151
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Nishikawa Y, Tamura T, Hamachi I. Recent Advance in Organic Chemistry for Protein Labeling under Live Cell Conditions. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
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152
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Jung S, Kwon I. Expansion of bioorthogonal chemistries towards site-specific polymer–protein conjugation. Polym Chem 2016. [DOI: 10.1039/c6py00856a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bioorthogonal chemistries have been used to achieve polymer-protein conjugation with the retained critical properties.
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Affiliation(s)
- Secheon Jung
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
| | - Inchan Kwon
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
- Department of Chemical Engineering
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153
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Zheng Y, Cai S, Peng L, Jin Y, Xu H, Weng Z, Gao Z, Zhao B, Gao C. Group interval-controlled polymers: an example of epoxy functional polymers via step-growth thiol–yne polymerization. Polym Chem 2016. [DOI: 10.1039/c6py01343k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here, we successfully synthesized a series of epoxy GICPs via one-step UV-triggered thiol–yne polymerization of commercial glycidyl propargyl ether and dithiols at 0 °C..
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Affiliation(s)
- Yaochen Zheng
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Shengying Cai
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Li Peng
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Yu Jin
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Han Xu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Zhulin Weng
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Zhengguo Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Bo Zhao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Chao Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
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154
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Ko W, Kim S, Lee S, Jo K, Lee HS. Genetically encoded FRET sensors using a fluorescent unnatural amino acid as a FRET donor. RSC Adv 2016. [DOI: 10.1039/c6ra17375f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
FRET sensors based on fluorescent proteins have been powerful tools for probing protein–protein interactions and structural changes within proteins.
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Affiliation(s)
- Wooseok Ko
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Sanggil Kim
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
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155
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Imaging and manipulating proteins in live cells through covalent labeling. Nat Chem Biol 2015; 11:917-23. [PMID: 26575238 DOI: 10.1038/nchembio.1959] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/14/2015] [Indexed: 12/19/2022]
Abstract
The past 20 years have witnessed the advent of numerous technologies to specifically and covalently label proteins in cellulo and in vivo with synthetic probes. These technologies range from self-labeling proteins tags to non-natural amino acids, and the question is no longer how we can specifically label a given protein but rather with what additional functionality we wish to equip it. In addition, progress in fields such as super-resolution microscopy and genome editing have either provided additional motivation to label proteins with advanced synthetic probes or removed some of the difficulties of conducting such experiments. By focusing on two particular applications, live-cell imaging and the generation of reversible protein switches, we outline the opportunities and challenges of the field and how the synergy between synthetic chemistry and protein engineering will make it possible to conduct experiments that are not feasible with conventional approaches.
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156
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Broichhagen J, Damijonaitis A, Levitz J, Sokol KR, Leippe P, Konrad D, Isacoff EY, Trauner D. Orthogonal Optical Control of a G Protein-Coupled Receptor with a SNAP-Tethered Photochromic Ligand. ACS CENTRAL SCIENCE 2015; 1:383-393. [PMID: 27162996 PMCID: PMC4827557 DOI: 10.1021/acscentsci.5b00260] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Indexed: 05/30/2023]
Abstract
The covalent attachment of synthetic photoswitches is a general approach to impart light sensitivity onto native receptors. It mimics the logic of natural photoreceptors and significantly expands the reach of optogenetics. Here we describe a novel photoswitch design-the photoswitchable orthogonal remotely tethered ligand (PORTL)-that combines the genetically encoded SNAP-tag with photochromic ligands connected to a benzylguanine via a long flexible linker. We use the method to convert the G protein-coupled receptor mGluR2, a metabotropic glutamate receptor, into a photoreceptor (SNAG-mGluR2) that provides efficient optical control over the neuronal functions of mGluR2: presynaptic inhibition and control of excitability. The PORTL approach enables multiplexed optical control of different native receptors using distinct bioconjugation methods. It should be broadly applicable since SNAP-tags have proven to be reliable, many SNAP-tagged receptors are already available, and photochromic ligands on a long leash are readily designed and synthesized.
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Affiliation(s)
- Johannes Broichhagen
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - Arunas Damijonaitis
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - Joshua Levitz
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - Kevin R. Sokol
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - Philipp Leippe
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - David Konrad
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
| | - Ehud Y. Isacoff
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Helen
Wills Neuroscience Institute, University
of California, Berkeley, California 94720, United States
- Physical
Bioscience Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Dirk Trauner
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse
5-13, 81377 München, Germany
- Munich Center for Integrated Protein Science, Butenandtstrasse 5-13, 81377 München, Germany
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157
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Liao GP, Abdelraheem EMM, Neochoritis CG, Kurpiewska K, Kalinowska-Tłuścik J, McGowan DC, Dömling A. Versatile Multicomponent Reaction Macrocycle Synthesis Using α-Isocyano-ω-carboxylic Acids. Org Lett 2015; 17:4980-3. [PMID: 26439710 DOI: 10.1021/acs.orglett.5b02419] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The direct macrocycle synthesis of α-isocyano-ω-carboxylic acids via an Ugi multicomponent reaction is introduced. This multicomponent reaction (MCR) protocol differs by being especially short, convergent, and versatile, giving access to 12-22 membered rings.
