cells. J Am Chem Soc 2010; 132:6183-93. [PMID: 20392038 DOI: 10.1021/ja100710j] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The photochemical regulation of biological systems represents a very precise means of achieving high-resolution control over gene expression in both a spatial and a temporal fashion. DNAzymes are enzymatically active deoxyoligonucleotides that enable the site-specific cleavage of RNA and have been used in a variety of in vitro applications. We have previously reported the photochemical activation of DNAzymes and antisense agents through the preparation of a caged DNA phosphoramidite and its site-specific incorporation into oligonucleotides. The presence of the caging group disrupts either DNA:RNA hybridization or catalytic activity until removed via a brief irradiation with UV light. Here, we are expanding this concept by investigating the photochemical deactivation of DNAzymes and antisense agents. Moreover, we report the application of light-activated and light-deactivated antisense agents to the regulation of gene function in mammalian cells. This represents the first example of gene silencing antisense agents that can be turned on and turned off in mammalian tissue culture.
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Affiliation(s)
- Douglas D Young
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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35
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Shen A. Allosteric regulation of protease activity by small molecules. MOLECULAR BIOSYSTEMS 2010; 6:1431-43. [PMID: 20539873 DOI: 10.1039/c003913f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Proteases regulate a plethora of biological processes. Because they irreversibly cleave peptide bonds, the activity of proteases is strictly controlled. While there are many ways to regulate protease activity, an emergent mechanism is the modulation of protease function by small molecules acting at allosteric sites. This mode of regulation holds the potential to allow for the specific and temporal control of a given biological process using small molecules. These compounds also serve as useful tools for studying protein dynamics and function. This review highlights recent advances in identifying and characterizing natural and synthetic small molecule allosteric regulators of proteases and discusses their utility in studies of protease function, drug discovery and protein engineering.
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Affiliation(s)
- Aimee Shen
- Department of Pathology, Stanford School of Medicine, Stanford, California 94305, USA.
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36
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Pastuszka MK, Mackay JA. Biomolecular engineering of intracellular switches in eukaryotes. J Drug Deliv Sci Technol 2010; 20:163-169. [PMID: 21209849 DOI: 10.1016/s1773-2247(10)50025-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Tools to selectively and reversibly control gene expression are useful to study and model cellular functions. When optimized, these cellular switches can turn a protein's function "on" and "off" based on cues designated by the researcher. These cues include small molecules, drugs, hormones, and even temperature variations. Here we review three distinct areas in gene expression that are commonly targeted when designing cellular switches. Transcriptional switches target gene expression at the level of mRNA polymerization, with examples including the tetracycline gene induction system as well as nuclear receptors. Translational switches target the process of turning the mRNA signal into protein, with examples including riboswitches and RNA interference. Post-translational switches control how proteins interact with one another to attenuate or relay signals. Examples of post-translational modification include dimerization and intein splicing. In general, the delay times between switch and effect decreases from transcription to translation to post-translation; furthermore, the fastest switches may offer the most elegant opportunities to influence and study cell behavior. We discuss the pros and cons of these strategies, which directly influence their usefulness to study and implement drug targeting at the tissue and cellular level.
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Affiliation(s)
- M K Pastuszka
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033-9121, United States
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37
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Deiters A. Light activation as a method of regulating and studying gene expression. Curr Opin Chem Biol 2009; 13:678-86. [PMID: 19857985 DOI: 10.1016/j.cbpa.2009.09.026] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 09/18/2009] [Accepted: 09/25/2009] [Indexed: 12/14/2022]
Abstract
Recently, several advances have been made in the activation and deactivation of gene expression using light. These developments are based on the application of small molecule inducers of gene expression, antisense- or RNA interference-mediated gene silencing, and the photochemical control of proteins regulating gene function. The majority of the examples employ a classical 'caging technology', through the chemical installation of a light-removable protecting group on the biological molecule (small molecule, oligonucleotide, or protein) of interest and rendering it inactive. UV light irradiation then removes the caging group and activates the molecule, enabling control over gene activity with high spatial and temporal resolution.
