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Articles de revues sur le sujet « Unnatural amino acids incorporation »

Auteur : Grafiati

Publié le 9 mars 2023

Mis à jour le 10 mars 2023

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1

Kigawa, Takanori, Shigeyuki Yokoyama, and Tatsuo Miyazawa. "Incorporation of unnatural amino acids proteins." Kobunshi 39, no. 7 (1990): 500–503. http://dx.doi.org/10.1295/kobunshi.39.500.

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Ko, Wooseok, Sanggil Kim, Kyubong Jo, and Hyun Soo Lee. "Genetic incorporation of recycled unnatural amino acids." Amino Acids 48, no. 2 (2015): 357–63. http://dx.doi.org/10.1007/s00726-015-2087-x.

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Adhikari, Anup, Bibek Raj Bhattarai, Ashika Aryal, et al. "Reprogramming natural proteins using unnatural amino acids." RSC Advances 11, no. 60 (2021): 38126–45. http://dx.doi.org/10.1039/d1ra07028b.

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Voloshchuk, Natalya, and Jin Kim Montclare. "Incorporation of unnatural amino acids for synthetic biology." Mol. BioSyst. 6, no. 1 (2010): 65–80. http://dx.doi.org/10.1039/b909200p.

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Nödling, Alexander R., Luke A. Spear, Thomas L. Williams, Louis Y. P. Luk, and Yu-Hsuan Tsai. "Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells." Essays in Biochemistry 63, no. 2 (2019): 237–66. http://dx.doi.org/10.1042/ebc20180042.

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Abstract Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.

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Gao, Wei, Ning Bu, and Yuan Lu. "Efficient Incorporation of Unnatural Amino Acids into Proteins with a Robust Cell-Free System." Methods and Protocols 2, no. 1 (2019): 16. http://dx.doi.org/10.3390/mps2010016.

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Unnatural proteins are crucial biomacromolecules and have been widely applied in fundamental science, novel biopolymer materials, enzymes, and therapeutics. Cell-free protein synthesis (CFPS) system can serve as a robust platform to synthesize unnatural proteins by highly effective site-specific incorporation of unnatural amino acids (UNAAs), without the limitations of cell membrane permeability and the toxicity of unnatural components. Here, we describe a quick and simple method to synthesize unnatural proteins in CFPS system based on Escherichia coli crude extract, with unnatural orthogonal aminoacyl-tRNA synthetase and suppressor tRNA evolved from Methanocaldococcus jannaschii. The superfolder green fluorescent protein (sfGFP) and p-propargyloxyphenylalanine (pPaF) were used as the model protein and UNAA. The synthesis of unnatural sfGFPs was characterized by microplate spectrophotometer, affinity chromatography, and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). This protocol provides a detailed procedure guiding how to use the powerful CFPS system to synthesize unnatural proteins on demand.

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Pless, Stephan A., and Christopher A. Ahern. "Incorporation of Unnatural Amino Acids into Trimeric Ion Channels." Biophysical Journal 104, no. 2 (2013): 542a. http://dx.doi.org/10.1016/j.bpj.2012.11.3001.

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Strømgaard, Anne, Anders A. Jensen, and Kristian Strømgaard. "Site-Specific Incorporation of Unnatural Amino Acids into Proteins." ChemBioChem 5, no. 7 (2004): 909–16. http://dx.doi.org/10.1002/cbic.200400060.

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Drienovská, Ivana, Ana Rioz-Martínez, Apparao Draksharapu, and Gerard Roelfes. "Novel artificial metalloenzymes by in vivo incorporation of metal-binding unnatural amino acids." Chemical Science 6, no. 1 (2015): 770–76. http://dx.doi.org/10.1039/c4sc01525h.

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Tookmanian, Elise M., Edward E. Fenlon, and Scott H. Brewer. "Synthesis and protein incorporation of azido-modified unnatural amino acids." RSC Advances 5, no. 2 (2015): 1274–81. http://dx.doi.org/10.1039/c4ra14244f.