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Affiliation(s)
- George P Liao
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Eman M M Abdelraheem
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Chemistry Department, Faculty of Science, Sohag University , Sohag 82524, Egypt
| | - Constantinos G Neochoritis
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University , 3 Ingardena Street, 30-060 Kraków, Poland
| | | | - David C McGowan
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Alexander Dömling
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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158
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Borba A, Gómez-Zavaglia A, Fausto R. Conformers, infrared spectrum, UV-induced photochemistry, and near-IR-induced generation of two rare conformers of matrix-isolated phenylglycine. J Chem Phys 2015; 141:154306. [PMID: 25338895 DOI: 10.1063/1.4897526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The conformational space of α-phenylglycine (PG) have been investigated theoretically at both the DFT/B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of approximation. Seventeen different minima were found on the investigated potential energy surfaces, which are characterized by different dominant intramolecular interactions: type I conformers are stabilized by hydrogen bonds of the type N-H···O=C, type II by a strong O-H···N hydrogen bond, type III by weak N-H···O-H hydrogen bonds, and type IV by a C=O···H-C contact. The calculations indicate also that entropic effects are relevant in determining the equilibrium populations of the conformers of PG in the gas phase, in particular in the case of conformers of type II, where the strong intramolecular O-H···N hydrogen bond considerably diminishes entropy by reducing the conformational mobility of the molecule. In consonance with the relative energies of the conformers and barriers for conformational interconversion, only 3 conformers of PG were observed for the compound isolated in cryogenic Ar, Xe, and N2 matrices: the conformational ground state (ICa), and forms ICc and IITa. All other significantly populated conformers existing in the gas phase prior to deposition convert either to conformer ICa or to conformer ICc during matrix deposition. The experimental observation of ICc had never been achieved hitherto. Narrowband near-IR irradiation of the first overtone of νOH vibrational mode of ICa and ICc in nitrogen matrices (at 6910 and 6930 cm(-1), respectively) led to selective generation of two additional conformers of high-energy, ITc and ITa, respectively, which were also observed experimentally for the first time. In addition, these experiments also provided the key information for the detailed vibrational characterization of the 3 conformers initially present in the matrices. On the other hand, UV irradiation (λ = 255 nm) of PG isolated in a xenon matrix revealed that PG undergoes facile photofragmentation through two photochemical pathways that are favored for different initial conformations of the reactant: (a) decarboxylation, leading to CO2 plus benzylamine (the dominant photofragmentation channel in PG cis-COOH conformers ICa and ICc) and (b) decarbonylation, with generation of CO plus benzonitrile, H2O and H2 (prevalent in the case of the trans-COOH conformer, IITa).
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Affiliation(s)
- Ana Borba
- Department of Chemistry, University of Coimbra, Coimbra P-3004-535, Portugal
| | | | - Rui Fausto
- Department of Chemistry, University of Coimbra, Coimbra P-3004-535, Portugal
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159
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Schumacher D, Helma J, Mann FA, Pichler G, Natale F, Krause E, Cardoso MC, Hackenberger CPR, Leonhardt H. Versatile and Efficient Site-Specific Protein Functionalization by Tubulin Tyrosine Ligase. Angew Chem Int Ed Engl 2015; 54:13787-91. [DOI: 10.1002/anie.201505456] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 08/17/2015] [Indexed: 12/20/2022]
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160
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Schumacher D, Helma J, Mann FA, Pichler G, Natale F, Krause E, Cardoso MC, Hackenberger CPR, Leonhardt H. Vielseitige, effiziente und ortsspezifische Proteinfunktionalisierung durch das Enzym Tubulin-Tyrosin-Ligase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505456] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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161
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Ravikumar Y, Nadarajan SP, Hyeon Yoo T, Lee CS, Yun H. Incorporating unnatural amino acids to engineer biocatalysts for industrial bioprocess applications. Biotechnol J 2015; 10:1862-76. [DOI: 10.1002/biot.201500153] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/13/2015] [Accepted: 09/02/2015] [Indexed: 12/22/2022]
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162
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Moatsou D, Li J, Ranji A, Pitto-Barry A, Ntai I, Jewett MC, O’Reilly RK. Self-Assembly of Temperature-Responsive Protein-Polymer Bioconjugates. Bioconjug Chem 2015; 26:1890-9. [PMID: 26083370 PMCID: PMC4577958 DOI: 10.1021/acs.bioconjchem.5b00264] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/12/2015] [Indexed: 12/13/2022]
Abstract
We report a simple temperature-responsive bioconjugate system comprising superfolder green fluorescent protein (sfGFP) decorated with poly[(oligo ethylene glycol) methyl ether methacrylate] (PEGMA) polymers. We used amber suppression to site-specifically incorporate the non-canonical azide-functional amino acid p-azidophenylalanine (pAzF) into sfGFP at different positions. The azide moiety on modified sfGFP was then coupled using copper-catalyzed "click" chemistry with the alkyne terminus of a PEGMA synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization. The protein in the resulting bioconjugate was found to remain functionally active (i.e., fluorescent) after conjugation. Turbidity measurements revealed that the point of attachment of the polymer onto the protein scaffold has an impact on the thermoresponsive behavior of the resultant bioconjugate. Furthermore, small-angle X-ray scattering analysis showed the wrapping of the polymer around the protein in a temperature-dependent fashion. Our work demonstrates that standard genetic manipulation combined with an expanded genetic code provides an easy way to construct functional hybrid biomaterials where the location of the conjugation site on the protein plays an important role in determining material properties. We anticipate that our approach could be generalized for the synthesis of complex functional materials with precisely defined domain orientation, connectivity, and composition.
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Affiliation(s)
- Dafni Moatsou
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Jian Li
- Department
of Chemical and Biological Engineering, Chemistry of Life Processes
Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Arnaz Ranji
- Department
of Chemical and Biological Engineering, Chemistry of Life Processes
Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Anaïs Pitto-Barry
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Ioanna Ntai
- Department
of Chemical and Biological Engineering, Chemistry of Life Processes
Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Chemistry of Life Processes
Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Rachel K. O’Reilly
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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163
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Library construction, selection and modification strategies to generate therapeutic peptide-based modulators of protein-protein interactions. Future Med Chem 2015; 6:2073-92. [PMID: 25531969 DOI: 10.4155/fmc.14.134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In the modern age of proteomics, vast numbers of protein-protein interactions (PPIs) are being identified as causative agents in pathogenesis, and are thus attractive therapeutic targets for intervention. Although traditionally regarded unfavorably as druggable agents relative to small molecules, peptides in recent years have gained considerable attention. Their previous dismissal had been largely due to the susceptibility of unmodified peptides to the barriers and pressures exerted by the circulation, immune system, proteases, membranes and other stresses. However, recent advances in high-throughput peptide isolation techniques, as well as a huge variety of direct modification options and approaches to allow targeted delivery, mean that peptides and their mimetics can now be designed to circumvent many of these traditional barriers. As a result, an increasing number of peptide-based drugs are reaching clinical trials and patients beyond.