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Affiliation(s)
- Alexander Deiters
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695-8204, USA.
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Thermodynamic basis for the optimization of binding-induced biomolecular switches and structure-switching biosensors. Proc Natl Acad Sci U S A 2009; 106:13802-7. [PMID: 19666496 DOI: 10.1073/pnas.0904005106] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Binding-induced biomolecular switches are used throughout nature and, increasingly, throughout biotechnology for the detection of chemical moieties and the subsequent transduction of this detection into useful outputs. Here we show that the thermodynamics of these switches are quantitatively described by a simple 3-state population-shift model, in which the equilibrium between a nonbinding, nonsignaling state and the binding-competent, signaling state is shifted toward the latter upon target binding. Because of this, their performance is determined by the tradeoff inherent to their switching thermodynamics; while a switching equilibrium constant favoring the nonbinding, nonsignaling, conformation ensures a larger signal change (more molecules are poised to respond), it also reduces affinity (binding must overcome a more unfavorable conformational free energy). We then derive and employ the relationship between switching thermodynamics and switch signaling to rationally tune the dynamic range and detection limit of a representative structure-switching biosensor, a molecular beacon, over 4 orders of magnitude. These findings demonstrate that the performance of biomolecular switches can be rationally tuned via mutations that alter their switching thermodynamics and suggest a mechanism by which the performance of naturally occurring switches may have evolved.
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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Abstract
Conditional gene expression systems are important tools to identify the function of essential genes or in terms of gene therapy approaches. Small molecule-binding aptamers can be used for efficient control of gene expression by inserting them into the 5' untranslated region of an mRNA with the ligand-bound form inhibiting gene expression by interfering with translation initiation. However, only a small fraction of in vitro selected aptamers has the potential to act as regulator of gene expression which originates the necessity to develop screening systems for the identification of regulatory active aptamers. We describe here a simple and powerful yeast-based screening system which allows the rapid identification of small molecule-binding aptamers with the potential to act as artificial riboswitches for conditional control of gene expression.
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Affiliation(s)
- Beatrix Suess
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität Frankfurt, Frankfurt, Germany
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41
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Sakamoto S, Kudo K. Supramolecular Control of Split-GFP Reassembly by Conjugation of β-Cyclodextrin and Coumarin Units. J Am Chem Soc 2008; 130:9574-82. [DOI: 10.1021/ja802313a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seiji Sakamoto
- Institute of Industrial Science, University of Tokyo, Komaba 4-6-1, Meguro-ku, Tokyo 153-8505, Japan
| | - Kazuaki Kudo
- Institute of Industrial Science, University of Tokyo, Komaba 4-6-1, Meguro-ku, Tokyo 153-8505, Japan
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Edwards WR, Busse K, Allemann RK, Jones DD. Linking the functions of unrelated proteins using a novel directed evolution domain insertion method. Nucleic Acids Res 2008; 36:e78. [PMID: 18559359 PMCID: PMC2490766 DOI: 10.1093/nar/gkn363] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We have successfully developed a new directed evolution method for generating integral protein fusions comprising of one domain inserted within another. Creating two connections between the insert and accepting parent domain can result in the inter-dependence of the separate protein activities, thus providing a general strategy for constructing molecular switches. Using an engineered transposon termed MuDel, contiguous trinucleotide sequences were removed at random positions from the bla gene encoding TEM-1 β-lactamase. The deleted trinucleotide sequence was then replaced by a DNA cassette encoding cytochrome b562 with differing linking sequences at each terminus and sampling all three reading frames. The result was a variety of chimeric genes encoding novel integral fusion proteins that retained TEM-1 activity. While most of the tolerated insertions were observed in loops, several also occurred close to the termini of α-helices and β-strands. Several variants conferred a switching phenotype on Escherichia coli, with bacterial tolerance to ampicillin being dependent on the presence of haem in the growth medium. The magnitude of the switching phenotype ranged from 4- to 128-fold depending on the insertion position within TEM-1 and the linker sequences that join the two domains.
