201
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Izumi M, Oka Y, Okamoto R, Seko A, Takeda Y, Ito Y, Kajihara Y. Synthesis of Glc1
Man9
-Glycoprotein Probes by a Misfolding/Enzymatic Glucosylation/Misfolding Sequence. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511491] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Masayuki Izumi
- Department of Chemistry; Graduate School of Science; Osaka University; 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Yukiho Oka
- Department of Chemistry; Graduate School of Science; Osaka University; 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Ryo Okamoto
- Department of Chemistry; Graduate School of Science; Osaka University; 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Akira Seko
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST); 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Yoichi Takeda
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST); 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Yukishige Ito
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST); 2-1 Hirosawa, Wako Saitama 351-0198 Japan
- Synthetic Cellular Chemistry Laboratory; RIKEN; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Yasuhiro Kajihara
- Department of Chemistry; Graduate School of Science; Osaka University; 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST); 2-1 Hirosawa, Wako Saitama 351-0198 Japan
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202
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Izumi M, Oka Y, Okamoto R, Seko A, Takeda Y, Ito Y, Kajihara Y. Synthesis of Glc1Man9-Glycoprotein Probes by a Misfolding/Enzymatic Glucosylation/Misfolding Sequence. Angew Chem Int Ed Engl 2016; 55:3968-71. [PMID: 26890995 DOI: 10.1002/anie.201511491] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Indexed: 12/12/2022]
Abstract
Glycoproteins in non-native conformations are often toxic to cells and may cause diseases, thus the quality control (QC) system eliminates these unwanted species. Lectin chaperone calreticulin and glucosidase II, both of which recognize the Glc1 Man9 oligosaccharide on glycoproteins, are important components of the glycoprotein QC system. Reported herein is the preparation of Glc1 Man9 -glycoproteins in both native and non-native conformations by using the following sequence: misfolding of chemically synthesized Man9 -glycoprotein, enzymatic glucosylation, and another misfolding step. By using synthetic glycoprotein probes, calreticulin was found to bind preferentially to a hydrophobic non-native glycoprotein whereas glucosidase II activity was not affected by glycoprotein conformation. The results demonstrate the ability of chemical synthesis to deliver homogeneous glycoproteins in several non-native conformations for probing the glycoprotein QC system.
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Affiliation(s)
- Masayuki Izumi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yukiho Oka
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Akira Seko
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoichi Takeda
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yukishige Ito
- ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan. .,ERATO Ito glycotrilogy project Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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203
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Rasale DB, Konda M, Biswas S, Das AK. Controlling Peptide Self-Assembly through a Native Chemical Ligation/Desulfurization Strategy. Chem Asian J 2016; 11:926-35. [DOI: 10.1002/asia.201501458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Dnyaneshwar B. Rasale
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 452020 India
| | - Maruthi Konda
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 452020 India
| | - Sagar Biswas
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 452020 India
| | - Apurba K. Das
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 452020 India
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204
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Masuda K, Furumitsu M, Ooyama H, Iwakoshi-Ukena E, Ukena K. Synthesis of neurosecretory protein GM composed of 88 amino acid residues by native chemical ligation. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.01.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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205
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Wang YJ, Szantai-Kis DM, Petersson EJ. Semi-synthesis of thioamide containing proteins. Org Biomol Chem 2016; 13:5074-81. [PMID: 25811732 DOI: 10.1039/c5ob00224a] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our laboratory has shown that the thioamide, a single atom O-to-S substitution, can be a versatile fluorescence quenching probe that is minimally-perturbing when placed at many locations in a protein sequence. In order to make these and other thioamide experiments applicable to full-sized proteins, we have developed methods for incorporating thioamides by generating thiopeptide fragments through solid phase synthesis and ligating them to protein fragments expressed in E. coli. To install donor fluorophores, we have adapted unnatural amino acid mutagenesis methods, including the generation of new tRNA synthetases for the incorporation of small, intrinsically fluorescent amino acids. We have used a combination of these two methods, as well as chemoenzymatic protein modification, to efficiently install sidechain and backbone modifications to generate proteins labeled with fluorophore/thioamide pairs.
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Affiliation(s)
- Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
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206
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Behrendt R, White P, Offer J. Advances in Fmoc solid-phase peptide synthesis. J Pept Sci 2016; 22:4-27. [PMID: 26785684 PMCID: PMC4745034 DOI: 10.1002/psc.2836] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 10/20/2015] [Indexed: 12/13/2022]
Abstract
Today, Fmoc SPPS is the method of choice for peptide synthesis. Very-high-quality Fmoc building blocks are available at low cost because of the economies of scale arising from current multiton production of therapeutic peptides by Fmoc SPPS. Many modified derivatives are commercially available as Fmoc building blocks, making synthetic access to a broad range of peptide derivatives straightforward. The number of synthetic peptides entering clinical trials has grown continuously over the last decade, and recent advances in the Fmoc SPPS technology are a response to the growing demand from medicinal chemistry and pharmacology. Improvements are being continually reported for peptide quality, synthesis time and novel synthetic targets. Topical peptide research has contributed to a continuous improvement and expansion of Fmoc SPPS applications.
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Affiliation(s)
- Raymond Behrendt
- Novabiochem, Merck & CieIm Laternenacker 58200SchaffhausenSwitzerland
| | - Peter White
- Novabiochem, Merck Chemicals LtdPadge RoadBeestonNG9 2JRUK
| | - John Offer
- The Francis Crick Institute215 Euston RoadLondonNW1 2BEUK
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207
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Abstract
Oxazetidine assisted KAHA ligation was developed by the Bode group as an efficient peptide segment ligation strategy at native serine residues. This milestone achievement should enable the chemical synthesis of difficult-to-prepare proteins for biological studies.