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164
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Genetic incorporation of recycled unnatural amino acids. Amino Acids 2015; 48:357-63. [PMID: 26358464 DOI: 10.1007/s00726-015-2087-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/25/2015] [Indexed: 01/24/2023]
Abstract
The genetic incorporation of unnatural amino acids (UAAs) into proteins has been a useful tool for protein engineering. However, most UAAs are expensive, and the method requires a high concentration of UAAs, which has been a drawback of the technology, especially for large-scale applications. To address this problem, a method to recycle cultured UAAs was developed. The method is based on recycling a culture medium containing the UAA, in which some of essential nutrients were resupplemented after each culture cycle, and induction of protein expression was controlled with glucose. Under optimal conditions, five UAAs were recycled for up to seven rounds of expression without a decrease in expression level, cell density, or incorporation fidelity. This method can generally be applied to other UAAs; therefore, it is useful for reducing the cost of UAAs for genetic incorporation and helpful for expanding the use of the technology to industrial applications.
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165
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Mezei PD, Csonka GI. Unified picture for the conformation and stabilization of the O-glycosidic linkage in glycopeptide model structures. Struct Chem 2015. [DOI: 10.1007/s11224-015-0666-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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166
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Ko W, Jin S, Lee J, Kim D, Park J, Kim S, Lee HS. Efficient and Site-Specific Antibody Labeling by Strain-promoted Azide-Alkyne Cycloaddition. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Wooseok Ko
- Department of Chemistry; Sogang University; Seoul 121-742 Korea
| | - Sunhwa Jin
- Department of Chemistry; Sogang University; Seoul 121-742 Korea
| | - Junmo Lee
- Department of Chemistry; Sogang University; Seoul 121-742 Korea
| | - Dongha Kim
- Department of Chemistry; Sogang University; Seoul 121-742 Korea
| | - Joohyun Park
- Department of Chemistry; Sogang University; Seoul 121-742 Korea
| | - Seongkyoung Kim
- Department of Chemistry; Sogang University; Seoul 121-742 Korea
| | - Hyun Soo Lee
- Department of Chemistry; Sogang University; Seoul 121-742 Korea
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167
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Leibfarth FA, Johnson JA, Jamison TF. Scalable synthesis of sequence-defined, unimolecular macromolecules by Flow-IEG. Proc Natl Acad Sci U S A 2015; 112:10617-22. [PMID: 26269573 PMCID: PMC4553786 DOI: 10.1073/pnas.1508599112] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We report a semiautomated synthesis of sequence and architecturally defined, unimolecular macromolecules through a marriage of multistep flow synthesis and iterative exponential growth (Flow-IEG). The Flow-IEG system performs three reactions and an in-line purification in a total residence time of under 10 min, effectively doubling the molecular weight of an oligomeric species in an uninterrupted reaction sequence. Further iterations using the Flow-IEG system enable an exponential increase in molecular weight. Incorporating a variety of monomer structures and branching units provides control over polymer sequence and architecture. The synthesis of a uniform macromolecule with a molecular weight of 4,023 g/mol is demonstrated. The user-friendly nature, scalability, and modularity of Flow-IEG provide a general strategy for the automated synthesis of sequence-defined, unimolecular macromolecules. Flow-IEG is thus an enabling tool for theory validation, structure-property studies, and advanced applications in biotechnology and materials science.
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Affiliation(s)
- Frank A Leibfarth
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Timothy F Jamison
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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168
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Frost JR, Jacob NT, Papa LJ, Owens AE, Fasan R. Ribosomal Synthesis of Macrocyclic Peptides in Vitro and in Vivo Mediated by Genetically Encoded Aminothiol Unnatural Amino Acids. ACS Chem Biol 2015; 10:1805-16. [PMID: 25933125 DOI: 10.1021/acschembio.5b00119] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A versatile method for orchestrating the formation of side chain-to-tail cyclic peptides from ribosomally derived polypeptide precursors is reported. Upon ribosomal incorporation into intein-containing precursor proteins, designer unnatural amino acids bearing side chain 1,3- or 1,2-aminothiol functionalities are able to promote the cyclization of a downstream target peptide sequence via a C-terminal ligation/ring contraction mechanism. Using this approach, peptide macrocycles of variable size and composition could be generated in a pH-triggered manner in vitro or directly in living bacterial cells. This methodology furnishes a new platform for the creation and screening of genetically encoded libraries of conformationally constrained peptides. This strategy was applied to identify and isolate a low-micromolar streptavidin binder (KD = 1.1 μM) from a library of cyclic peptides produced in Escherichia coli, thereby illustrating its potential toward aiding the discovery of functional peptide macrocycles.
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Affiliation(s)
- John R. Frost
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Nicholas T. Jacob
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Louis J. Papa
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Andrew E. Owens
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
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169
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Maza JC, McKenna JR, Raliski BK, Freedman MT, Young DD. Synthesis and Incorporation of Unnatural Amino Acids To Probe and Optimize Protein Bioconjugations. Bioconjug Chem 2015; 26:1884-9. [PMID: 26287719 DOI: 10.1021/acs.bioconjchem.5b00424] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The utilization of unnatural amino acids (UAAs) in bioconjugations is ideal due to their ability to confer a degree of bioorthogonality and specificity. In order to elucidate optimal conditions for the preparation of bioconjugates with UAAs, we synthesized 9 UAAs with variable methylene tethers (2-4) and either an azide, alkyne, or halide functional group. All 9 UAAs were then incorporated into green fluorescent protein (GFP) using a promiscuous aminoacyl-tRNA synthetase. The different bioconjugations were then analyzed for optimal tether length via reaction with either a fluorophore or a derivatized resin. Interestingly, the optimal tether length was found to be dependent on the type of reaction. Overall, these findings provide a better understanding of various parameters that can be optimized for the efficient preparation of bioconjugates.