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Affiliation(s)
- Wayne R Edwards
- School of Biosciences and School of Chemistry, Cardiff University, Cardiff, UK
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Blenner MA, Banta S. Characterization of the 4D5Flu single-chain antibody with a stimulus-responsive elastin-like peptide linker: a potential reporter of peptide linker conformation. Protein Sci 2008; 17:527-36. [PMID: 18218715 DOI: 10.1110/ps.073257308] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-chain antibodies (scFvs) are comprised of IgG variable light and variable heavy domains tethered together by a peptide linker whose length and sequence can affect antigen binding properties. The ability to modulate antigen binding affinity through the use of environmental triggers would be of great interest for many biotechnological applications. We have characterized the antigen binding properties of an anti-fluorescein scFv, 4D5Flu, containing stimulus-responsive short elastin-like peptide linkers and nonresponsive flexible linkers. Comparison of length-matched flexible and short elastin-like peptide linkers indicates that a stimulus-responsive linker can confer stimulus-responsive control of fluorescein binding. A linker length of either six or 10 amino acids proved to have the largest thermally induced response. Similar differences in binding free energy changes indicate a common underlying mechanism of thermal responsiveness. Contrary to the thermal behavior, the effect of salt, another elastin beta-turn-inducing stimulus, stabilized antigen binding in the six- and 10-amino-acid linkers such that elastin-like linkers became less stimulus-responsive as compared with flexible linkers. Again, the thermodynamic analysis indicates a common mechanism of salt responsiveness. Characterization of the room-temperature binding affinities and evidence indicating a dimeric state of the scFvs concomitantly suggest the major contribution to the stimulus-responsive behavior derives from the perturbation of interdomain associations, rather than the linker-constrained disruption of the intramolecular association. The ability to use stimulus-responsive peptide modules to exert a novel control over protein function will likely find application in the creation of allosteric antibodies and scFv-based biosensors, and as a platform to enable the evolution of new stimulus-responsive peptides.
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Stankunas K, Bayle JH, Havranek JJ, Wandless TJ, Baker D, Crabtree GR, Gestwicki JE. Rescue of degradation-prone mutants of the FK506-rapamycin binding (FRB) protein with chemical ligands. Chembiochem 2007; 8:1162-9. [PMID: 17525916 DOI: 10.1002/cbic.200700087] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We recently reported that certain mutations in the FK506-rapamycin binding (FRB) domain disrupt its stability in vitro and in vivo (Stankunas et al. Mol. Cell, 2003, 12, 1615). To determine the precise residues that cause instability, we calculated the folding free energy (Delta G) of a collection of FRB mutants by measuring their intrinsic tryptophan fluorescence during reversible chaotropic denaturation. Our results implicate the T2098L point mutation as a key determinant of instability. Further, we found that some of the mutants in this collection were destabilized by up to 6 kcal mol(-1) relative to the wild type. To investigate how these mutants behave in cells, we expressed firefly luciferase fused to FRB mutants in African green monkey kidney (COS) cell lines and mouse embryonic fibroblasts (MEFs). When unstable FRB mutants were used, we found that the protein levels and the luminescence intensities were low. However, addition of a chemical ligand for FRB, rapamycin, restored luciferase activity. Interestingly, we found a roughly linear relationship between the Delta G of the FRB mutants calculated in vitro and the relative chemical rescue in cells. Because rapamycin is capable of simultaneously binding both FRB and the chaperone, FK506-binding protein (FKBP), we next examined whether FKBP might contribute to the protection of FRB mutants. Using both in vitro experiments and a cell-based model, we found that FKBP stabilizes the mutants. These findings are consistent with recent models that suggest damage to intrinsic Delta G can be corrected by pharmacological chaperones. Further, these results provide a collection of conditionally stable fusion partners for use in controlling protein stability.