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Iida, Shin, Noriyuki Asakura, Kenji Tabata, Ichiro Okura, and Toshiaki Kamachi. "Incorporation of Unnatural Amino Acids into Cytochrome c3 and Specific Viologen Binding to the Unnatural Amino Acid." ChemBioChem 7, no. 12 (2006): 1853–55. http://dx.doi.org/10.1002/cbic.200600347.

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12

Rut, Wioletta, Mikolaj Zmudzinski, Scott J. Snipas, Miklos Bekes, Tony T. Huang, and Marcin Drag. "Engineered unnatural ubiquitin for optimal detection of deubiquitinating enzymes." Chemical Science 11, no. 23 (2020): 6058–69. http://dx.doi.org/10.1039/d0sc01347a.

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13

Rudack, Till, Christian Teuber, Marvin Scherlo, et al. "The Ras dimer structure." Chemical Science 12, no. 23 (2021): 8178–89. http://dx.doi.org/10.1039/d1sc00957e.

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By combining the incorporation of unnatural amino acids, click chemistry, FRET and EPR distance measurements, protein modeling and biomolecular simulations, we obtained an unambiguous Ras dimer structural model and disrupt the dimer by mutagenesis.

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14

Ugwumba, Isaac N., Kiyoshi Ozawa, Zhi-Qiang Xu, et al. "Improving a Natural Enzyme Activity through Incorporation of Unnatural Amino Acids." Journal of the American Chemical Society 133, no. 2 (2011): 326–33. http://dx.doi.org/10.1021/ja106416g.

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Wang, Feng, Scott Robbins, Jiantao Guo, Weijun Shen, and Peter G. Schultz. "Genetic Incorporation of Unnatural Amino Acids into Proteins in Mycobacterium tuberculosis." PLoS ONE 5, no. 2 (2010): e9354. http://dx.doi.org/10.1371/journal.pone.0009354.

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Liu, Wenshe, Ansgar Brock, Shuo Chen, Shuibing Chen, and Peter G. Schultz. "Genetic incorporation of unnatural amino acids into proteins in mammalian cells." Nature Methods 4, no. 3 (2007): 239–44. http://dx.doi.org/10.1038/nmeth1016.

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Ryu, Youngha, and Peter G. Schultz. "Efficient incorporation of unnatural amino acids into proteins in Escherichia coli." Nature Methods 3, no. 4 (2006): 263–65. http://dx.doi.org/10.1038/nmeth864.

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18

Wang, Qian, and Lei Wang. "New Methods Enabling Efficient Incorporation of Unnatural Amino Acids in Yeast." Journal of the American Chemical Society 130, no. 19 (2008): 6066–67. http://dx.doi.org/10.1021/ja800894n.

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19

Lee, Byeong Sung, Seunggun Shin, Jong Yeob Jeon, et al. "Incorporation of Unnatural Amino Acids in Response to the AGG Codon." ACS Chemical Biology 10, no. 7 (2015): 1648–53. http://dx.doi.org/10.1021/acschembio.5b00230.

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Lang, Kathrin, and Jason W. Chin. "Cellular Incorporation of Unnatural Amino Acids and Bioorthogonal Labeling of Proteins." Chemical Reviews 114, no. 9 (2014): 4764–806. http://dx.doi.org/10.1021/cr400355w.

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Won, Yumi, Amol D. Pagar, Mahesh D. Patil, Philip E. Dawson, and Hyungdon Yun. "Recent Advances in Enzyme Engineering through Incorporation of Unnatural Amino Acids." Biotechnology and Bioprocess Engineering 24, no. 4 (2019): 592–604. http://dx.doi.org/10.1007/s12257-019-0163-x.