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Affiliation(s)
- Johnathan C Maza
- Department of Chemistry, College of William & Mary P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Jaclyn R McKenna
- Department of Chemistry, College of William & Mary P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Benjamin K Raliski
- Department of Chemistry, College of William & Mary P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Matthew T Freedman
- Department of Chemistry, College of William & Mary P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Douglas D Young
- Department of Chemistry, College of William & Mary P.O. Box 8795, Williamsburg, Virginia 23187, United States
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170
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Ding B, Panahi A, Ho JJ, Laaser JE, Brooks CL, Zanni MT, Chen Z. Probing Site-Specific Structural Information of Peptides at Model Membrane Interface In Situ. J Am Chem Soc 2015; 137:10190-8. [PMID: 26241117 DOI: 10.1021/jacs.5b04024] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isotope labeling is a powerful technique to probe detailed structures of biological molecules with a variety of analytical methods such as NMR and vibrational spectroscopies. It is important to obtain molecular structural information on biological molecules at interfaces such as cell membranes, but it is challenging to use the isotope labeling method to study interfacial biomolecules. Here, by individually (13)C═(16)O labeling ten residues of a peptide, Ovispirin-1, we have demonstrated for the first time that a site-specific environment of membrane associated peptide can be probed by the submonolayer surface sensitive sum frequency generation (SFG) vibrational spectroscopy in situ. With the peptide associated with a single lipid bilayer, the sinusoidal trend of the SFG line width and peak-center frequency suggests that the peptide is located at the interface beneath the lipid headgroup region. The constructive interferences between the isotope labeled peaks and the main peptide amide I peak contributed by the unlabeled components were used to determine the membrane orientation of the peptide. From the SFG spectral peak-center frequency, line width, and polarization dependence of the isotope labeled units, we deduced structural information on individual units of the peptide associated with a model cell membrane. We also performed molecular dynamics (MD) simulations to understand peptide-membrane interactions. The physical pictures described by simulation agree well with the SFG experimental result. This research demonstrates the feasibility and power of using isotope labeling SFG to probe molecular structures of interfacial biological molecules in situ in real time.
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Affiliation(s)
- Bei Ding
- †Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Afra Panahi
- †Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jia-Jung Ho
- ‡Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53703, United States
| | - Jennifer E Laaser
- ‡Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53703, United States
| | - Charles L Brooks
- †Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Martin T Zanni
- ‡Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53703, United States
| | - Zhan Chen
- †Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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171
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Heinz N, Dolg M, Berkessel A. A theoretical study of imine hydrocyanation catalyzed by halogen-bonding. J Comput Chem 2015; 36:1812-7. [PMID: 26149792 DOI: 10.1002/jcc.23999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/29/2015] [Accepted: 05/30/2015] [Indexed: 01/14/2023]
Abstract
A detailed theoretical study of the mechanism and energetics of an organocatalysis based on C=N activation by halogen-bonding is presented for the hydrocyanation of N-benzylidenemethylamine. The calculations at the level of scalar-relativistic gradient-corrected density functional theory give an insight in this catalytic concept and provide information on the characteristics of four different monodentate catalyst candidates acting as halogen-bond donors during the reaction.
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Affiliation(s)
- Norah Heinz
- Department of Chemistry, Institute for Theoretical Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Michael Dolg
- Department of Chemistry, Institute for Theoretical Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Albrecht Berkessel
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
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172
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Lampkowski JS, Villa JK, Young TS, Young DD. Development and Optimization of Glaser-Hay Bioconjugations. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502676] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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173
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Lampkowski JS, Villa JK, Young TS, Young DD. Development and Optimization of Glaser-Hay Bioconjugations. Angew Chem Int Ed Engl 2015; 54:9343-6. [DOI: 10.1002/anie.201502676] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/24/2015] [Indexed: 12/18/2022]
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174
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Ravikumar Y, Nadarajan SP, Yoo TH, Lee CS, Yun H. Unnatural amino acid mutagenesis-based enzyme engineering. Trends Biotechnol 2015; 33:462-70. [PMID: 26088007 DOI: 10.1016/j.tibtech.2015.05.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 02/09/2023]
Abstract
Traditional enzyme engineering relies on substituting one amino acid by one of the other 19 natural amino acids to change the functional properties of an enzyme. However, incorporation of unnatural amino acids (UAAs) has been harnessed to engineer efficient enzymes for biocatalysis. Residue-specific and site-specific in vivo incorporation methods are becoming the preferred approach for producing enzymes with altered or improved functions. We describe the contribution of in vivo UAA incorporation methodologies to enzyme engineering as well as the future prospects for the field, including the integration of UAAs with other new advances in enzyme engineering.
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Affiliation(s)
- Yuvaraj Ravikumar
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | | | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Chong-soon Lee
- School of Biotechnology, Department of Biochemistry, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Korea.
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175
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Peters C, Brown S. Antibody-drug conjugates as novel anti-cancer chemotherapeutics. Biosci Rep 2015; 35:e00225. [PMID: 26182432 PMCID: PMC4613712 DOI: 10.1042/bsr20150089] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/18/2015] [Accepted: 05/29/2015] [Indexed: 12/19/2022] Open
Abstract
Over the past couple of decades, antibody-drug conjugates (ADCs) have revolutionized the field of cancer chemotherapy. Unlike conventional treatments that damage healthy tissues upon dose escalation, ADCs utilize monoclonal antibodies (mAbs) to specifically bind tumour-associated target antigens and deliver a highly potent cytotoxic agent. The synergistic combination of mAbs conjugated to small-molecule chemotherapeutics, via a stable linker, has given rise to an extremely efficacious class of anti-cancer drugs with an already large and rapidly growing clinical pipeline. The primary objective of this paper is to review current knowledge and latest developments in the field of ADCs. Upon intravenous administration, ADCs bind to their target antigens and are internalized through receptor-mediated endocytosis. This facilitates the subsequent release of the cytotoxin, which eventually leads to apoptotic cell death of the cancer cell. The three components of ADCs (mAb, linker and cytotoxin) affect the efficacy and toxicity of the conjugate. Optimizing each one, while enhancing the functionality of the ADC as a whole, has been one of the major considerations of ADC design and development. In addition to these, the choice of clinically relevant targets and the position and number of linkages have also been the key determinants of ADC efficacy. The only marketed ADCs, brentuximab vedotin and trastuzumab emtansine (T-DM1), have demonstrated their use against both haematological and solid malignancies respectively. The success of future ADCs relies on improving target selection, increasing cytotoxin potency, developing innovative linkers and overcoming drug resistance. As more research is conducted to tackle these issues, ADCs are likely to become part of the future of targeted cancer therapeutics.