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Affiliation(s)
- Kryn Stankunas
- Department of Pathology, Stanford University, 279 Campus Drive, Beckman Building, Stanford, CA 94305, USA
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Young DD, Deiters A. Photochemical activation of protein expression in bacterial cells. Angew Chem Int Ed Engl 2007; 46:4290-2. [PMID: 17458846 DOI: 10.1002/anie.200700057] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Douglas D Young
- North Carolina State University, Department of Chemistry, Campus Box 8204, Raleigh, NC 27695-8204, USA
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46
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Young D, Deiters A. Photochemical Activation of Protein Expression in Bacterial Cells. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Wright CM, Heins RA, Ostermeier M. As easy as flipping a switch? Curr Opin Chem Biol 2007; 11:342-6. [PMID: 17466569 DOI: 10.1016/j.cbpa.2007.04.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 04/17/2007] [Indexed: 11/15/2022]
Abstract
Proteins that behave as switches help to establish the complex molecular logic that is central to biological systems. Aspiring to be nature's equal, researchers have successfully created protein switches of their own design; in particular, numerous and varied zinc-triggered switches have been made. Recent studies in which such switches have been readily identified from combinatorial protein libraries support the notion that proteins are primed to show allosteric behavior and that newly created ligand-binding sites will often be functionally coupled to the original activity of the protein. If true, this notion suggests that switch engineering might be more tractable than previously thought, boding well for the basic science, sensing and biomedical applications for which protein switches hold much promise.
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Affiliation(s)
- Chapman M Wright
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218-2681, USA
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Umarye JD, Lessmann T, García AB, Mamane V, Sommer S, Waldmann H. Biology-Oriented Synthesis of Stereochemically Diverse Natural-Product-Derived Compound Collections by Iterative Allylations on a Solid Support. Chemistry 2007; 13:3305-19. [PMID: 17310497 DOI: 10.1002/chem.200601698] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A strategy aiming at the introduction of stereocenters into polymer-bound natural-product-derived and -inspired compound collections is presented. Treatment of immobilized aldehydes with Brown's pinene-derived allylboranes results in the stereoselective formation of homoallylic alcohols with up to 89 % ee (ee=enantiomeric excess). Subsequent iterative ozonolysis-allylation sequences with up to three allylations on a solid support give access to 1,3-polyols with different relative configurations. Esterification with acryloyl chloride and final ring-closing metathesis yields alpha,beta-unsaturated delta-lactones with multiply oxygenated side chains, a substructure found in a group of natural products with a broad range of biological activity. The flexibility of the approach is exemplified by the parallel synthesis of all eight diastereomers of cryptocarya diacetate on a solid support. The individual isomers are obtained in overall yields of 40-60 % over 10 steps and with 63-85 % diastereoselectivity for the major isomer.
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Affiliation(s)
- Jayant D Umarye
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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49
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Dai CF, Cheng F, Xu HC, Ruan YP, Huang PQ. Diversity-Oriented Asymmetric Synthesis of Hapalosin: Construction of Three Small C9/C4/C3-Modified Hapalosin Analogue Libraries. ACTA ACUST UNITED AC 2007; 9:386-94. [PMID: 17358084 DOI: 10.1021/cc060166h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A flexible approach to the beta-hydroxy gamma-amino acid residue (fragment C) of hapalosin has been developed on the basis of the the regio- and diastereoselective Grignard reaction. The method allows the introduction of different side chains at the C9 of hapalosin. Asymmetric syntheses of hapalosin (1a), 9-homohapalosin (1b), 9-i-butyl-hapalosin (1c), 8-epi-hapalosin (epi-1a), and three small libraries diversified at C9 (3-member, 1L3), C9/ C4 (9-member, 1L9), or C9/C4/C3 (27-member, 1L27) have been produced using this method.
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Affiliation(s)
- Chao-Feng Dai
- Department of Chemistry and Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
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