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22

Bąchor, Urszula, Agnieszka Lizak, Remigiusz Bąchor та Marcin Mączyński. "5-Amino-3-methyl-Isoxazole-4-carboxylic Acid as a Novel Unnatural Amino Acid in the Solid Phase Synthesis of α/β-Mixed Peptides". Molecules 27, № 17 (2022): 5612. http://dx.doi.org/10.3390/molecules27175612.

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The hybrid peptides consisting of α and β-amino acids show great promise as peptidomimetics that can be used as therapeutic agents. Therefore, the development of new unnatural amino acids and the methods of their incorporation into the peptide chain is an important task. Here, we described our investigation of the possibility of 5-amino-3-methyl-isoxazole-4-carboxylic acid (AMIA) application in the solid phase peptide synthesis. This new unnatural β-amino acid, presenting various biological activities, was successfully coupled to a resin-bound peptide using different reaction conditions, including classical and ultrasonic agitated solid-phase synthesis. All the synthesized compounds were characterized by tandem mass spectrometry. The obtained results present the possibility of the application of this β-amino acid in the synthesis of a new class of bioactive peptides.

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Curnew, Leah Jane Fitzgerald, Kate McNicholas, Bridgette Green, et al. "Visualizing HCV Core Protein via Fluorescent Unnatural Amino Acid Incorporation." Proceedings 50, no. 1 (2020): 129. http://dx.doi.org/10.3390/proceedings2020050129.

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Introduction: Unnatural amino acids (UAAs) share the same basic structure as proteinogenic amino acids. However, UAAs permit additional functions and applications to proteins due to their different side chains. Recent UAA applications include using fluorescent UAAs to label proteins. The UAA system provides an alternative method to traditional protein labeling mechanisms (antibodies, GFP, and tags, such as HA and HIS), which can affect protein functionality and topology. The purpose of this study was to visualize the hepatitis C virus (HCV) core protein using the fluorescent UAA Anap (3-[(6-acetyl-2-naphthalenyl)amino]-L-alanine). Methods: Huh-7.5 cells were co-transfected with HCV core plasmids containing amber stop codons at various positions throughout the coding sequence and a second plasmid encoding the orthogonal tRNA/synthetase pair that facilitates Anap incorporation. Three days post transfection, cells were stained for core protein and lipid droplets (LDs) and visualized using immunofluorescence or confocal microscopy. Results: We have optimized transfection protocols for the efficient expression of the tRNA/synthetase pair required for Anap incorporation and are able to visualize our core mutant proteins containing Anap. We have successfully substituted Anap into 11 different positions within the core, including substitutions for tryptophan, tyrosine, and phenylalanine residues. In addition, we have shown that our core mutants associate with cellular LDs, suggesting that the incorporation of the UAA did not disrupt core protein expression, stability, or cellular localization. Conclusions: We have demonstrated the establishment of a UAA incorporation system in an HCV protein without any obvious impact on core protein function. The ability to label viral proteins using fluorescent UAAs eliminates the requirement of antibodies or tags for protein visualization. In conclusion, the UAA system is a useful method to study HCV proteins and can potentially be used to label viruses for live cell and animal studies.

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24

Jung, Jae-Eun, Sang Yeul Lee, Hyojin Park та ін. "Genetic incorporation of unnatural amino acids biosynthesized from α-keto acids by an aminotransferase". Chemical Science 5, № 5 (2014): 1881. http://dx.doi.org/10.1039/c3sc51617b.

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25

Minaba, Masaomi, and Yusuke Kato. "High-Yield, Zero-Leakage Expression System with a Translational Switch Using Site-Specific Unnatural Amino Acid Incorporation." Applied and Environmental Microbiology 80, no. 5 (2013): 1718–25. http://dx.doi.org/10.1128/aem.03417-13.

