1
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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2
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Coram AE, Morewood R, Voss S, Price JL, Nitsche C. Exploring biocompatible chemistry to create stapled and photoswitchable variants of the antimicrobial peptide aurein 1.2. J Pept Sci 2024; 30:e3551. [PMID: 37926859 DOI: 10.1002/psc.3551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 11/07/2023]
Abstract
Antibiotic resistance is an escalating global health threat. Due to their diverse mechanisms of action and evasion of traditional resistance mechanisms, peptides hold promise as future antibiotics. Their ability to disrupt bacterial membranes presents a potential strategy to combat drug-resistant infections and address the increasing need for effective antimicrobial treatments. Amphipathic α-helical peptides possess a distinctive molecular structure with both charged/hydrophilic and hydrophobic regions that interact with the bacterial cell membrane, disrupting its structural integrity. The α-helical amphipathic peptide aurein 1.2, secreted by the Australian frog Litoria aurea, is one of the shortest known antimicrobial peptides, spanning only 13 amino acids. The primary objective of this study was to investigate stapled and photoswitchable modifications of short helical peptides employing biocompatible chemistry, utilising aurein 1.2 as a model system. We developed various stapled versions of aurein 1.2 using biocompatible conjugation chemistry between dicyanopyridine and 1,2-aminothiols. While the commonly employed stapling pattern for longer staples is i, i + 7, we observed superior helicity in peptides stapled at positions i, i + 8. Molecular dynamics simulations confirmed both stapling patterns to support an α-helical peptide conformation. Additionally, we utilised a cysteine-selective photosensitive staple, perfluoro azobenzene, to explore photoswitchable variants of aurein 1.2. A double-cysteine variant stapled at i, i + 7 indeed exhibited a change in overall helicity induced by light. We further demonstrated the applicability of this staple to attach to cysteine residues in i, i + 7 positions of a helix in a model protein. While some of the stapled variants displayed substantial increase in helicity, minimal inhibitory concentration assays revealed that none of the stapled aurein 1.2 variants exhibited increased antimicrobial activity compared to the wildtype.
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Affiliation(s)
- Alexandra E Coram
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Richard Morewood
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Saan Voss
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Joshua L Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, Australia
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3
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Axelrod S, Shakhnovich E, Gómez-Bombarelli R. Mapping the Space of Photoswitchable Ligands and Photodruggable Proteins with Computational Modeling. J Chem Inf Model 2023; 63:5794-5802. [PMID: 37671878 DOI: 10.1021/acs.jcim.3c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Light-activated drugs are a promising way to localize biological activity and minimize side effects. However, their development is complicated by the numerous photophysical and biological properties that must be simultaneously optimized. To accelerate the design of photoactive drugs, we describe a procedure that combines ligand-protein docking with chemical property prediction based on machine learning (ML). We apply this procedure to 58 proteins and 9000 photo-drug candidates based on azobenzene cis-trans isomerism. We find that most proteins display a preference for trans isomers over cis and that the binding affinities of nominally active/inactive pairs are in fact highly correlated. These findings have significant value for photopharmacology research, and reinforce the need for virtual screening to identify compounds with rare desirable properties. Further, we combine our procedure with quantum chemical validation to identify promising candidates for the photoactive inhibition of PARP1, an enzyme that is over-expressed in cancer cells. The top compounds are predicted to have long-lived active forms, differential bioactivity, and absorption in the near-infrared therapeutic window.
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Affiliation(s)
- Simon Axelrod
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Rafael Gómez-Bombarelli
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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4
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Yamaguchi T, Ogawa M. Photoinduced movement: how photoirradiation induced the movements of matter. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2022; 23:796-844. [PMID: 36465797 PMCID: PMC9718566 DOI: 10.1080/14686996.2022.2142955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Pioneered by the success on active transport of ions across membranes in 1980 using the regulation of the binding properties of crown ethers with covalently linked photoisomerizable units, extensive studies on the movements by using varied interactions between moving objects and environments have been reported. Photoinduced movements of various objects ranging from molecules, polymers to microscopic particles were discussed from the aspects of the driving for the movements, materials design to achieve the movements and systems design to see and to utilize the movements are summarized in this review.
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Affiliation(s)
- Tetsuo Yamaguchi
- Department of Energy and Materials Engineering, Dongguk University-Seoul, Seoul, South Korea
| | - Makoto Ogawa
- School of Energy Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
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5
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Willems S, Morstein J, Hinnah K, Trauner D, Merk D. A Photohormone for Light-Dependent Control of PPARα in Live Cells. J Med Chem 2021; 64:10393-10402. [PMID: 34213899 DOI: 10.1021/acs.jmedchem.1c00810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Photopharmacology enables the optical control of several biochemical processes using small-molecule photoswitches that exhibit different bioactivities in their cis- and trans-conformations. Such tool compounds allow for high spatiotemporal control of biological signaling, and the approach also holds promise for the development of drug molecules that can be locally activated to reduce target-mediated adverse effects. Herein, we present the expansion of the photopharmacological arsenal to two new members of the peroxisome proliferator-activated receptor (PPAR) family, PPARα and PPARδ. We have developed a set of highly potent PPARα and PPARδ targeting photohormones derived from the weak pan-PPAR agonist GL479 that can be deactivated by light. The photohormone 6 selectively activated PPARα in its trans-conformation with high selectivity over the related PPAR subtypes and was used in live cells to switch PPARα activity on and off in a light- and time-dependent fashion.