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Affiliation(s)
- Yi-Ming Li
- School of Medical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China.
| | - Yi-Chao Huang
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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208
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Hayashi G, Sueoka T, Okamoto A. In vitro and in cell analysis of chemically synthesized histone H2A with multiple modifications. Chem Commun (Camb) 2016; 52:4999-5002. [DOI: 10.1039/c5cc10555b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The chemical synthetic route to histone H2A is described. An H2A–H2B dimer, histone octamer, and nucleosome were reconstituted with the synthetic H2A.
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Affiliation(s)
- Gosuke Hayashi
- Department of Chemistry and Biotechnology
- The University of Tokyo
- Bunkyo-ku
- Japan
| | - Takuma Sueoka
- Department of Chemistry and Biotechnology
- The University of Tokyo
- Bunkyo-ku
- Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology
- The University of Tokyo
- Bunkyo-ku
- Japan
- Address Research Center for Advanced Science and Technology
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209
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Cottam Jones JM, Harris PWR, Scanlon DB, Forbes BE, Brimble MA, Abell AD. Fluorescent IGF-II analogues for FRET-based investigations into the binding of IGF-II to the IGF-1R. Org Biomol Chem 2016; 14:2698-705. [DOI: 10.1039/c5ob02110c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Convergent-based synthesis of native IGF-II and two IGF-II analogues, with coumarin fluorescent probes incorporated at residues 19 and 28, and their use in FRET-based identification of interactions with the type 1 insulin-like growth factor receptor (IGF-IR).
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Affiliation(s)
| | - P. W. R. Harris
- School of Chemical Sciences
- The University of Auckland
- Auckland 1010
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
| | - D. B. Scanlon
- Department of Chemistry
- The University of Adelaide
- Adelaide 5001
- Australia
| | - B. E. Forbes
- School of Molecular and Biomedical Sciences
- The University of Adelaide
- Adelaide 5005
- Australia
- School of Medicine
| | - M. A. Brimble
- School of Chemical Sciences
- The University of Auckland
- Auckland 1010
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
| | - A. D. Abell
- Department of Chemistry
- The University of Adelaide
- Adelaide 5001
- Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)
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210
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Weidmann J, Dimitrijević E, Hoheisel JD, Dawson PE. Boc-SPPS: Compatible Linker for the Synthesis of Peptide o-Aminoanilides. Org Lett 2015; 18:164-7. [DOI: 10.1021/acs.orglett.5b03111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joachim Weidmann
- Division
of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
- Departments of Chemistry and Cell & Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Elena Dimitrijević
- Departments of Chemistry and Cell & Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jörg D. Hoheisel
- Division
of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Philip E. Dawson
- Departments of Chemistry and Cell & Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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211
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Brieke C, Kratzig V, Haslinger K, Winkler A, Cryle MJ. Rapid access to glycopeptide antibiotic precursor peptides coupled with cytochrome P450-mediated catalysis: towards a biomimetic synthesis of glycopeptide antibiotics. Org Biomol Chem 2015; 13:2012-21. [PMID: 25501135 DOI: 10.1039/c4ob02452d] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Understanding the mechanisms underpinning glycopeptide antibiotic biosynthesis is key to the future ability to reinvent these compounds. For effective in vitro characterization of the crucial later steps of the biosynthesis, facile access to a wide range of substrate peptides as their Coenzyme A (CoA) conjugates is essential. Here we report the development of a rapid route to glycopeptide precursor CoA conjugates that affords both high yields and excellent purities. This synthesis route is applicable to the synthesis of peptide CoA-conjugates containing racemization-prone arylglycine residues: such residues are hallmarks of non-ribosomal peptide synthesis and have previously been inaccessible to peptide synthesis using Fmoc-type chemistry. We have applied this route to generate glycopeptide precursor peptides in their carrier protein-bound form as substrates to explore the specificity of the first oxygenase enzyme from vancomycin biosynthesis (OxyBvan). Our results indicate that OxyBvan is a highly promiscuous catalyst for phenolic coupling of diverse glycopeptide precursors that accepts multiple carrier protein substrates, even on carrier protein domains from alternate glycopeptide biosynthetic machineries. These results represent the first important steps in the development of an in vitro biomimetic synthesis of modified glycopeptide aglycones.