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ABSTRACTSynthetic biologists construct complex biological circuits by combinations of various genetic parts. Many genetic parts that are orthogonal to one another and are independent of existing cellular processes would be ideal for use in synthetic biology. However, our toolbox is still limited with respect to the bacteriumEscherichia coli, which is important for both research and industrial use. The site-specific incorporation of unnatural amino acids is a technique that incorporates unnatural amino acids into proteins using a modified exogenous aminoacyl-tRNA synthetase/tRNA pair that is orthogonal to any native pairs in a host and is independent from other cellular functions. Focusing on the orthogonality and independency that are suitable for the genetic parts, we designed novel AND gate and translational switches using the unnatural amino acid 3-iodo-l-tyrosine incorporation system inE. coli. A translational switch was turned on after addition of 3-iodo-l-tyrosine in the culture medium within minutes and allowed tuning of switchability and translational efficiency. As an application, we also constructed a gene expression system that produced large amounts of proteins under induction conditions and exhibited zero-leakage expression under repression conditions. Similar translational switches are expected to be applicable also for eukaryotes such as yeasts, nematodes, insects, mammalian cells, and plants.

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26

Stein, Alina, Alexandria Deliz Liang, Reyhan Sahin, and Thomas R. Ward. "Incorporation of metal-chelating unnatural amino acids into halotag for allylic deamination." Journal of Organometallic Chemistry 962 (March 2022): 122272. http://dx.doi.org/10.1016/j.jorganchem.2022.122272.

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Chen, Mingjie, Lei Cai, Zhengzhi Fang, Hong Tian, Xiangdong Gao, and Wenbing Yao. "Site-specific incorporation of unnatural amino acids into urate oxidase inEscherichia coli." Protein Science 17, no. 10 (2008): 1827–33. http://dx.doi.org/10.1110/ps.034587.108.

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Johnson, David B. F., Jianfeng Xu, Zhouxin Shen, et al. "RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites." Nature Chemical Biology 7, no. 11 (2011): 779–86. http://dx.doi.org/10.1038/nchembio.657.

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29

Xiao, Han, Abhishek Chatterjee, Sei-hyun Choi, Krishna M. Bajjuri, Subhash C. Sinha, and Peter G. Schultz. "Genetic Incorporation of Multiple Unnatural Amino Acids into Proteins in Mammalian Cells." Angewandte Chemie 125, no. 52 (2013): 14330–33. http://dx.doi.org/10.1002/ange.201308137.

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Xiao, Han, Abhishek Chatterjee, Sei-hyun Choi, Krishna M. Bajjuri, Subhash C. Sinha, and Peter G. Schultz. "Genetic Incorporation of Multiple Unnatural Amino Acids into Proteins in Mammalian Cells." Angewandte Chemie International Edition 52, no. 52 (2013): 14080–83. http://dx.doi.org/10.1002/anie.201308137.

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31

Ye, Shixin, Caroline Köhrer, Thomas Huber, et al. "Site-specific Incorporation of Keto Amino Acids into Functional G Protein-coupled Receptors Using Unnatural Amino Acid Mutagenesis." Journal of Biological Chemistry 283, no. 3 (2007): 1525–33. http://dx.doi.org/10.1074/jbc.m707355200.

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G protein-coupled receptors (GPCRs) are ubiquitous heptahelical transmembrane proteins involved in a wide variety of signaling pathways. The work described here on application of unnatural amino acid mutagenesis to two GPCRs, the chemokine receptor CCR5 (a major co-receptor for the human immunodeficiency virus) and rhodopsin (the visual photoreceptor), adds a new dimension to studies of GPCRs. We incorporated the unnatural amino acids p-acetyl-l-phenylalanine (Acp) and p-benzoyl-l-phenylalanine (Bzp) into CCR5 at high efficiency in mammalian cells to produce functional receptors harboring reactive keto groups at three specific positions. We obtained functional mutant CCR5, at levels up to ∼50% of wild type as judged by immunoblotting, cell surface expression, and ligand-dependent calcium flux. Rhodopsin containing Acp at three different sites was also purified in high yield (0.5–2 μg/107 cells) and reacted with fluorescein hydrazide in vitro to produce fluorescently labeled rhodopsin. The incorporation of reactive keto groups such as Acp or Bzp into GPCRs allows their reaction with different reagents to introduce a variety of spectroscopic and other probes. Bzp also provides the possibility of photo-cross-linking to identify precise sites of protein-protein interactions, including GPCR binding to G proteins and arrestins, and for understanding the molecular basis of ligand recognition by chemokine receptors.