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Affiliation(s)
- Sabine Willems
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Johannes Morstein
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Konstantin Hinnah
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Dirk Trauner
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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6
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Dwyer BG, Wang C, Abegg D, Racioppo B, Qiu N, Zhao Z, Pechalrieu D, Shuster A, Hoch DG, Adibekian A. Chemoproteomics-Enabled De Novo Discovery of Photoswitchable Carboxylesterase Inhibitors for Optically Controlled Drug Metabolism. Angew Chem Int Ed Engl 2021; 60:3071-3079. [PMID: 33035395 DOI: 10.1002/anie.202011163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/07/2020] [Indexed: 12/28/2022]
Abstract
Herein, we report arylazopyrazole ureas and sulfones as a novel class of photoswitchable serine hydrolase inhibitors and present a chemoproteomic platform for rapid discovery of optically controlled serine hydrolase targets in complex proteomes. Specifically, we identify highly potent and selective photoswitchable inhibitors of the drug-metabolizing enzymes carboxylesterases 1 and 2 and demonstrate their pharmacological application by optically controlling the metabolism of the immunosuppressant drug mycophenolate mofetil. Collectively, this proof-of-concept study provides a first example of photopharmacological tools to optically control drug metabolism by modulating the activity of a metabolizing enzyme. Our arylazopyrazole ureas and sulfones offer synthetically accessible scaffolds that can be expanded to identify specific photoswitchable inhibitors for other serine hydrolases, including lipases, peptidases, and proteases. Our chemoproteomic platform can be applied to other photoswitches and scaffolds to achieve optical control over diverse protein classes.
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Affiliation(s)
- Brendan G Dwyer
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Chao Wang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA.,Current address: Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Daniel Abegg
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Brittney Racioppo
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Nan Qiu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Zhensheng Zhao
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Dany Pechalrieu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Anton Shuster
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Dominic G Hoch
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA.,Current address: Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
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7
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Dwyer BG, Wang C, Abegg D, Racioppo B, Qiu N, Zhao Z, Pechalrieu D, Shuster A, Hoch DG, Adibekian A. Chemoproteomics‐Enabled De Novo Discovery of Photoswitchable Carboxylesterase Inhibitors for Optically Controlled Drug Metabolism. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Brendan G. Dwyer
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Chao Wang
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
- Current address: Department of Molecular Medicine The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Daniel Abegg
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Brittney Racioppo
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Nan Qiu
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Zhensheng Zhao
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Dany Pechalrieu
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Anton Shuster
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Dominic G. Hoch
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
- Current address: Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
| | - Alexander Adibekian
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
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8
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Cheng B, Morstein J, Ladefoged LK, Maesen JB, Schiøtt B, Sinning S, Trauner D. A Photoswitchable Inhibitor of the Human Serotonin Transporter. ACS Chem Neurosci 2020; 11:1231-1237. [PMID: 32275382 DOI: 10.1021/acschemneuro.9b00521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The human serotonin transporter (hSERT) terminates serotonergic signaling through reuptake of neurotransmitter into presynaptic neurons and is a target for many antidepressant drugs. We describe here the development of a photoswitchable hSERT inhibitor, termed azo-escitalopram, that can be reversibly switched between trans and cis configurations using light of different wavelengths. The dark-adapted trans isomer was found to be significantly less active than the cis isomer, formed upon irradiation.
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Affiliation(s)
- Bichu Cheng
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Johannes Morstein
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Lucy Kate Ladefoged
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jannick Bang Maesen
- Department of Forensic Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Steffen Sinning
- Department of Forensic Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Dirk Trauner
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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9
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10
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Vanuytsel S, Carniello J, Wallace MI. Artificial Signal Transduction across Membranes. Chembiochem 2019; 20:2569-2580. [DOI: 10.1002/cbic.201900254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/09/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Steven Vanuytsel
- Department of ChemistryKing's College London Britannia House 7 Trinity Street London SE1 1DB UK
- London Centre for Nanotechnology Strand London WC2R 2LS UK
| | - Joanne Carniello
- Department of ChemistryKing's College London Britannia House 7 Trinity Street London SE1 1DB UK
- London Centre for Nanotechnology Strand London WC2R 2LS UK
| | - Mark Ian Wallace
- Department of ChemistryKing's College London Britannia House 7 Trinity Street London SE1 1DB UK
- London Centre for Nanotechnology Strand London WC2R 2LS UK
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11
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Mutter NL, Volarić J, Szymanski W, Feringa BL, Maglia G. Reversible Photocontrolled Nanopore Assembly. J Am Chem Soc 2019; 141:14356-14363. [PMID: 31469268 PMCID: PMC6743218 DOI: 10.1021/jacs.9b06998] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Self-assembly
is a fundamental feature of biological systems, and
control of such processes offers fascinating opportunities to regulate
function. Fragaceatoxin C (FraC) is a toxin that upon binding to the
surface of sphingomyelin-rich cells undergoes a structural metamorphosis,
leading to the assembly of nanopores at the cell membrane and causing
cell death. In this study we attached photoswitchable azobenzene pendants
to various locations near the sphingomyelin binding pocket of FraC
with the aim of remote controlling the nanopore assembly using light.