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Affiliation(s)
- Clara Brieke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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212
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Moyle PM, Dai W, Liu TY, Hussein WM, Maruthayanar P, Wells JW, McMillan NA, Skwarczynski M, Toth I. Combined synthetic and recombinant techniques for the development of lipoprotein-based, self-adjuvanting vaccines targeting human papillomavirus type-16 associated tumors. Bioorg Med Chem Lett 2015; 25:5570-5. [DOI: 10.1016/j.bmcl.2015.10.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 11/28/2022]
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213
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Lichtenstein BR, Bialas C, Cerda JF, Fry BA, Dutton PL, Moser CC. Designing Light-Activated Charge-Separating Proteins with a Naphthoquinone Amino Acid. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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214
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Loibl SF, Harpaz Z, Seitz O. A Type of Auxiliary for Native Chemical Peptide Ligation beyond Cysteine and Glycine Junctions. Angew Chem Int Ed Engl 2015; 54:15055-9. [DOI: 10.1002/anie.201505274] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/17/2015] [Indexed: 11/11/2022]
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215
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Loibl SF, Harpaz Z, Seitz O. Ein Auxiliartyp für die native chemische Peptidligation jenseits von Cystein und Glycin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505274] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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216
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Mitchell NJ, Malins LR, Liu X, Thompson RE, Chan B, Radom L, Payne RJ. Rapid Additive-Free Selenocystine–Selenoester Peptide Ligation. J Am Chem Soc 2015; 137:14011-4. [DOI: 10.1021/jacs.5b07237] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Lara R. Malins
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Xuyu Liu
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Robert E. Thompson
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bun Chan
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Leo Radom
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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217
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Wang J, Liao Y, Shao S. An NBD-based Fluorescent Probe with High Selectivity to Cysteine over Homocysteine under Neutral Physiological Conditions. CHEM LETT 2015. [DOI: 10.1246/cl.150544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jiamin Wang
- Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences
- University of Chinese Academy of Sciences
| | - Yuan Liao
- Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences
- University of Chinese Academy of Sciences
| | - Shijun Shao
- Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences
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218
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Sun XH, Yu HZ, Pei SQ, Dang ZM. Theoretical investigations on the thiol–thioester exchange steps of different thioesters. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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219
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Reinhardt U, Lotze J, Mörl K, Beck-Sickinger AG, Seitz O. Rapid Covalent Fluorescence Labeling of Membrane Proteins on Live Cells via Coiled-Coil Templated Acyl Transfer. Bioconjug Chem 2015; 26:2106-17. [PMID: 26367072 DOI: 10.1021/acs.bioconjchem.5b00387] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fluorescently labeled proteins enable the microscopic imaging of protein localization and function in live cells. In labeling reactions targeted against specific tag sequences, the size of the fluorophore-tag is of major concern. The tag should be small to prevent interference with protein function. Furthermore, rapid and covalent labeling methods are desired to enable the analysis of fast biological processes. Herein, we describe the development of a method in which the formation of a parallel coiled coil triggers the transfer of a fluorescence dye from a thioester-linked coil peptide conjugate onto a cysteine-modified coil peptide. This labeling method requires only small tag sequences (max 23 aa) and occurs with high tag specificity. We show that size matching of the coil peptides and a suitable thioester reactivity allow the acyl transfer reaction to proceed within minutes (rather than hours). We demonstrate the versatility of this method by applying it to the labeling of different G-protein coupled membrane receptors including the human neuropeptide Y receptors 1, 2, 4, 5, the neuropeptide FF receptors 1 and 2, and the dopamine receptor 1. The labeled receptors are fully functional and able to bind the respective ligand with high affinity. Activity is not impaired as demonstrated by activation, internalization, and recycling experiments.
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Affiliation(s)
- Ulrike Reinhardt
- Institut für Chemie, Humboldt-Universität zu Berlin , Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
| | - Jonathan Lotze
- Institut für Biochemie, Universität Leipzig , Brüderstrasse 34, D-04103 Leipzig, Germany
| | - Karin Mörl
- Institut für Biochemie, Universität Leipzig , Brüderstrasse 34, D-04103 Leipzig, Germany
| | | | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin , Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
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220
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Todorovski T, Suñol D, Riera A, Macias MJ. Addition of HOBt improves the conversion of thioester-Amine chemical ligation. Biopolymers 2015; 104:693-702. [PMID: 26396113 DOI: 10.1002/bip.22745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/10/2015] [Accepted: 09/18/2015] [Indexed: 11/07/2022]
Abstract
The syntheses of large peptides and of those containing non-natural amino acids can be facilitated by the application of convergent approaches, dissecting the native sequence into segments connected through a ligation reaction. We describe an improvement of the ligation protocol used to prepare peptides and proteins without cysteine residues at the ligation junction. We have found that the addition of HOBt to the ligation, improves the conversion of the ligation reaction without affecting the epimerization rate or chemoselectivity, and it can be efficiently used with peptides containing phosphorylated amino acids.
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Affiliation(s)
- Toni Todorovski
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - David Suñol
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.,Departament de Química Orgànica, University of Barcelona, Martí i Franquès, 1, Barcelona, 08028, Spain
| | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys, Barcelona, 23 08010, Spain
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221
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Terrier VP, Adihou H, Arnould M, Delmas AF, Aucagne V. A straightforward method for automated Fmoc-based synthesis of bio-inspired peptide crypto-thioesters. Chem Sci 2015; 7:339-345. [PMID: 29861986 PMCID: PMC5952550 DOI: 10.1039/c5sc02630j] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/22/2015] [Indexed: 01/19/2023] Open
Abstract
A bio-inspired method for the synthesis of peptide thioester surrogates for native chemical ligation was developed. The process can be fully automated and does not require postsynthetic steps.
Despite recent advances, the direct Fmoc-based solid phase synthesis of peptide α-thioesters for the convergent synthesis of proteins via native chemical ligation (NCL) remains a challenge in the field. We herein report a simple and general methodology, enabling access to peptide thioester surrogates. A novel C-terminal N-(2-hydroxybenzyl)cysteine thioesterification device based on an amide-to-thioester rearrangement was developed, and the resulting peptide crypto-thioesters can be directly used in NCL reactions with fast N → S shift kinetics at neutral pH. These fast kinetics arise from our bio-inspired design, via intein-like intramolecular catalysis. Due to a well-positioned phenol moiety, an impressive >50 fold increase in the kinetic rate is observed compared to an O-methylated derivative. Importantly, the synthesis of this new device can be fully automated using inexpensive commercially available materials and does not require any post-synthetic steps prior to NCL. We successfully applied this new method to the synthesis of two long naturally-occurring cysteine-rich peptide sequences.