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32

Zeynaloo, Elnaz, Elsayed M. Zahran, Yu-Ping Yang, et al. "Reagentless electrochemical biosensors through incorporation of unnatural amino acids on the protein structure." Biosensors and Bioelectronics 200 (March 2022): 113861. http://dx.doi.org/10.1016/j.bios.2021.113861.

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Rodriguez, E. A., H. A. Lester, and D. A. Dougherty. "In vivo incorporation of multiple unnatural amino acids through nonsense and frameshift suppression." Proceedings of the National Academy of Sciences 103, no. 23 (2006): 8650–55. http://dx.doi.org/10.1073/pnas.0510817103.

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Noren, C., S. Anthony-Cahill, M. Griffith, and P. Schultz. "A general method for site-specific incorporation of unnatural amino acids into proteins." Science 244, no. 4901 (1989): 182–88. http://dx.doi.org/10.1126/science.2649980.

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Maza, Johnathan C., Jaclyn R. McKenna, Benjamin K. Raliski, Matthew T. Freedman, and Douglas D. Young. "Synthesis and Incorporation of Unnatural Amino Acids To Probe and Optimize Protein Bioconjugations." Bioconjugate Chemistry 26, no. 9 (2015): 1884–89. http://dx.doi.org/10.1021/acs.bioconjchem.5b00424.

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Monahan, Sarah L., Henry A. Lester, and Dennis A. Dougherty. "Site-Specific Incorporation of Unnatural Amino Acids into Receptors Expressed in Mammalian Cells." Chemistry & Biology 10, no. 6 (2003): 573–80. http://dx.doi.org/10.1016/s1074-5521(03)00124-8.

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Wang, Jinfan, and Anthony C. Forster. "Ribosomal incorporation of unnatural amino acids: lessons and improvements from fast kinetics studies." Current Opinion in Chemical Biology 46 (October 2018): 180–87. http://dx.doi.org/10.1016/j.cbpa.2018.07.009.

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Hicks, Rickey P., Jayendra B. Bhonsle, Divakaramenon Venugopal, Brandon W. Koser, and Alan J. Magill. "De Novo Design of Selective Antibiotic Peptides by Incorporation of Unnatural Amino Acids." Journal of Medicinal Chemistry 50, no. 13 (2007): 3026–36. http://dx.doi.org/10.1021/jm061489v.

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Chollet, Andre, and Gerardo Turcatti. "ChemInform Abstract: Biosynthetic Incorporation of Unnatural Amino Acids into G Protein-Coupled Receptors." ChemInform 30, no. 51 (2010): no. http://dx.doi.org/10.1002/chin.199951288.

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Edan, Dawood Salim, Inkyung Choi, and Jungchan Park. "Establishment of a Selection System for the Site-Specific Incorporation of Unnatural Amino Acids into Protein." Korean Journal of Microbiology 50, no. 1 (2014): 1–7. http://dx.doi.org/10.7845/kjm.2014.4012.

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41

Hou, Jiaqi, Xinjie Chen, Nan Jiang, et al. "Toward efficient multiple-site incorporation of unnatural amino acids using cell-free translation system." Synthetic and Systems Biotechnology 7, no. 1 (2022): 522–32. http://dx.doi.org/10.1016/j.synbio.2021.12.007.