We found several constructs in which the affinity of the toxin for
biological membranes could be activated or deactivated by irradiation,
thus enabling reversible photocontrol of pore formation. Notably,
one construct was completely inactive in the thermally adapted state;
it however induced full lysis of cultured cancer cells upon light
irradiation. Selective irradiation also allowed isolation of individual
nanopores in artificial lipid membranes. Photocontrolled FraC might
find applications in photopharmacology for cancer therapeutics and
has potential to be used for the fabrication of nanopore arrays in
nanopore sensing devices, where the reconstitution, with high spatiotemporal
precision, of single nanopores must be controlled.
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Affiliation(s)
| | | | - Wiktor Szymanski
- University Medical Center Groningen, Department of Radiology , University of Groningen , Hanzeplein 1 , 9713 GZ , Groningen , The Netherlands
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12
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Fu X, Bai H, Qi R, Zhao H, Peng K, Lv F, Liu L, Wang S. Optically-controlled supramolecular self-assembly of an antibiotic for antibacterial regulation. Chem Commun (Camb) 2019; 55:14466-14469. [DOI: 10.1039/c9cc07999h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A new supramolecular photo-responsive antibiotic (azobenzene-norfloxacin/αCD) exhibited a higher “on–off” ratio of antibacterial ability than Azo-Nor alone.
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Affiliation(s)
- Xuancheng Fu
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Organic Solids
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Haotian Bai
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Organic Solids
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Ruilian Qi
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Organic Solids
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Hao Zhao
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Organic Solids
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Ke Peng
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Organic Solids
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Organic Solids
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Organic Solids
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Organic Solids
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
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13
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Luo J, Samanta S, Convertino M, Dokholyan NV, Deiters A. Reversible and Tunable Photoswitching of Protein Function through Genetic Encoding of Azobenzene Amino Acids in Mammalian Cells. Chembiochem 2018; 19:2178-2185. [PMID: 30277634 DOI: 10.1002/cbic.201800226] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 12/30/2022]
Abstract
The genetic encoding of three different azobenzene phenylalanines with different photochemical properties was achieved in human cells by using an engineered pyrrolysyl tRNA/tRNA synthetase pair. In order to demonstrate reversible light control of protein function, azobenzenes were site-specifically introduced into firefly luciferase. Computational strategies were applied to guide the selection of potential photoswitchable sites that lead to a reversibly controlled luciferase enzyme. In addition, the new azobenzene analogues provide enhanced thermal stability, high photoconversion, and responsiveness to visible light. These small-molecule photoswitches can reversibly photocontrol protein function with excellent spatiotemporal resolution, and preferred sites for incorporation can be computationally determined, thus providing a new tool for investigating biological processes.
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Affiliation(s)
- Ji Luo
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA, 15260, USA
| | - Subhas Samanta
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA, 15260, USA
| | - Marino Convertino
- University of North Carolina at Chapel Hill, Department of Biochemistry and Biophysics, Chapel Hill, NC, 27599, USA
| | - Nikolay V Dokholyan
- University of North Carolina at Chapel Hill, Department of Biochemistry and Biophysics, Chapel Hill, NC, 27599, USA
| | - Alexander Deiters
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA, 15260, USA
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14
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Heu W, Choi JM, Kyeong HH, Choi Y, Kim HY, Kim HS. Repeat Module-Based Rational Design of a Photoswitchable Protein for Light-Driven Control of Biological Processes. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Woosung Heu
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Jung Min Choi
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hyun-Ho Kyeong
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Yoonjoo Choi
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hee Yeon Kim
- Graduate school of Nanoscience and Technology; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hak-Sung Kim
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
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15
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Heu W, Choi JM, Kyeong HH, Choi Y, Kim HY, Kim HS. Repeat Module-Based Rational Design of a Photoswitchable Protein for Light-Driven Control of Biological Processes. Angew Chem Int Ed Engl 2018; 57:10859-10863. [DOI: 10.1002/anie.201803993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Woosung Heu
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Jung Min Choi
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hyun-Ho Kyeong
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Yoonjoo Choi
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hee Yeon Kim
- Graduate school of Nanoscience and Technology; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hak-Sung Kim
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
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16
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Abstract
The last few years have witnessed significant advances in the use of light as a stimulus to control biomolecular interactions. Great efforts have been devoted to the development of genetically encoded optobiological and small photochromic switches. Newly discovered small molecules now allow researchers to build molecular systems that are sensitive to a wider range of wavelengths of light than ever before with improved switching fidelities and increased lifetimes of the photoactivated states. Because these molecules are relatively small and adopt predictable conformations they are well suited as tools to interrogate cellular function in a spatially and temporally contolled fashion and for applications in photopharmacology.