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Affiliation(s)
- Christina Peters
- School of Life Sciences, Nottingham Medical School, Queen's Medical Centre, Nottingham NG7 2UH, U.K
| | - Stuart Brown
- School of Life Sciences, Nottingham Medical School, Queen's Medical Centre, Nottingham NG7 2UH, U.K.
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176
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Lim RKV, Yu S, Cheng B, Li S, Kim NJ, Cao Y, Chi V, Kim JY, Chatterjee AK, Schultz PG, Tremblay MS, Kazane SA. Targeted Delivery of LXR Agonist Using a Site-Specific Antibody-Drug Conjugate. Bioconjug Chem 2015; 26:2216-22. [PMID: 25945727 DOI: 10.1021/acs.bioconjchem.5b00203] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liver X receptor (LXR) agonists have been explored as potential treatments for atherosclerosis and other diseases based on their ability to induce reverse cholesterol transport and suppress inflammation. However, this therapeutic potential has been hindered by on-target adverse effects in the liver mediated by excessive lipogenesis. Herein, we report a novel site-specific antibody-drug conjugate (ADC) that selectively delivers a LXR agonist to monocytes/macrophages while sparing hepatocytes. The unnatural amino acid para-acetylphenylalanine (pAcF) was site-specifically incorporated into anti-CD11a IgG, which binds the α-chain component of the lymphocyte function-associated antigen 1 (LFA-1) expressed on nearly all monocytes and macrophages. An aminooxy-modified LXR agonist was conjugated to anti-CD11a IgG through a stable, cathepsin B cleavable oxime linkage to afford a chemically defined ADC. The anti-CD11a IgG-LXR agonist ADC induced LXR activation specifically in human THP-1 monocyte/macrophage cells in vitro (EC50-27 nM), but had no significant effect in hepatocytes, indicating that payload delivery is CD11a-mediated. Moreover, the ADC exhibited higher-fold activation compared to a conventional synthetic LXR agonist T0901317 (Tularik) (3-fold). This novel ADC represents a fundamentally different strategy that uses tissue targeting to overcome the limitations of LXR agonists for potential use in treating atherosclerosis.
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Affiliation(s)
- Reyna K V Lim
- California Institute for Biomedical Research (Calibr) , 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shan Yu
- California Institute for Biomedical Research (Calibr) , 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Bo Cheng
- California Institute for Biomedical Research (Calibr) , 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sijia Li
- California Institute for Biomedical Research (Calibr) , 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nam-Jung Kim
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yu Cao
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Victor Chi
- California Institute for Biomedical Research (Calibr) , 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ji Young Kim
- California Institute for Biomedical Research (Calibr) , 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Arnab K Chatterjee
- California Institute for Biomedical Research (Calibr) , 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G Schultz
- California Institute for Biomedical Research (Calibr) , 11119 North Torrey Pines Road, La Jolla, California 92037, United States.,Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Matthew S Tremblay
- California Institute for Biomedical Research (Calibr) , 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Stephanie A Kazane
- California Institute for Biomedical Research (Calibr) , 11119 North Torrey Pines Road, La Jolla, California 92037, United States
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177
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Nikić I, Kang JH, Girona GE, Aramburu IV, Lemke EA. Labeling proteins on live mammalian cells using click chemistry. Nat Protoc 2015; 10:780-91. [DOI: 10.1038/nprot.2015.045] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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178
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Lesne A, Foray N, Cathala G, Forné T, Wong H, Victor JM. Chromatin fiber allostery and the epigenetic code. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064114. [PMID: 25563208 DOI: 10.1088/0953-8984/27/6/064114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The notion of allostery introduced for proteins about fifty years ago has been extended since then to DNA allostery, where a locally triggered DNA structural transition remotely controls other DNA-binding events. We further extend this notion and propose that chromatin fiber allosteric transitions, induced by histone-tail covalent modifications, may play a key role in transcriptional regulation. We present an integrated scenario articulating allosteric mechanisms at different scales: allosteric transitions of the condensed chromatin fiber induced by histone-tail acetylation modify the mechanical constraints experienced by the embedded DNA, thus possibly controlling DNA-binding of allosteric transcription factors or further allosteric mechanisms at the linker DNA level. At a higher scale, different epigenetic constraints delineate different statistically dominant subsets of accessible chromatin fiber conformations, which each favors the assembly of dedicated regulatory complexes, as detailed on the emblematic example of the mouse Igf2-H19 gene locus and its parental imprinting. This physical view offers a mechanistic and spatially structured explanation of the observed correlation between transcriptional activity and histone modifications. The evolutionary origin of allosteric control supports to speak of an 'epigenetic code', by which events involved in transcriptional regulation are encoded in histone modifications in a context-dependent way.
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Affiliation(s)
- Annick Lesne
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, UPMC Université Paris 06, Sorbonne Universités, F-75005, Paris, France. Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535, Université de Montpellier, F-34293, Montpellier, France. CNRS GDR 3536, UPMC Université Paris 06, F-75005, Paris, France
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179
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Mahmoodi MM, Rashidian M, Zhang Y, Distefano MD. Application of meta- and para-Phenylenediamine as Enhanced Oxime Ligation Catalysts for Protein Labeling, PEGylation, Immobilization, and Release. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2015; 79:15.4.1-15.4.28. [PMID: 25640893 PMCID: PMC4357315 DOI: 10.1002/0471140864.ps1504s79] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Meta- and para-phenylenediamines have recently been shown to catalyze oxime and hydrazone ligation reactions at rates much faster than aniline, a commonly used catalyst. Here, we demonstrate how these new catalysts can be used in a generally applicable procedure for fluorescent labeling, PEGylation, immobilization, and release of aldehyde- and ketone- functionalized proteins. The chemical orthogonality of phenylenediamine-catalyzed oxime ligation versus copper-catalyzed click reaction has also been harnessed for simultaneous dual labeling of bifunctional proteins containing both aldehyde and alkyne groups in high yield.