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Affiliation(s)
- Victor P Terrier
- Centre de Biophysique Moléculaire , CNRS UPR 4301 , Rue Charles Sadron , 45071 Orléans Cedex 2 , France .
| | - Hélène Adihou
- Centre de Biophysique Moléculaire , CNRS UPR 4301 , Rue Charles Sadron , 45071 Orléans Cedex 2 , France .
| | - Mathieu Arnould
- Centre de Biophysique Moléculaire , CNRS UPR 4301 , Rue Charles Sadron , 45071 Orléans Cedex 2 , France .
| | - Agnès F Delmas
- Centre de Biophysique Moléculaire , CNRS UPR 4301 , Rue Charles Sadron , 45071 Orléans Cedex 2 , France .
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire , CNRS UPR 4301 , Rue Charles Sadron , 45071 Orléans Cedex 2 , France .
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222
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Lichtenstein BR, Bialas C, Cerda JF, Fry BA, Dutton PL, Moser CC. Designing Light-Activated Charge-Separating Proteins with a Naphthoquinone Amino Acid. Angew Chem Int Ed Engl 2015; 54:13626-9. [PMID: 26366882 DOI: 10.1002/anie.201507094] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 11/09/2022]
Abstract
The first principles design of manmade redox-protein maquettes is used to clarify the physical/chemical engineering supporting the mechanisms of natural enzymes with a view to recapitulate and surpass natural performance. Herein, we use intein-based protein semisynthesis to pair a synthetic naphthoquinone amino acid (Naq) with histidine-ligated photoactive metal-tetrapyrrole cofactors, creating a 100 μs photochemical charge separation unit akin to photosynthetic reaction centers. By using propargyl groups to protect the redox-active para-quinone during synthesis and assembly while permitting selective activation, we gain the ability to employ the quinone amino acid redox cofactor with the full set of natural amino acids in protein design. Direct anchoring of quinone to the protein backbone permits secure and adaptable control of intraprotein electron-tunneling distances and rates.
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Affiliation(s)
- Bruce R Lichtenstein
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059 (USA).,Present address: Max Planck Institute for Developmental Biology, Tübingen, 72076 (Germany)
| | - Chris Bialas
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059 (USA)
| | - José F Cerda
- Department of Chemistry, St. Joseph's University, Philadelphia, PA 19131 (USA)
| | - Bryan A Fry
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059 (USA)
| | - P Leslie Dutton
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059 (USA)
| | - Christopher C Moser
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059 (USA).
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223
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Han C, Pao KC, Kazlauskaite A, Muqit MMK, Virdee S. A Versatile Strategy for the Semisynthetic Production of Ser65 Phosphorylated Ubiquitin and Its Biochemical and Structural Characterisation. Chembiochem 2015; 16:1574-9. [PMID: 26010437 PMCID: PMC4581463 DOI: 10.1002/cbic.201500185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/22/2015] [Indexed: 11/10/2022]
Abstract
Ubiquitin phosphorylation is emerging as an important regulatory layer in the ubiquitin system. This is exemplified by the phosphorylation of ubiquitin on Ser65 by the Parkinson's disease-associated kinase PINK1, which mediates the activation of the E3 ligase Parkin. Additional phosphorylation sites on ubiquitin might also have important cellular roles. Here we report a versatile strategy for preparing phosphorylated ubiquitin. We biochemically and structurally characterise semisynthetic phospho-Ser65-ubiquitin. Unexpectedly, we observed disulfide bond formation between ubiquitin molecules, and hence a novel crystal form. The method outlined provides a direct approach to study the combinatorial effects of phosphorylation on ubiquitin function. Our analysis also suggests that disulfide engineering of ubiquitin could be a useful strategy for obtaining alternative crystal forms of ubiquitin species thereby facilitating structural validation.
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Affiliation(s)
- Cong Han
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK)
| | - Kuan-Chuan Pao
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK)
| | - Agne Kazlauskaite
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK)
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK)
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK).
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224
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Pardo A, Hogenauer TJ, Cai Z, Vellucci JA, Castillo EM, Dirk CW, Franz AH, Michael K. Efficient Photochemical Synthesis of Peptide-α-Phenylthioesters. Chembiochem 2015; 16:1884-1889. [DOI: 10.1002/cbic.201500266] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Indexed: 01/16/2023]
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225
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Translocation of Non-Canonical Polypeptides into Cells Using Protective Antigen. Sci Rep 2015; 5:11944. [PMID: 26178180 PMCID: PMC4503955 DOI: 10.1038/srep11944] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 04/09/2015] [Indexed: 11/09/2022] Open
Abstract
A variety of pathogenic bacteria infect host eukaryotic cells using protein toxins, which enter the cytosol and exert their cytotoxic effects. Anthrax lethal toxin, for example, utilizes the membrane-spanning translocase, protective antigen (PA) pore, to deliver the protein toxin lethal factor (LF) from the endosome into the cytosol of cells. Previous work has investigated the delivery of natural peptides and enzymatic domains appended to the C-terminus of the PA-binding domain of lethal factor (LFN) into the cytosol via PA pore. Here, we move beyond natural amino acids and systematically investigate the translocation of polypeptide cargo containing non-canonical amino acids and functionalities through PA pore. Our results indicate translocation is not perturbed with alterations to the peptide backbone or side-chain. Moreover, despite their structural complexity, we found that the small molecule drugs, doxorubicin and monomethyl auristatin F (MMAF) translocated efficiently through PA pore. However, we found cyclic peptides and the small molecule drug docetaxel abrogated translocation due to their large size and structural rigidity. For cargos that reached the cytosol, we demonstrated that each remained intact after translocation. These studies show PA is capable of translocating non-canonical cargo provided it is in a conformational state conducive for passage through the narrow pore.