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Affiliation(s)
- Robert J Mart
- School of Chemistry & Cardiff Catalysis Institute, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - Rudolf K Allemann
- School of Chemistry & Cardiff Catalysis Institute, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
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17
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Li X, Wu B, Chen H, Nan K, Jin Y, Sun L, Wang B. Recent developments in smart antibacterial surfaces to inhibit biofilm formation and bacterial infections. J Mater Chem B 2018; 6:4274-4292. [PMID: 32254504 DOI: 10.1039/c8tb01245h] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Since their development over 70 years, antibiotics are still the most effective strategy to treat bacterial biofilms and infections.
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Affiliation(s)
- Xi Li
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University
- Wenzhou
- China
| | - Biao Wu
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University
- Wenzhou
- China
| | - Hao Chen
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University
- Wenzhou
- China
- Wenzhou Institute of Biomaterials and Engineering, Chinese Academy of Sciences
- Wenzhou
| | - Kaihui Nan
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University
- Wenzhou
- China
- Wenzhou Institute of Biomaterials and Engineering, Chinese Academy of Sciences
- Wenzhou
| | - Yingying Jin
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University
- Wenzhou
- China
| | - Lin Sun
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University
- Wenzhou
- China
| | - Bailiang Wang
- School of Ophthalmology & Optometry, Eye Hospital, Wenzhou Medical University
- Wenzhou
- China
- Wenzhou Institute of Biomaterials and Engineering, Chinese Academy of Sciences
- Wenzhou
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18
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Okamoto K, Nanya A, Eguchi A, Ohe K. Asymmetric Synthesis of 2H
-Azirines with a Tetrasubstituted Stereocenter by Enantioselective Ring Contraction of Isoxazoles. Angew Chem Int Ed Engl 2017; 57:1039-1043. [DOI: 10.1002/anie.201710920] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Kazuhiro Okamoto
- Department of Energy and Hydrocarbon Chemistry; Graduate School of Engineering; Kyoto University; Katsura Nishikyo-ku Kyoto 615-8510 Japan
| | - Atsushi Nanya
- Department of Energy and Hydrocarbon Chemistry; Graduate School of Engineering; Kyoto University; Katsura Nishikyo-ku Kyoto 615-8510 Japan
| | - Akira Eguchi
- Department of Energy and Hydrocarbon Chemistry; Graduate School of Engineering; Kyoto University; Katsura Nishikyo-ku Kyoto 615-8510 Japan
| | - Kouichi Ohe
- Department of Energy and Hydrocarbon Chemistry; Graduate School of Engineering; Kyoto University; Katsura Nishikyo-ku Kyoto 615-8510 Japan
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19
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Okamoto K, Nanya A, Eguchi A, Ohe K. Asymmetric Synthesis of 2H
-Azirines with a Tetrasubstituted Stereocenter by Enantioselective Ring Contraction of Isoxazoles. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710920] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Kazuhiro Okamoto
- Department of Energy and Hydrocarbon Chemistry; Graduate School of Engineering; Kyoto University; Katsura Nishikyo-ku Kyoto 615-8510 Japan
| | - Atsushi Nanya
- Department of Energy and Hydrocarbon Chemistry; Graduate School of Engineering; Kyoto University; Katsura Nishikyo-ku Kyoto 615-8510 Japan
| | - Akira Eguchi
- Department of Energy and Hydrocarbon Chemistry; Graduate School of Engineering; Kyoto University; Katsura Nishikyo-ku Kyoto 615-8510 Japan
| | - Kouichi Ohe
- Department of Energy and Hydrocarbon Chemistry; Graduate School of Engineering; Kyoto University; Katsura Nishikyo-ku Kyoto 615-8510 Japan
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20
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Let there be light: how to use photoswitchable cross-linker to reprogram proteins. Biochem Soc Trans 2017; 45:831-837. [PMID: 28620044 DOI: 10.1042/bst20160386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/04/2017] [Accepted: 04/07/2017] [Indexed: 12/19/2022]
Abstract
Azobenzene is a photo-isomerizing molecule whose end-to-end distance changes upon external illumination. When combined with site-specific reactive groups, it can be used as molecular tweezers to remote-control the structure and function of protein targets. The present study gives a brief overview over the rational design strategies that use an azobenzene-based photoswitchable cross-linker to engineer ON/OFF switches into functional proteins or to reprogram proteins for novel functions. The re-engineered proteins may be used as remote controls for cellular pathways, as light-gated drug delivery platforms or as light-powered machinery of synthetic cells and micro-scaled factories.
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21
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Lubbe AS, van Leeuwen T, Wezenberg SJ, Feringa BL. Designing dynamic functional molecular systems. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.06.049] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Dübner M, Cadarso VJ, Gevrek TN, Sanyal A, Spencer ND, Padeste C. Reversible Light-Switching of Enzymatic Activity on Orthogonally Functionalized Polymer Brushes. ACS APPLIED MATERIALS & INTERFACES 2017; 9:9245-9249. [PMID: 28266210 DOI: 10.1021/acsami.7b01154] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Copolymer brushes, composed of glycidyl methacrylate and a furan-protected maleimide-containing monomer, were grafted from radical initiators at the surface of irradiation-activated fluoropolymer foils. After postpolymerization modification with enzymatically active microperoxidase-11 and photochromic spiropyran moieties, the polymer brushes catalyzed the oxidation of 3,3'5,5'-tetramethylbenzidine. Exposure to either UV or visible-light allowed switching the turnover by more than 1 order of magnitude, as consequence of the reversible, light-induced spiropyran-merocyanine transition. The modified samples were integrated into an optofluidic device that allowed the reversible switching of enzymatic activity for several cycles under flow, validating the potential for application in smart lab-on-a-chip systems.