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Affiliation(s)
| | - Mohammad Rashidian
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
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180
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Fan CW, Xu GC, Ma BD, Bai YP, Zhang J, Xu JH. A novel d-mandelate dehydrogenase used in three-enzyme cascade reaction for highly efficient synthesis of non-natural chiral amino acids. J Biotechnol 2015; 195:67-71. [DOI: 10.1016/j.jbiotec.2014.10.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/16/2014] [Accepted: 10/19/2014] [Indexed: 11/30/2022]
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181
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Schiller SM. Protein Tectons in Synthetic Biology. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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182
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Tsukiji S, Hamachi I. Ligand-directed tosyl chemistry for selective native protein labeling in vitro, in cells, and in vivo. Methods Mol Biol 2015; 1266:243-263. [PMID: 25560080 DOI: 10.1007/978-1-4939-2272-7_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Introducing nongenetically encoded, synthetic probes into specific proteins is now recognized as a key component in chemical biology. In particular, the ability to chemically modify specific "native" proteins in various contexts from in vitro to cellular systems is of fundamental importance to study biological systems. We developed a protein-labeling technique termed ligand-directed tosyl (LDT) chemistry for this purpose. This method is capable of labeling specific native proteins with diverse synthetic probes with high site specificity and target selectivity without compromising protein function. Here we describe the principle of the LDT chemistry and the protocol for selective chemical labeling of native carbonic anhydrase in vitro, in blood cells (ex vivo), and in living mice (in vivo).
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Affiliation(s)
- Shinya Tsukiji
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
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183
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FRET-based analysis of protein-nucleic acid interactions by genetically incorporating a fluorescent amino acid. Amino Acids 2014; 47:729-34. [PMID: 25540052 DOI: 10.1007/s00726-014-1900-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/12/2014] [Indexed: 10/24/2022]
Abstract
Protein-nucleic acid interaction is an important process in many biological phenomena. In this study, a fluorescence resonance energy transfer (FRET)-based protein-DNA binding assay has been developed, in which a fluorescent amino acid is genetically incorporated into a DNA-binding protein. A coumarin-containing amino acid was incorporated into a DNA-binding protein, and the mutant protein specifically produced a FRET signal upon binding to its cognate DNA labeled with a fluorophore. The protein-DNA binding affinity was then measured under equilibrium conditions. This method is advantageous for studying protein-nucleic acid interactions, because it is performed under equilibrium conditions, technically easy, and applicable to any nucleic acid-binding protein.
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184
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Padilla MS, Young DD. Photosensitive GFP mutants containing an azobenzene unnatural amino acid. Bioorg Med Chem Lett 2014; 25:470-3. [PMID: 25563892 DOI: 10.1016/j.bmcl.2014.12.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 11/19/2022]
Abstract
The incorporation of unnatural amino acids represents a unique mechanism for the modulation of protein function. This approach has been utilized to generate photoswitchable GFP mutants, capable of demonstrating modulated fluorescence upon exposure to UV irradiation. Overall these photosensitive GFP mutants can be employed in various biosensing and diagnostic techniques to better understand protein function and processing.
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Affiliation(s)
- Marshall S Padilla
- Department of Chemistry, College of William & Mary, Williamsburg, VA 23187, USA
| | - Douglas D Young
- Department of Chemistry, College of William & Mary, Williamsburg, VA 23187, USA
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185
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Nischan N, Herce HD, Natale F, Bohlke N, Budisa N, Cardoso MC, Hackenberger CPR. Kovalente Verknüpfung cyclischer TAT-Peptide mit GFP resultiert in der direkten Aufnahme in lebende Zellen mit sofortiger biologischer Verfügbarkeit. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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186
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Nischan N, Herce HD, Natale F, Bohlke N, Budisa N, Cardoso MC, Hackenberger CPR. Covalent attachment of cyclic TAT peptides to GFP results in protein delivery into live cells with immediate bioavailability. Angew Chem Int Ed Engl 2014; 54:1950-3. [PMID: 25521313 DOI: 10.1002/anie.201410006] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Indexed: 11/08/2022]
Abstract
The delivery of free molecules into the cytoplasm and nucleus by using arginine-rich cell-penetrating peptides (CPPs) has been limited to small cargoes, while large cargoes such as proteins are taken up and trapped in endocytic vesicles. Based on recent work, in which we showed that the transduction efficiency of arginine-rich CPPs can be greatly enhanced by cyclization, the aim was to use cyclic CPPs to transport full-length proteins, in this study green fluorescent protein (GFP), into the cytosol of living cells. Cyclic and linear CPP-GFP conjugates were obtained by using azido-functionalized CPPs and an alkyne-functionalized GFP. Our findings reveal that the cyclic-CPP-GFP conjugates are internalized into live cells with immediate bioavailability in the cytosol and the nucleus, whereas linear CPP analogues do not confer GFP transduction. This technology expands the application of cyclic CPPs to the efficient transport of functional full-length proteins into live cells.
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Affiliation(s)
- Nicole Nischan
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin (Germany); Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, 14195 Berlin (Germany)
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187
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Al Toma RS, Kuthning A, Exner MP, Denisiuk A, Ziegler J, Budisa N, Süssmuth RD. Site-Directed and Global Incorporation of Orthogonal and Isostructural Noncanonical Amino Acids into the Ribosomal Lasso Peptide Capistruin. Chembiochem 2014; 16:503-9. [DOI: 10.1002/cbic.201402558] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Indexed: 02/01/2023]
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188
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Piscotta FJ, Tharp JM, Liu WR, Link AJ. Expanding the chemical diversity of lasso peptide MccJ25 with genetically encoded noncanonical amino acids. Chem Commun (Camb) 2014; 51:409-12. [PMID: 25407838 DOI: 10.1039/c4cc07778d] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Using the amber suppression approach, four noncanonical amino acids (ncAAs) were used to replace existing amino acids at four positions in lasso peptide microcin J25 (MccJ25). The lasso peptide biosynthesis enzymes tolerated all four ncAAs and produced antibiotics with efficacy equivalent to wild-type in some cases. Given the rapid expansion of the genetically encoded ncAA pool, this study is the first to demonstrate an expedient method to significantly increase the chemical diversity of lasso peptides.