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226
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Raibaut L, Drobecq H, Melnyk O. Selectively Activatable Latent Thiol and Selenolesters Simplify the Access to Cyclic or Branched Peptide Scaffolds. Org Lett 2015; 17:3636-9. [DOI: 10.1021/acs.orglett.5b01817] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Laurent Raibaut
- UMR CNRS
8161 Pasteur Institute of Lille, Univ Lille, 1 rue du Pr Calmette, 59021 Lille, France
| | - Hervé Drobecq
- UMR CNRS
8161 Pasteur Institute of Lille, Univ Lille, 1 rue du Pr Calmette, 59021 Lille, France
| | - Oleg Melnyk
- UMR CNRS
8161 Pasteur Institute of Lille, Univ Lille, 1 rue du Pr Calmette, 59021 Lille, France
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227
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Kwon B, Tietze D, White PB, Liao SY, Hong M. Chemical ligation of the influenza M2 protein for solid-state NMR characterization of the cytoplasmic domain. Protein Sci 2015; 24:1087-99. [PMID: 25966817 PMCID: PMC4500309 DOI: 10.1002/pro.2690] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 04/13/2015] [Accepted: 04/24/2015] [Indexed: 12/17/2022]
Abstract
Solid-state NMR-based structure determination of membrane proteins and large protein complexes faces the challenge of limited spectral resolution when the proteins are uniformly (13)C-labeled. A strategy to meet this challenge is chemical ligation combined with site-specific or segmental labeling. While chemical ligation has been adopted in NMR studies of water-soluble proteins, it has not been demonstrated for membrane proteins. Here we show chemical ligation of the influenza M2 protein, which contains a transmembrane (TM) domain and two extra-membrane domains. The cytoplasmic domain, which contains an amphipathic helix (AH) and a cytoplasmic tail, is important for regulating virus assembly, virus budding, and the proton channel activity. A recent study of uniformly (13)C-labeled full-length M2 by spectral simulation suggested that the cytoplasmic tail is unstructured. To further test this hypothesis, we conducted native chemical ligation of the TM segment and part of the cytoplasmic domain. Solid-phase peptide synthesis of the two segments allowed several residues to be labeled in each segment. The post-AH cytoplasmic residues exhibit random-coil chemical shifts, low bond order parameters, and a surface-bound location, thus indicating that this domain is a dynamic random coil on the membrane surface. Interestingly, the protein spectra are similar between a model membrane and a virus-mimetic membrane, indicating that the structure and dynamics of the post-AH segment is insensitive to the lipid composition. This chemical ligation approach is generally applicable to medium-sized membrane proteins to provide site-specific structural constraints, which complement the information obtained from uniformly (13)C, (15)N-labeled proteins.
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Affiliation(s)
- Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Daniel Tietze
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Paul B White
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Shu Y Liao
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of TechnologyCambridge, Massachusetts, 02139
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228
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Desmet R, Pauzuolis M, Boll E, Drobecq H, Raibaut L, Melnyk O. Synthesis of Unprotected Linear or Cyclic O-Acyl Isopeptides in Water Using Bis(2-sulfanylethyl)amido Peptide Ligation. Org Lett 2015; 17:3354-7. [PMID: 26075704 DOI: 10.1021/acs.orglett.5b01614] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
SEA ligation proceeds chemoselectively at pH 3, i.e., at a pH where the O-acyl isopeptides are protected by protonation. This property was used for synthesizing unprotected O-acyl isopeptides in water, starting from peptide segments which are easily accessible by the Fmoc SPPS.
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Affiliation(s)
- Rémi Desmet
- UMR CNRS 8161, Université Lille, Pasteur Institute of Lille 59021 Lille, France
| | - Mindaugas Pauzuolis
- UMR CNRS 8161, Université Lille, Pasteur Institute of Lille 59021 Lille, France
| | - Emmanuelle Boll
- UMR CNRS 8161, Université Lille, Pasteur Institute of Lille 59021 Lille, France
| | - Hervé Drobecq
- UMR CNRS 8161, Université Lille, Pasteur Institute of Lille 59021 Lille, France
| | - Laurent Raibaut
- UMR CNRS 8161, Université Lille, Pasteur Institute of Lille 59021 Lille, France
| | - Oleg Melnyk
- UMR CNRS 8161, Université Lille, Pasteur Institute of Lille 59021 Lille, France
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229
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Janssen BMG, van Ommeren SPFI, Merkx M. Efficient Synthesis of Peptide and Protein Functionalized Pyrrole-Imidazole Polyamides Using Native Chemical Ligation. Int J Mol Sci 2015; 16:12631-47. [PMID: 26053396 PMCID: PMC4490465 DOI: 10.3390/ijms160612631] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/25/2015] [Accepted: 05/28/2015] [Indexed: 01/02/2023] Open
Abstract
The advancement of DNA-based bionanotechnology requires efficient strategies to functionalize DNA nanostructures in a specific manner with other biomolecules, most importantly peptides and proteins. Common DNA-functionalization methods rely on laborious and covalent conjugation between DNA and proteins or peptides. Pyrrole-imidazole (Py-Im) polyamides, based on natural minor groove DNA-binding small molecules, can bind to DNA in a sequence specific fashion. In this study, we explore the use of Py-Im polyamides for addressing proteins and peptides to DNA in a sequence specific and non-covalent manner. A generic synthetic approach based on native chemical ligation was established that allows efficient conjugation of both peptides and recombinant proteins to Py-Im polyamides. The effect of Py-Im polyamide conjugation on DNA binding was investigated by Surface Plasmon Resonance (SPR). Although the synthesis of different protein-Py-Im-polyamide conjugates was successful, attenuation of DNA affinity was observed, in particular for the protein-Py-Im-polyamide conjugates. The practical use of protein-Py-Im-polyamide conjugates for addressing DNA structures in an orthogonal but non-covalent manner, therefore, remains to be established.