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Affiliation(s)
- Matthias Dübner
- Laboratory for Micro- and Nanotechnology, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
- Laboratory for Surface Science and Technology, Department of Materials, ETH Zürich , 8093 Zurich, Switzerland
| | - Victor J Cadarso
- Laboratory for Micro- and Nanotechnology, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Tugce N Gevrek
- Department of Chemistry, Bogazici University , 34342 Bebek, Istanbul, Turkey
| | - Amitav Sanyal
- Department of Chemistry, Bogazici University , 34342 Bebek, Istanbul, Turkey
| | - Nicholas D Spencer
- Laboratory for Surface Science and Technology, Department of Materials, ETH Zürich , 8093 Zurich, Switzerland
| | - Celestino Padeste
- Laboratory for Micro- and Nanotechnology, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
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23
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Hoersch D. Engineering a light-controlled F1 ATPase using structure-based protein design. PeerJ 2016; 4:e2286. [PMID: 27547581 PMCID: PMC4974930 DOI: 10.7717/peerj.2286] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 07/04/2016] [Indexed: 12/03/2022] Open
Abstract
The F1 sub-complex of ATP synthase is a biological nanomotor that converts the free energy of ATP hydrolysis into mechanical work with an astonishing efficiency of up to 100% (Kinosita et al., 2000). To probe the principal mechanics of the machine, I re-engineered the active site of E.coli F1 ATPase with a structure-based protein design approach: by incorporation of a site-specific, photoswitchable crosslinker, whose end-to-end distance can be modulated by illumination with light of two different wavelengths, a dynamic constraint was imposed on the inter-atomic distances of the α and β subunits. Crosslinking reduced the ATP hydrolysis activity of four designs tested in vitro and in one case created a synthetic ATPase whose activity can be reversibly modulated by subsequent illumination with near UV and blue light. The work is a first step into the direction of the long-term goal to design nanoscaled machines based on biological parts that can be precisely controlled by light.
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Affiliation(s)
- Daniel Hoersch
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin , Berlin , Germany
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24
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Lerch MM, Hansen MJ, van Dam GM, Szymanski W, Feringa BL. Emerging Targets in Photopharmacology. Angew Chem Int Ed Engl 2016; 55:10978-99. [DOI: 10.1002/anie.201601931] [Citation(s) in RCA: 413] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/29/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Michael M. Lerch
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Mickel J. Hansen
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Gooitzen M. van Dam
- Department of Surgery, Nuclear Medicine and Molecular Imaging and Intensive Care, University of Groningen; University Medical Center Groningen; Hanzeplein 1, P.O. Box 30001 9700 RB Groningen The Netherlands
| | - Wiktor Szymanski
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Department of Radiology, University of Groningen; University Medical Center Groningen; Hanzeplein 1, P.O. Box 30001 9700 RB Groningen The Netherlands
| | - Ben L. Feringa
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 7 9747 AG Groningen The Netherlands
- Department of Radiology, University of Groningen; University Medical Center Groningen; Hanzeplein 1, P.O. Box 30001 9700 RB Groningen The Netherlands
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25
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Lerch MM, Hansen MJ, van Dam GM, Szymanski W, Feringa BL. Neue Ziele für die Photopharmakologie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601931] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Michael M. Lerch
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen Niederlande
| | - Mickel J. Hansen
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen Niederlande
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 7 9747 AG Groningen Niederlande
| | - Gooitzen M. van Dam
- Department of Surgery, Nuclear Medicine and Molecular Imaging and Intensive Care, University of Groningen; University Medical Center Groningen; Hanzeplein 1, P.O. Box 30001 9700 RB Groningen Niederlande
| | - Wiktor Szymanski
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen Niederlande
- Department of Radiology, University of Groningen; University Medical Center Groningen; Hanzeplein 1, P.O. Box 30001 9700 RB Groningen Niederlande
| | - Ben L. Feringa
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen Niederlande
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 7 9747 AG Groningen Niederlande
- Department of Radiology, University of Groningen; University Medical Center Groningen; Hanzeplein 1, P.O. Box 30001 9700 RB Groningen Niederlande
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26
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Everhart SC, Jayasundara UK, Kim H, Procúpez-Schtirbu R, Stanbery WA, Mishler CH, Frost BJ, Cline JI, Bell TW. Synthesis and Photoisomerization of Substituted Dibenzofulvene Molecular Rotors. Chemistry 2016; 22:11291-302. [PMID: 27363530 DOI: 10.1002/chem.201600854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 12/18/2022]
Abstract
The synthesis, spectral and structural characterization, and photoisomerization of a family of 2-substituted dibenzofulvene molecular actuators based on (2,2,2-triphenylethylidene)fluorene (TEF) are reported. The 2-substituted species investigated are nitro (NTEF), cyano (CTEF), and iodo (ITEF). X-ray structures of these three compounds and three intermediates were determined to assign alkene configuration and investigate the effects of the 2-substituents on steric gearing. The addition-elimination reaction of Z-9 with trityl anion to form Z-10 proceeded with complete retention of configuration. Rates of photoisomerization were measured at irradiation wavelengths between 266-355 nm in acetonitrile/dioxane solutions at room temperature. Photoisomerization quantum yields (φ) were calculated by means of a mathematical model that accounts for a certain degree of photodecomposition in the cases of CTEF and ITEF. Quantum yields vary significantly with substituent, having maximum values of φ=0.26 for NTEF, 0.39 for CTEF, and 0.50 for ITEF. NTEF is photochemically robust and has a large quantum yield for photoisomerization in the near-UV, making it a particularly promising drive rotor moiety for light-powered molecular devices.