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Affiliation(s)
- Frank J Piscotta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
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189
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Raliski BK, Howard CA, Young DD. Site-Specific Protein Immobilization Using Unnatural Amino Acids. Bioconjug Chem 2014; 25:1916-20. [DOI: 10.1021/bc500443h] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Benjamin K. Raliski
- Department of Chemistry, College of William & Mary P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Christina A. Howard
- Department of Chemistry, College of William & Mary P.O. Box 8795, Williamsburg, Virginia 23187, United States
| | - Douglas D. Young
- Department of Chemistry, College of William & Mary P.O. Box 8795, Williamsburg, Virginia 23187, United States
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190
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Abstract
Antibody drug conjugates (ADCs) are an emerging class of targeted therapeutics with the potential to improve therapeutic index over traditional chemotherapy. Drugs and linkers have been the current focus of ADC development, in addition to antibody and target selection. Recently, however, the importance of conjugate homogeneity has been realized. The current methods for drug attachment lead to a heterogeneous mixture, and some populations of that mixture have poor in vivo performance. New methods for site-specific drug attachment lead to more homogeneous conjugates and allow control of the site of drug attachment. These subtle improvements can have profound effects on in vivo efficacy and therapeutic index. This review examines current methods for site-specific drug conjugation to antibodies, and compares in vivo results with their non-specifically conjugated counterparts. The apparent improvement in pharmacokinetics and the reduced off target toxicity warrant further development of this site-specific modification approach for future ADC development.
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191
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Lu X, Yi J, Zhang ZQ, Dai JJ, Liu JH, Xiao B, Fu Y, Liu L. Expedient synthesis of chiral α-amino acids through nickel-catalyzed reductive cross-coupling. Chemistry 2014; 20:15339-43. [PMID: 25314635 DOI: 10.1002/chem.201405296] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Indexed: 11/08/2022]
Abstract
A novel method for the synthesis of non-natural L- and D-amino acids by a Ni-catalyzed reductive cross-coupling reaction is described. This strategy enables the racemization-free cross-coupling of serine/homoserine- derived iodides with aryl/acyl/alkyl halides. It provides convenient access to varieties of enantiopure and functionalized amino acids, which are important building blocks in bioactive compounds and pharmaceuticals.
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Affiliation(s)
- Xi Lu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026 (China); State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Department of Chemistry, Tsinghua University, Beijing 100084 (China)
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192
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Warner JB, Muthusamy AK, Petersson EJ. Specific modulation of protein activity by using a bioorthogonal reaction. Chembiochem 2014; 15:2508-14. [PMID: 25256385 DOI: 10.1002/cbic.201402423] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Indexed: 11/06/2022]
Abstract
Unnatural amino acids with bioorthogonal reactive groups have the potential to provide a rapid and specific mechanism for covalently inhibiting a protein of interest. Here, we use mutagenesis to insert an unnatural amino acid containing an azide group (Z) into the target protein at positions such that a "click" reaction with an alkyne modulator (X) will alter the function of the protein. This bioorthogonally reactive pair can engender specificity of X for the Z-containing protein, even if the target is otherwise identical to another protein, allowing for rapid target validation in living cells. We demonstrate our method using inhibition of the Escherichia coli enzyme aminoacyl transferase by both active-site occlusion and allosteric mechanisms. We have termed this a "clickable magic bullet" strategy, and it should be generally applicable to studying the effects of protein inhibition, within the limits of unnatural amino acid mutagenesis.
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Affiliation(s)
- John B Warner
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323 (USA)
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193
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Bionda N, Cryan AL, Fasan R. Bioinspired strategy for the ribosomal synthesis of thioether-bridged macrocyclic peptides in bacteria. ACS Chem Biol 2014; 9:2008-13. [PMID: 25079213 PMCID: PMC4168796 DOI: 10.1021/cb500311k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
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Inspired
by the biosynthetic logic of lanthipeptide natural products,
a new methodology was developed to direct the ribosomal synthesis
of macrocyclic peptides constrained by an intramolecular thioether
bond. As a first step, a robust and versatile strategy was implemented
to enable the cyclization of ribosomally derived peptide sequences
via a chemoselective reaction between a genetically encoded cysteine
and a cysteine-reactive unnatural amino acid (O-(2-bromoethyl)-tyrosine).
Combination of this approach with intein-catalyzed protein splicing
furnished an efficient route to achieve the spontaneous, post-translational
formation of structurally diverse macrocyclic peptides in bacterial
cells. The present peptide cyclization strategy was also found to
be amenable to integration with split intein-mediated circular ligation,
resulting in the intracellular synthesis of conformationally constrained
peptides featuring a bicyclic architecture.
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Affiliation(s)
- Nina Bionda
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Abby L. Cryan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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194
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Sinz A. The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks. Expert Rev Proteomics 2014; 11:733-43. [DOI: 10.1586/14789450.2014.960852] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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195
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Huber T, Sakmar T. Chemical Biology Methods for Investigating G Protein-Coupled Receptor Signaling. ACTA ACUST UNITED AC 2014; 21:1224-37. [DOI: 10.1016/j.chembiol.2014.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/21/2014] [Accepted: 08/20/2014] [Indexed: 11/26/2022]
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196
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Wang Q, Sun T, Xu J, Shen Z, Briggs SP, Zhou D, Wang L. Response and adaptation of Escherichia coli to suppression of the amber stop codon. Chembiochem 2014; 15:1744-9. [PMID: 25044429 PMCID: PMC4156322 DOI: 10.1002/cbic.201402235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Indexed: 11/08/2022]
Abstract
Some extant organisms reassign the amber stop codon to a sense codon through evolution, and suppression of the amber codon with engineered tRNAs has been exploited to expand the genetic code for incorporating non-canonical amino acids (ncAAs) in live systems. However, it is unclear how the host cells respond and adapt to such amber suppression. Herein we suppressed the amber codon in Escherichia coli with an orthogonal tRNA/synthetase pair and cultured the cells under such a pressure for about 500 generations. We discovered that E. coli quickly counteracted the suppression with transposon insertion to inactivate the orthogonal synthetase. Persistent amber suppression evading transposon inactivation led to global proteomic changes with a notable up-regulation of a previously uncharacterized protein (YdiI) for which we identified an unexpected function of expelling plasmids. These results should be valuable for understanding codon reassignment in genetic code evolution and for improving the efficiency of ncAA incorporation.