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Affiliation(s)
- Brian M G Janssen
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
| | - Sven P F I van Ommeren
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, The Netherlands.
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230
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Blanco-Canosa JB, Nardone B, Albericio F, Dawson PE. Chemical Protein Synthesis Using a Second-Generation N-Acylurea Linker for the Preparation of Peptide-Thioester Precursors. J Am Chem Soc 2015; 137:7197-209. [DOI: 10.1021/jacs.5b03504] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Brunello Nardone
- Departments
of Chemistry and Biology, University of Salerno, Via Giovanni
Paolo II 132, Fisciano 84084, Italy
| | - Fernando Albericio
- Department
of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, Barcelona 08028, Spain
| | - Philip E. Dawson
- Department
of Chemistry, The Scripps Research Institute (TSRI), 10550 N. Torrey
Pines Road, La Jolla, California 92037, United States
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231
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Reimann O, Glanz M, Hackenberger CP. Native chemical ligation between asparagine and valine: Application and limitations for the synthesis of tri-phosphorylated C-terminal tau. Bioorg Med Chem 2015; 23:2890-4. [DOI: 10.1016/j.bmc.2015.03.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/05/2015] [Accepted: 03/10/2015] [Indexed: 12/29/2022]
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232
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Niu LY, Chen YZ, Zheng HR, Wu LZ, Tung CH, Yang QZ. Design strategies of fluorescent probes for selective detection among biothiols. Chem Soc Rev 2015; 44:6143-60. [PMID: 26027649 DOI: 10.1039/c5cs00152h] [Citation(s) in RCA: 543] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Simple thiol derivatives, such as cysteine (Cys), homocysteine (Hcy), and glutathione (GSH), play key roles in biological processes, and the fluorescent probes to detect such thiols in vivo selectively with high sensitivity and fast response times are critical for understanding their numerous functions. However, the similar structures and reactivities of these thiols pose considerable challenges to the development of such probes. This review focuses on various strategies for the design of fluorescent probes for the selective detection of biothiols. We classify the fluorescent probes for discrimination among biothiols according to reaction types between the probes and thiols such as cyclization with aldehydes, conjugate addition-cyclization with acrylates, native chemical ligation, and aromatic substitution-rearrangement.
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Affiliation(s)
- Li-Ya Niu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
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233
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Koniev O, Wagner A. Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation. Chem Soc Rev 2015; 44:5495-551. [PMID: 26000775 DOI: 10.1039/c5cs00048c] [Citation(s) in RCA: 391] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.
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Affiliation(s)
- Oleksandr Koniev
- Laboratory of Functional Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg, 74 Route du Rhin, 67401 Illkirch-Graffenstaden, France.
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234
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Yang R, Bi X, Li F, Cao Y, Liu CF. Native chemical ubiquitination using a genetically incorporated azidonorleucine. Chem Commun (Camb) 2015; 50:7971-4. [PMID: 24915456 DOI: 10.1039/c4cc03721a] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A robust chemical ubiquitination method was developed. The method employed a genetically incorporated azidonorleucine as an orthogonal lysine precursor for the installation of a Gly residue bearing an Nα-auxiliary which mediated the ligation between ubiquitin(1-75)-thioester and the target protein. To demonstrate our methodology, a model protein, K48-linked diubiquitin, was synthesized with an overall yield of 35%.
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Affiliation(s)
- Renliang Yang
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.
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235
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Chen M, Heimer P, Imhof D. Synthetic strategies for polypeptides and proteins by chemical ligation. Amino Acids 2015; 47:1283-99. [DOI: 10.1007/s00726-015-1982-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/02/2015] [Indexed: 11/30/2022]
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236
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Saito F, Noda H, Bode JW. Critical evaluation and rate constants of chemoselective ligation reactions for stoichiometric conjugations in water. ACS Chem Biol 2015; 10:1026-33. [PMID: 25572124 DOI: 10.1021/cb5006728] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Chemoselective ligation reactions have contributed immensely to the development of organic synthesis and chemical biology. However, the ligation of stoichiometric amounts of large molecules for applications such as protein-protein conjugates is still challenging. Conjugation reactions need to be fast enough to proceed under dilute conditions and chemoselective in the presence of unprotected functional groups; the starting materials and products must be stable under the reaction conditions. To compare known ligation reactions for their suitability under these conditions, we determined the second-order rate constants of ligation reactions using peptide substrates with unprotected functional groups. The reaction conditions, the chemoselectivity of the reactions, and the stability of the starting materials and products were carefully evaluated. In some cases, the stability could be improved by modifying the substrate structure. These data obtained under the ligation conditions provide a useful guide to choose an appropriate ligation reaction for synthesis of large molecules by covalent ligation reactions of unprotected substrates in water.
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Affiliation(s)
- Fumito Saito
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Hidetoshi Noda
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Jeffrey W. Bode
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
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237
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Nadler C, Nadler A, Hansen C, Diederichsen U. A Photocleavable Auxiliary for Extended Native Chemical Ligation. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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238
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Panda SS, Jones RA, Hall CD, Katritzky AR. Applications of Chemical Ligation in Peptide Synthesis via Acyl Transfer. Top Curr Chem (Cham) 2015; 362:229-65. [PMID: 25805142 DOI: 10.1007/128_2014_608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The utility of native chemical ligation (NCL) in the solution or solid phase synthesis of peptides, cyclic peptides, glycopeptides, and neoglycoconjugates is reviewed. In addition, the mechanistic details of inter- or intra-molecular NCLs are discussed from experimental and computational points of view.