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Affiliation(s)
- Stephanie C Everhart
- Department of Chemistry and Program in Chemical Physics, University of Nevada, Reno, NV, 89557-0216, USA
| | - Udaya K Jayasundara
- Department of Chemistry and Program in Chemical Physics, University of Nevada, Reno, NV, 89557-0216, USA
| | - HyunJong Kim
- Department of Chemistry and Program in Chemical Physics, University of Nevada, Reno, NV, 89557-0216, USA
| | - Rolando Procúpez-Schtirbu
- Department of Chemistry and Program in Chemical Physics, University of Nevada, Reno, NV, 89557-0216, USA.,Coordinador Sección Química General, Escuela de Química, Universidad de Costa Rica, P.O. Box 11501-2060, Costa Rica
| | - Wayne A Stanbery
- Department of Chemistry and Program in Chemical Physics, University of Nevada, Reno, NV, 89557-0216, USA
| | - Clay H Mishler
- Department of Chemistry and Program in Chemical Physics, University of Nevada, Reno, NV, 89557-0216, USA
| | - Brian J Frost
- Department of Chemistry and Program in Chemical Physics, University of Nevada, Reno, NV, 89557-0216, USA
| | - Joseph I Cline
- Department of Chemistry and Program in Chemical Physics, University of Nevada, Reno, NV, 89557-0216, USA
| | - Thomas W Bell
- Department of Chemistry and Program in Chemical Physics, University of Nevada, Reno, NV, 89557-0216, USA.
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27
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Müller A, Lindhorst TK. Synthesis of Hetero-bifunctional Azobenzene Glycoconjugates for Bioorthogonal Cross-Linking of Proteins. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600136] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Müller A, Kobarg H, Chandrasekaran V, Gronow J, Sönnichsen FD, Lindhorst TK. Synthesis of Bifunctional Azobenzene Glycoconjugates for Cysteine-Based Photosensitive Cross-Linking with Bioactive Peptides. Chemistry 2015; 21:13723-31. [DOI: 10.1002/chem.201501571] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 01/31/2023]
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29
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Wang J, Zhang YM, Zhang XJ, Zhao XJ, Liu Y. Light-Controlled [3]Pseudorotaxane Based on Tetrasulfonated 1,5-Dinaphtho-32-Crown-8 and α-Cyclodextrin. ASIAN J ORG CHEM 2015. [DOI: 10.1002/ajoc.201402238] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Perur N, Yahara M, Kamei T, Tamaoki N. A non-nucleoside triphosphate for powering kinesin-microtubule motility with photo-tunable velocity. Chem Commun (Camb) 2014; 49:9935-7. [PMID: 24037324 DOI: 10.1039/c3cc45933k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three non-nucleoside triphosphates, one containing an azobenzene moiety, power a kinesin-microtubule system with high motile activity, with an observed maximum velocity of almost half of that obtained with ATP. The cis-trans photoisomerization of the azobenzene unit allows reversible and repeated control over the motile properties of kinesin.
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Affiliation(s)
- Nishad Perur
- Research Institute for Electronic Science, Hokkaido University, N20, W10, Kita-ku, Sapporo, Hokkaido, Japan.
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31
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Poloni C, Szymański W, Hou L, Browne WR, Feringa BL. A Fast, Visible-Light-Sensitive Azobenzene for Bioorthogonal Ligation. Chemistry 2014; 20:946-51. [DOI: 10.1002/chem.201304129] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Indexed: 12/22/2022]
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32
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SzymaŃski W, Yilmaz D, Koçer A, Feringa BL. Bright ion channels and lipid bilayers. Acc Chem Res 2013; 46:2910-23. [PMID: 23597020 DOI: 10.1021/ar4000357] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
If we look at a simple organism such as a zebrafish under a microscope, we would see many cells working in harmony. If we zoomed in, we would observe each unit performing its own tasks in a special aqueous environment isolated from the other units by a lipid bilayer approximately 5 nm thick. These confined units are social: they communicate with one another by sensing and responding to the chemical changes in their environment through receptors and ion channels. These channels control the highly specific and selective passage of ions from one side of the cell to the other and are embedded in lipid bilayers. The movement of ions through ion channels supports excitation and electrical signaling in the nervous system. Ion channels have fascinated scientists not only because of their specificity and selectivity, but also for their functions, the serious consequences when they malfunction, and the other potential applications of these molecules. Light is a useful trigger to control and manipulate ion channels externally. With the many state-of-the-art optical technologies available, light offers a high degree of spatial and temporal control, millisecond precision, and noninvasive intervention and does not change the chemical environment of the system of interest. In this Account, we discuss research toward the dynamic control of lipid bilayer assembly and channel function, particularly the transport across the lipid bilayer-ion channel barrier of cells using light. We first summarize the manipulation of ion channel activity with light to modulate the channel's natural activity. Based on the type of photoswitch employed, we can achieve novel functionalities with these channels, and control neural activity. Then we discuss the recent developments in light-induced transport through lipid bilayers. We focus on three different approaches: the incorporation of photoswitchable copolymers into the lipids, the doping of the lipid bilayer with photosensitive amphiphiles and the preparation of the lipid bilayers solely from photoswitchable lipids. These examples reflect the versatility of what we can achieve by manipulating biological systems with light, from triggering the permeability of a specific area of a lipid bilayer to controlling the behavior of a whole organism.