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Affiliation(s)
- Qian Wang
- Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193 (China)
| | - Tingting Sun
- Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing, 100191 (China)
| | - Jianfeng Xu
- Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Zhouxin Shen
- Section of Cell and Development Biology, University of California at San Diego, La Jolla, CA 92093 (USA)
| | - Steven P. Briggs
- Section of Cell and Development Biology, University of California at San Diego, La Jolla, CA 92093 (USA)
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing, 100191 (China)
| | - Lei Wang
- Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
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197
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Tsukiji S, Hamachi I. Ligand-directed tosyl chemistry for in situ native protein labeling and engineering in living systems: from basic properties to applications. Curr Opin Chem Biol 2014; 21:136-43. [DOI: 10.1016/j.cbpa.2014.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/11/2014] [Accepted: 07/14/2014] [Indexed: 11/17/2022]
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198
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Pippig DA, Baumann F, Strackharn M, Aschenbrenner D, Gaub HE. Protein-DNA chimeras for nano assembly. ACS NANO 2014; 8:6551-6555. [PMID: 24897163 DOI: 10.1021/nn501644w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In synthetic biology, "understanding by building" requires exquisite control of the molecular constituents and their spatial organization. Site-specific coupling of DNA to proteins allows arrangement of different protein functionalities with emergent properties by self-assembly on origami-like DNA scaffolds or by direct assembly via Single-Molecule Cut & Paste (SMC&P). Here, we employed the ybbR-tag/Sfp system to covalently attach Coenzyme A-modified DNA to GFP and, as a proof of principle, arranged the chimera in different patterns by SMC&P. Fluorescence recordings of individual molecules proved that the proteins remained folded and fully functional throughout the assembly process. The high coupling efficiency and specificity as well as the negligible size (11 amino acids) of the ybbR-tag represent a mild, yet versatile, general and robust way of adding a freely programmable and highly selective attachment site to virtually any protein of interest.
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Affiliation(s)
- Diana A Pippig
- Center for Nanoscience and Department of Physics, University of Munich , Amalienstraße 54, 80799 Munich, Germany
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199
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Wang L, Zhao M, Li S, Erasquin UJ, Wang H, Ren L, Chen C, Wang Y, Cai C. "Click" immobilization of a VEGF-mimetic peptide on decellularized endothelial extracellular matrix to enhance angiogenesis. ACS APPLIED MATERIALS & INTERFACES 2014; 6:8401-8406. [PMID: 24749832 PMCID: PMC4059262 DOI: 10.1021/am501309d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 04/21/2014] [Indexed: 05/29/2023]
Abstract
We show that coating of decellularized extracellular matrix (DC-ECM) on substrate surfaces is an efficient way to generate a platform mimicking the native ECM environment. Moreover, the DC-ECM can be modified with a peptide (QK) mimicking vascular endothelial growth factor without apparently compromising its integrity. The modification was achieved through metabolic incorporation of a "clickable" handle to DC-ECM followed by rapid attachment of the QK peptide with an azido tag using copper-catalyzed click reaction. The attachment of the QK peptide on to DC-ECM in this way further enhanced the angiogenic responses (formation of branched tubular networks) of endothelial cells.
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Affiliation(s)
- Lin Wang
- Department
of Chemistry, University of Houston, Houston, Texas 77204, United States
- Biomaterials
Research Center, South China University
of Technology, Guangzhou 510640, China
| | - Meirong Zhao
- Department
of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Siheng Li
- Department
of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Uriel J. Erasquin
- Department
of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hao Wang
- Molecular
Surgeon Research Center, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Li Ren
- Biomaterials
Research Center, South China University
of Technology, Guangzhou 510640, China
| | - Changyi Chen
- Molecular
Surgeon Research Center, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Yingjun Wang
- Biomaterials
Research Center, South China University
of Technology, Guangzhou 510640, China
| | - Chengzhi Cai
- Department
of Chemistry, University of Houston, Houston, Texas 77204, United States
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200
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González de Torre I, Santos M, Quintanilla L, Testera A, Alonso M, Rodríguez Cabello JC. Elastin-like recombinamer catalyst-free click gels: characterization of poroelastic and intrinsic viscoelastic properties. Acta Biomater 2014; 10:2495-505. [PMID: 24530853 DOI: 10.1016/j.actbio.2014.02.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 01/23/2014] [Accepted: 02/03/2014] [Indexed: 02/08/2023]
Abstract
Elastin-like recombinamer catalyst-free click gels (ELR-CFCGs) have been prepared and characterized by modifying both a structural ELR (VKVx24) and a biofunctionalized ELR-bearing RGD cell-adhesion sequence (HRGD6) to bear the reactive groups needed to form hydrogels via a click reaction. Prior to formation of the ELR-CFCGs, azide-bearing and cyclooctyne-modified ELRs were also synthesized. Subsequent covalent crosslinking was based on the reaction between these azide and cyclooctyne groups, which takes place under physiological conditions and without the need for a catalyst. The correlation among SEM micrographs, porosity, swelling ratio, and rheological measurements have been carried out. The storage and loss moduli at 1Hz are in the range 1-10kPa and 100-1000Pa, respectively. The linear dependence of |G∗| on f(½) and the peak value of tan δ were considered to be consistent with a poroelastic mechanism dominating the frequency range 0.3-70Hz. The discrete relaxation spectrum was obtained from stress relaxation measurements (t>5s). The good fit of the relaxation modulus to decrease exponential functions suggests that an intrinsic viscoelastic mechanism dominates the transients. Several recombinamer concentrations and temperatures were tested to obtain gels with fully tuneable properties that could find applications in the biomedical field.
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