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Affiliation(s)
- Siva S Panda
- Department of Chemistry, Center for Heterocyclic Compounds, University of Florida, Gainesville, FL, 32611-7200, USA,
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239
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Tsuda S, Yoshiya T, Mochizuki M, Nishiuchi Y. Synthesis of Cysteine-Rich Peptides by Native Chemical Ligation without Use of Exogenous Thiols. Org Lett 2015; 17:1806-9. [DOI: 10.1021/acs.orglett.5b00624] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shugo Tsuda
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan
| | - Taku Yoshiya
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan
| | | | - Yuji Nishiuchi
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan
- Graduate
School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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240
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Holt M, Muir T. Application of the protein semisynthesis strategy to the generation of modified chromatin. Annu Rev Biochem 2015; 84:265-90. [PMID: 25784050 DOI: 10.1146/annurev-biochem-060614-034429] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Histone proteins are subject to a host of posttranslational modifications (PTMs) that modulate chromatin structure and function. Such control is achieved by the direct alteration of the intrinsic physical properties of the chromatin fiber or by regulating the recruitment and activity of a host of trans-acting nuclear factors. The sheer number of histone PTMs presents a formidable barrier to understanding the molecular mechanisms at the heart of epigenetic regulation of eukaryotic genomes. One aspect of this multifarious problem, namely how to access homogeneously modified chromatin for biochemical studies, is well suited to the sensibilities of the organic chemist. Indeed, recent years have witnessed a critical role for synthetic protein chemistry methods in generating the raw materials needed for studying how histone PTMs regulate chromatin biochemistry. This review focuses on what is arguably the most powerful, and widely employed, of these chemical strategies, namely histone semisynthesis via the chemical ligation of peptide fragments.
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Affiliation(s)
- Matthew Holt
- Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544; ,
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241
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Deng FK. Ultrafiltration, a useful method for isolation of intermediates in native chemical ligation exemplified with the total synthesis of Sortase AΔN59. J Pept Sci 2015; 21:257-64. [PMID: 25754699 DOI: 10.1002/psc.2745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 12/23/2014] [Accepted: 12/23/2014] [Indexed: 11/07/2022]
Abstract
In this paper, ultrafiltration was employed to facilitate the isolation of intermediates in native chemical ligation. Depending on the molecular weight cutoff of the membrane used, molecules with different sizes could be purified, separated, or concentrated by the ultrafiltration process. Total chemical synthesis of the polypeptide chain of the enzyme Sortase AΔN59 was used as an example of the application of ultrafiltration in chemical protein synthesis. Sortase A is a ligase that catalyzes transpeptidation reactions between proteins that have C-terminal LPXTG recognition sequence and Gly5- on the peptidoglycan of bacterial cell walls. Ultrafiltration technique facilitated synthesis of Sortase AΔN59 and was a promising tool in isolation of intermediates in native chemical ligation.
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Affiliation(s)
- Fang-kun Deng
- Department of Chemistry, The University of Chicago, 929 East 57th street, Chicago, IL, 60615, USA; Department of Biochemistry, School of Medicine Room1017, Jinan University, Huangpu West Road 601, Tianhe District, Guangzhou, Guangdong Province, 510000, China
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242
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Izumi M, Dedola S, Ito Y, Kajihara Y. Chemical Synthesis of Homogeneous Glycoproteins for the Study of Glycoprotein Quality Control System. Isr J Chem 2015. [DOI: 10.1002/ijch.201400154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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243
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Tailhades J, Patil NA, Hossain MA, Wade JD. Intramolecular acyl transfer in peptide and protein ligation and synthesis. J Pept Sci 2015; 21:139-47. [DOI: 10.1002/psc.2749] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/25/2014] [Accepted: 12/27/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Julien Tailhades
- The Florey Institute of Neuroscience and Mental Health; University of Melbourne; Victoria 3010 Australia
| | - Nitin A. Patil
- The Florey Institute of Neuroscience and Mental Health; University of Melbourne; Victoria 3010 Australia
- School of Chemistry; University of Melbourne; Victoria 3010 Australia
| | - Mohammed Akhter Hossain
- The Florey Institute of Neuroscience and Mental Health; University of Melbourne; Victoria 3010 Australia
- School of Chemistry; University of Melbourne; Victoria 3010 Australia
| | - John D. Wade
- The Florey Institute of Neuroscience and Mental Health; University of Melbourne; Victoria 3010 Australia
- School of Chemistry; University of Melbourne; Victoria 3010 Australia
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244
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Brimble MA, Edwards PJ, Harris PWR, Norris GE, Patchett ML, Wright TH, Yang SH, Carley SE. Synthesis of the Antimicrobial S-Linked Glycopeptide, Glycocin F. Chemistry 2015; 21:3556-61. [DOI: 10.1002/chem.201405692] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 12/23/2022]
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245
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Boll E, Drobecq H, Ollivier N, Blanpain A, Raibaut L, Desmet R, Vicogne J, Melnyk O. One-pot chemical synthesis of small ubiquitin-like modifier protein-peptide conjugates using bis(2-sulfanylethyl)amido peptide latent thioester surrogates. Nat Protoc 2015; 10:269-92. [PMID: 25591010 DOI: 10.1038/nprot.2015.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Small ubiquitin-like modifier (SUMO) post-translational modification (PTM) of proteins has a crucial role in the regulation of important cellular processes. This protocol describes the chemical synthesis of functional SUMO-peptide conjugates. The two crucial stages of this protocol are the solid-phase synthesis of peptide segments derivatized by thioester or bis(2-sulfanylethyl)amido (SEA) latent thioester functionalities and the one-pot assembly of the SUMO-peptide conjugate by a sequential native chemical ligation (NCL)/SEA native peptide ligation reaction sequence. This protocol also enables the isolation of a SUMO SEA latent thioester, which can be attached to a target peptide or protein in a subsequent step. It is compatible with 9-fluorenylmethoxycarbonyl (Fmoc) chemistry, and it gives access to homogeneous, reversible and functional SUMO conjugates that are not easily produced using living systems. The synthesis of SUMO-peptide conjugates on a milligram scale takes 20 working days.