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Affiliation(s)
- Wiktor SzymaŃski
- Center for Systems Chemistry, Stratingh Institute for Chemistry and ‡Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Duygu Yilmaz
- Center for Systems Chemistry, Stratingh Institute for Chemistry and ‡Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - ArmaĞan Koçer
- Center for Systems Chemistry, Stratingh Institute for Chemistry and ‡Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Ben L. Feringa
- Center for Systems Chemistry, Stratingh Institute for Chemistry and ‡Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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Abstract
Bacterial resistance is a major problem in the modern world, stemming in part from the build-up of antibiotics in the environment. Novel molecular approaches that enable an externally triggered increase in antibiotic activity with high spatiotemporal resolution and auto-inactivation are highly desirable. Here we report a responsive, broad-spectrum, antibacterial agent that can be temporally activated with light, whereupon it auto-inactivates on the scale of hours. The use of such a 'smart' antibiotic might prevent the build-up of active antimicrobial material in the environment. Reversible optical control over active drug concentration enables us to obtain pharmacodynamic information. Precisely localized control of activity is achieved, allowing the growth of bacteria to be confined to defined patterns, which has potential for the development of treatments that avoid interference with the endogenous microbial population in other parts of the organism.
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34
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Lycklama a Nijeholt JA, de Keyzer J, Prabudiansyah I, Driessen AJM. Characterization of the supporting role of SecE in protein translocation. FEBS Lett 2013; 587:3083-8. [PMID: 23954289 DOI: 10.1016/j.febslet.2013.07.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 11/17/2022]
Abstract
SecYEG functions as a membrane channel for protein export. SecY constitutes the protein-conducting pore, which is enwrapped by SecE in a V-shaped manner. In its minimal form SecE consists of a single transmembrane segment that is connected to a surface-exposed amphipathic α-helix via a flexible hinge. These two domains are the major sites of interaction between SecE and SecY. Specific cleavage of SecE at the hinge region, which destroys the interaction between the two SecE domains, reduced translocation. When SecE and SecY were disulfide bonded at the two sites of interaction, protein translocation was not affected. This suggests that the SecY and SecE interactions are static, while the hinge region provides flexibility to allow the SecY pore to open.
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Affiliation(s)
- Jelger A Lycklama a Nijeholt
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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35
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Velema WA, van der Toorn M, Szymanski W, Feringa BL. Design, Synthesis, and Inhibitory Activity of Potent, Photoswitchable Mast Cell Activation Inhibitors. J Med Chem 2013; 56:4456-64. [DOI: 10.1021/jm400115k] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Willem A. Velema
- Centre for Systems Chemistry,
Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Marco van der Toorn
- Laboratory of Allergology and
Pulmonary Diseases, Department of Pathology and Medical Biology, University
Medical Centre Groningen, 9713 GZ Groningen, The Netherlands
| | - Wiktor Szymanski
- Centre for Systems Chemistry,
Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Ben L. Feringa
- Centre for Systems Chemistry,
Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
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36
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Szymański W, Beierle JM, Kistemaker HAV, Velema WA, Feringa BL. Reversible Photocontrol of Biological Systems by the Incorporation of Molecular Photoswitches. Chem Rev 2013; 113:6114-78. [DOI: 10.1021/cr300179f] [Citation(s) in RCA: 847] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wiktor Szymański
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - John M. Beierle
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Hans A. V. Kistemaker
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Willem A. Velema
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Ben L. Feringa
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
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37
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London G, Carroll GT, Feringa BL. Silanization of quartz, silicon and mica surfaces with light-driven molecular motors: construction of surface-bound photo-active nanolayers. Org Biomol Chem 2013; 11:3477-83. [PMID: 23592007 DOI: 10.1039/c3ob40276b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The attachment of molecular rotary motors containing triethoxysilane functional groups to quartz, silicon and mica surfaces is described. Motors containing silane coupling agents in their structure form stable molecular layers on quartz and silicon surfaces. Motors attached to these surfaces were found to undergo photochemical and thermal isomerization steps similar to those observed in solution. Additionally, successful formation of molecular "carpets" on atomically flat mica extending micrometer-sized length scales is presented. These "carpets" were found to undergo morphological changes upon irradiation with UV-light.