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Pastrnak, M. "Phage selection for site-specific incorporation of unnatural amino acids into proteins in vivo." Bioorganic & Medicinal Chemistry 9, no. 9 (2001): 2373–79. http://dx.doi.org/10.1016/s0968-0896(01)00157-2.

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Klarmann, George J., Brian M. Eisenhauer, Yi Zhang, et al. "Site- and subunit-specific incorporation of unnatural amino acids into HIV-1 reverse transcriptase." Protein Expression and Purification 38, no. 1 (2004): 37–44. http://dx.doi.org/10.1016/j.pep.2004.07.019.

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Katragadda, Madan, and John D. Lambris. "Expression of compstatin in Escherichia coli: Incorporation of unnatural amino acids enhances its activity." Protein Expression and Purification 47, no. 1 (2006): 289–95. http://dx.doi.org/10.1016/j.pep.2005.11.016.

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Oh, Su-Jin, Kyung-Ho Lee, Ho-Cheol Kim, Christy Catherine, Hyungdon Yun, and Dong-Myung Kim. "Translational incorporation of multiple unnatural amino acids in a cell-free protein synthesis system." Biotechnology and Bioprocess Engineering 19, no. 3 (2014): 426–32. http://dx.doi.org/10.1007/s12257-013-0849-4.

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Niu, Wei, and Jiantao Guo. "Expanding the chemistry of fluorescent protein biosensors through genetic incorporation of unnatural amino acids." Molecular BioSystems 9, no. 12 (2013): 2961. http://dx.doi.org/10.1039/c3mb70204a.

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Jones, Chloe M., Itthipol Sungwienwong, and E. James Petersson. "The Development of Intrinsically Fluorescent Unnatural Amino Acids for In Vivo Incorporation into Proteins." Biophysical Journal 116, no. 3 (2019): 473a. http://dx.doi.org/10.1016/j.bpj.2018.11.2555.

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48

Arthur, Isaac N., James E. Hennessy, Dharshana Padmakshan, et al. "In Situ Deprotection and Incorporation of Unnatural Amino Acids during Cell-Free Protein Synthesis." Chemistry - A European Journal 19, no. 21 (2013): 6824–30. http://dx.doi.org/10.1002/chem.201203923.

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Dippel, Andrew B., Gregory M. Olenginski, Nicole Maurici, Melanie T. Liskov, Scott H. Brewer, and Christine M. Phillips-Piro. "Probing the effectiveness of spectroscopic reporter unnatural amino acids: a structural study." Acta Crystallographica Section D Structural Biology 72, no. 1 (2016): 121–30. http://dx.doi.org/10.1107/s2059798315022858.

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The X-ray crystal structures of superfolder green fluorescent protein (sfGFP) containing the spectroscopic reporter unnatural amino acids (UAAs) 4-cyano-L-phenylalanine (pCNF) or 4-ethynyl-L-phenylalanine (pCCF) at two unique sites in the protein have been determined. These UAAs were genetically incorporated into sfGFP in a solvent-exposed loop region and/or a partially buried site on the β-barrel of the protein. The crystal structures containing the UAAs at these two sites permit the structural implications of UAA incorporation for the native protein structure to be assessed with high resolution and permit a direct correlation between the structure and spectroscopic data to be made. The structural implications were quantified by comparing the root-mean-square deviation (r.m.s.d.) between the crystal structure of wild-type sfGFP and the protein constructs containing either pCNF or pCCF in the local environment around the UAAs and in the overall protein structure. The results suggest that the selective placement of these spectroscopic reporter UAAs permits local protein environments to be studied in a relatively nonperturbative fashion with site-specificity.

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Zhou, Han, Jenny W. Cheung, Tomaya Carpenter, et al. "Enhancing the incorporation of lysine derivatives into proteins with methylester forms of unnatural amino acids." Bioorganic & Medicinal Chemistry Letters 30, no. 2 (2020): 126876. http://dx.doi.org/10.1016/j.bmcl.2019.126876.

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