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Affiliation(s)
- Emmanuelle Boll
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Hervé Drobecq
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Nathalie Ollivier
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Annick Blanpain
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Laurent Raibaut
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Rémi Desmet
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Jérôme Vicogne
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Oleg Melnyk
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
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246
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Schmalisch J, Seitz O. Acceleration of thiol additive-free native chemical ligation by intramolecular S → S acyl transfer. Chem Commun (Camb) 2015; 51:7554-7. [DOI: 10.1039/c5cc01447f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The old dog and a new trick; mercaptopropionylcysteine (MPA–Cys) peptide thioesters show a surprisingly high reactivity in native chemical ligation (NCL) and allow thiol-additive free reactions. This facilitates sequential NCL reactions and ligation–desulfurization reactions in one-pot formats. The synthetic utility is demonstrated by the synthesis of a SH3 domain.
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Affiliation(s)
- J. Schmalisch
- Humboldt-Universität zu Berlin
- Institut für Chemie
- 12489 Berlin
- Germany
| | - O. Seitz
- Humboldt-Universität zu Berlin
- Institut für Chemie
- 12489 Berlin
- Germany
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247
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Malins LR, Payne RJ. Synthetic Amino Acids for Applications in Peptide Ligation–Desulfurization Chemistry. Aust J Chem 2015. [DOI: 10.1071/ch14568] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Native chemical ligation is a powerful tool for the convergent assembly of homogeneous peptide and protein targets from unprotected peptide fragments. The method involves the chemoselective coupling of a peptide thioester with a peptide bearing an N-terminal cysteine (Cys) residue and is mediated by the nucleophilic Cys thiol functionality. A widely adopted extension of the technique for the disconnection of protein targets at alanine (Ala) ligation junctions has been the application of post-ligation desulfurization protocols for the mild removal of the Cys thiol moiety. Recently, attention has turned to the construction of synthetic amino acid building blocks bearing suitably positioned β-, γ-, or δ-thiol ligation auxiliaries with a view to expanding the scope of the ligation–desulfurization manifold. To date, several thiol-derived amino acids have been prepared, greatly increasing the generality and flexibility of chemoselective ligation technologies for the chemical synthesis of diverse protein targets. This review will highlight the current synthetic approaches to these important amino acid building blocks.
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248
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Cowper B, Sze TM, Premdjee B, Bongat White AF, Hacking A, Macmillan D. Examination of mercaptobenzyl sulfonates as catalysts for native chemical ligation: application to the assembly of a glycosylated Glucagon-Like Peptide 1 (GLP-1) analogue. Chem Commun (Camb) 2015; 51:3208-10. [DOI: 10.1039/c4cc09502b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
3/4-Mercaptobenzyl sulfonates were investigated as aryl thiol catalysts for native chemical ligation (NCL).
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Affiliation(s)
- Ben Cowper
- Department of Chemistry
- University College London
- London
- UK
| | - Tsz Mei Sze
- Department of Chemistry
- University College London
- London
- UK
| | | | | | - Andrew Hacking
- Dextra Laboratories Ltd
- Science and Technology Centre
- Earley Gate
- Reading
- UK
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249
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Pan J, Zhang Y, Xu J, Liu J, Zeng L, Bao GM. A smart fluorescent probe for simultaneous detection of GSH and Cys in human plasma and cells. RSC Adv 2015. [DOI: 10.1039/c5ra21025a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A smart fluorescent probe was developed to simultaneously detect Cys and GSH in different emission channel with low detection limit.
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Affiliation(s)
- Jian Pan
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion
- School of Chemistry & Chemical Engineering
- Tianjin University of Technology
- Tianjin
- P. R. China
| | - Yue Zhang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion
- School of Chemistry & Chemical Engineering
- Tianjin University of Technology
- Tianjin
- P. R. China
| | - Junchao Xu
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion
- School of Chemistry & Chemical Engineering
- Tianjin University of Technology
- Tianjin
- P. R. China
| | - Jinbiao Liu
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion
- School of Chemistry & Chemical Engineering
- Tianjin University of Technology
- Tianjin
- P. R. China
| | - Lintao Zeng
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion
- School of Chemistry & Chemical Engineering
- Tianjin University of Technology
- Tianjin
- P. R. China
| | - Guang-Ming Bao
- Department of Veterinary Medicine
- School of Animal Science and Technology
- Jiangxi Agricultural University
- Nanchang 330045
- P. R. China
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250
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Giuliano MW, Miller SJ. Site-Selective Reactions with Peptide-Based Catalysts. SITE-SELECTIVE CATALYSIS 2015; 372:157-201. [DOI: 10.1007/128_2015_653] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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