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Affiliation(s)
- Gábor London
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
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38
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Szymański W, Wu B, Poloni C, Janssen DB, Feringa BL. Azobenzene Photoswitches for Staudinger-Bertozzi Ligation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208596] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Szymański W, Wu B, Poloni C, Janssen DB, Feringa BL. Azobenzene Photoswitches for Staudinger-Bertozzi Ligation. Angew Chem Int Ed Engl 2013; 52:2068-72. [DOI: 10.1002/anie.201208596] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/03/2012] [Indexed: 11/07/2022]
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40
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Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Light-controlled tools. Angew Chem Int Ed Engl 2012; 51:8446-76. [PMID: 22829531 DOI: 10.1002/anie.201202134] [Citation(s) in RCA: 738] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Indexed: 12/21/2022]
Abstract
Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems--from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.
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Affiliation(s)
- Clara Brieke
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438 Frankfurt/Main, Germany
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Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Lichtgesteuerte Werkzeuge. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202134] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clara Brieke
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
| | - Falk Rohrbach
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Gottschalk
- Buchmann‐Institut für Molekulare Lebenswissenschaften, Institut für Biochemie, Max‐von‐Laue‐Straße 15, 60438 Frankfurt/Main (Deutschland)
| | - Günter Mayer
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Heckel
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
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Kamei T, Fukaminato T, Tamaoki N. A photochromic ATP analogue driving a motor protein with reversible light-controlled motility: controlling velocity and binding manner of a kinesin-microtubule system in an in vitro motility assay. Chem Commun (Camb) 2012; 48:7625-7. [PMID: 22735457 DOI: 10.1039/c2cc33552b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We synthesized two photochromic ATP analogues (ATP-Azos) featuring azobenzene derivatives tethered at the 2' position of the ribose ring. In the presence of the ATP-Azo tethering p-tert-butylazobenzene, we observed reversible photo-control of the motility, velocity and binding manner, of a kinesin-microtubule system in an in vitro motility assay.
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Affiliation(s)
- Takashi Kamei
- Research Institute for Electronic Science, Hokkaido University, N20, W10, Kita-ku, Sapporo, Hokkaido, Japan
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Lycklama A Nijeholt JA, Driessen AJM. The bacterial Sec-translocase: structure and mechanism. Philos Trans R Soc Lond B Biol Sci 2012; 367:1016-28. [PMID: 22411975 DOI: 10.1098/rstb.2011.0201] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most bacterial secretory proteins pass across the cytoplasmic membrane via the translocase, which consists of a protein-conducting channel SecYEG and an ATP-dependent motor protein SecA. The ancillary SecDF membrane protein complex promotes the final stages of translocation. Recent years have seen a major advance in our understanding of the structural and biochemical basis of protein translocation, and this has led to a detailed model of the translocation mechanism.
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Affiliation(s)
- Jelger A Lycklama A Nijeholt
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands.
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Wilson D, Branda NR. Turning “On” and “Off” a Pyridoxal 5′-Phosphate Mimic Using Light. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201447] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wilson D, Branda NR. Turning “On” and “Off” a Pyridoxal 5′-Phosphate Mimic Using Light. Angew Chem Int Ed Engl 2012; 51:5431-4. [DOI: 10.1002/anie.201201447] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 03/03/2012] [Indexed: 11/09/2022]
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Stephenson A, Ward MD. Coordination chemistry of Ag(i) with bridging ligands based on pyrazolyl–pyridine termini: polymers, helicates and a bow-tie. RSC Adv 2012. [DOI: 10.1039/c2ra21757k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Bonardi F, Nouwen N, Feringa BL, Driessen AJM. Protein conducting channels—mechanisms, structures and applications. MOLECULAR BIOSYSTEMS 2012; 8:709-19. [DOI: 10.1039/c2mb05433g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Lycklama A Nijeholt JA, Wu ZC, Driessen AJM. Conformational dynamics of the plug domain of the SecYEG protein-conducting channel. J Biol Chem 2011; 286:43881-43890. [PMID: 22033919 PMCID: PMC3243504 DOI: 10.1074/jbc.m111.297507] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 10/20/2011] [Indexed: 11/06/2022] Open
Abstract
The central pore of the SecYEG preprotein-conducting channel is closed at the periplasmic face of the membrane by a plug domain. To study its conformational dynamics, the plug was labeled site-specifically with an environment-sensitive fluorophore. In the presence of a stable preprotein translocation inter-mediate, the SecY plug showed an enhanced solvent exposure consistent with a displacement from the hydrophobic central pore region. In contrast, binding and insertion of a ribosome-bound nascent membrane protein did not alter the plug conformation. These data indicate different plug dynamics depending on the ligand bound state of the SecYEG channel.
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Affiliation(s)
- Jelger A Lycklama A Nijeholt
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology institute, and the Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Zht Cheng Wu
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology institute, and the Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology institute, and the Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.
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Fehrentz T, Schönberger M, Trauner D. Optochemical Genetics. Angew Chem Int Ed Engl 2011; 50:12156-82. [DOI: 10.1002/anie.201103236] [Citation(s) in RCA: 316] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Indexed: 11/09/2022]
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