1
|
Kambanis L, Kulkarni SS, Payne RJ. Side-Chain Anchoring Strategies for the Synthesis of Peptide Thioesters and Selenoesters. Methods Mol Biol 2022; 2530:125-140. [PMID: 35761046 DOI: 10.1007/978-1-0716-2489-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Peptides bearing C-terminal thioester and selenoester functionalities are essential precursors for the chemical synthesis of larger proteins using ligation chemistry, including native chemical ligation (NCL) and diselenide-selenoester ligation (DSL). The use of a side-chain anchoring thioesterification or selenoesterification approach offers a robust method to access peptide thioesters or peptide selenoesters in excellent yields and in high purity. Importantly, this methodology overcomes solubility issues and epimerization of the C-terminal amino acid residue that can occur using solution-phase approaches. Detailed methods for the solid-phase synthesis of peptide thioesters and selenoesters using a side-chain anchoring approach are outlined in this article.
Collapse
Affiliation(s)
- Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia
| | - Sameer S Kulkarni
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia
| | - Richard J Payne
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia.
| |
Collapse
|
2
|
Abstract
Genetic code expansion is one of the most powerful technologies in protein engineering. In addition to the 20 canonical amino acids, the expanded genetic code is supplemented by unnatural amino acids, which have artificial side chains that can be introduced into target proteins in vitro and in vivo. A wide range of chemical groups have been incorporated co-translationally into proteins in single cells and multicellular organisms by using genetic code expansion. Incorporated unnatural amino acids have been used for novel structure-function relationship studies, bioorthogonal labelling of proteins in cellulo for microscopy and in vivo for tissue-specific proteomics, the introduction of post-translational modifications and optical control of protein function, to name a few examples. In this Minireview, the development of genetic code expansion technology is briefly introduced, then its applications in neurobiology are discussed, with a focus on studies using mammalian cells and mice as model organisms.
Collapse
Affiliation(s)
- Ivana Nikić‐Spiegel
- Werner Reichardt Centre for Integrative NeuroscienceUniversity of TübingenOtfried-Müller-Strasse 2572076TübingenGermany
| |
Collapse
|
3
|
Lin JD, Liu X. Recent Development in Ligation Methods for Glycopeptide and Glycoprotein Synthesis. Chem Asian J 2020; 15:2548-2557. [DOI: 10.1002/asia.202000566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/28/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Junjie Desmond Lin
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore
| | - Xue‐Wei Liu
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore
| |
Collapse
|
4
|
Liu J, Ekanayake O, Santoleri D, Walker K, Rozovsky S. Efficient Generation of Hydrazides in Proteins by RadA Split Intein. Chembiochem 2020; 21:346-352. [PMID: 31265209 DOI: 10.1002/cbic.201900160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/30/2019] [Indexed: 12/27/2022]
Abstract
Protein C-terminal hydrazides are useful for bioconjugation and construction of proteins from multiple fragments through native chemical ligation. To generate C-terminal hydrazides in proteins, an efficient intein-based preparation method has been developed by using thiols and hydrazine to accelerate the formation of the transient thioester intermediate and subsequent hydrazinolysis. This approach not only increases the yield, but also improves biocompatibility. The scope of the method has been expanded by employing Pyrococcus horikoshii RadA split intein, which can accommodate a broad range of extein residues before the site of cleavage. The use of split RadA minimizes premature intein N cleavage in vivo and offers control over the initiation of the intein N cleavage reaction. It is expected that this versatile preparation method will expand the utilization of protein C-terminal hydrazides in protein preparation and modification.
Collapse
Affiliation(s)
- Jun Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, CA, 94158, USA
| | - Oshini Ekanayake
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Dominic Santoleri
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.,Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kelsi Walker
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| |
Collapse
|
5
|
Zuo C, Zhang B, Yan B, Zheng JS. One-pot multi-segment condensation strategies for chemical protein synthesis. Org Biomol Chem 2019; 17:727-744. [DOI: 10.1039/c8ob02610f] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This paper describes recent advances of one-pot multi-segment condensation strategies based on kinetically controlled strategies and/or protecting group-removal strategies in chemical protein synthesis.
Collapse
Affiliation(s)
- Chong Zuo
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230027
- China
- Department of Chemistry
| | - Baochang Zhang
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Bingjia Yan
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Ji-Shen Zheng
- School of Life Sciences
- University of Science and Technology of China
- Hefei 230027
- China
| |
Collapse
|
6
|
Sereikaitė V, Jensen TMT, Bartling CRO, Jemth P, Pless SA, Strømgaard K. Probing Backbone Hydrogen Bonds in Proteins by Amide-to-Ester Mutations. Chembiochem 2018; 19:2136-2145. [PMID: 30073762 DOI: 10.1002/cbic.201800350] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 01/09/2023]
Abstract
All proteins contain characteristic backbones formed of consecutive amide bonds, which can engage in hydrogen bonds. However, the importance of these is not easily addressed by conventional technologies that only allow for side-chain substitutions. By contrast, technologies such as nonsense suppression mutagenesis and protein ligation allow for manipulation of the protein backbone. In particular, replacing the backbone amide groups with ester groups, that is, amide-to-ester mutations, is a powerful tool to examine backbone-mediated hydrogen bonds. In this minireview, we showcase examples of how amide-to-ester mutations can be used to uncover pivotal roles of backbone-mediated hydrogen bonds in protein recognition, folding, function, and structure.
Collapse
Affiliation(s)
- Vita Sereikaitė
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Thomas M T Jensen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Christian R O Bartling
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, 75123, Uppsala, Sweden
| | - Stephan A Pless
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| |
Collapse
|
7
|
Carlo U, Yasuhiro K. Recent advances in the chemical synthesis of N-linked glycoproteins. Curr Opin Chem Biol 2018; 46:130-137. [PMID: 30144649 DOI: 10.1016/j.cbpa.2018.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 11/15/2022]
Abstract
Glycoproteins have many biological roles. Due to the heterogeneity of natural glycoproteins in the sugar part resulting in glycoforms the evaluation of the biochemical roles of individual glycans remains difficult to investigate. Since pure glycoforms are still not accessible via recombinant or chromatographic methods, the synthesis of proteins with uniform posttranslational modifications using ligation methods or glycan remodeling are currently the best options for accessing these targets. Recent developments in chemical protein synthesis, the assembly of N-glycans and the use of enzymatic procedures have provided access to many glycoproteins with modifications as well as their analogs.
Collapse
Affiliation(s)
- Unverzagt Carlo
- Bioorganic Chemistry, Gebäude NWI, University of Bayreuth, 95440 Bayreuth, Germany.
| | - Kajihara Yasuhiro
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
| |
Collapse
|
8
|
Chisholm TS, Clayton D, Dowman LJ, Sayers J, Payne RJ. Native Chemical Ligation-Photodesulfurization in Flow. J Am Chem Soc 2018; 140:9020-9024. [PMID: 29792427 DOI: 10.1021/jacs.8b03115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Native chemical ligation (NCL) combined with desulfurization chemistry has revolutionized the way in which large polypeptides and proteins are accessed by chemical synthesis. Herein, we outline the use of flow chemistry for the ligation-based assembly of polypeptides. We also describe the development of a novel photodesulfurization transformation that, when coupled with flow NCL, enables efficient access to native polypeptides on time scales up to 2 orders of magnitude faster than current batch NCL-desulfurization methods. The power of the new ligation-photodesulfurization flow platform is showcased through the rapid synthesis of the 36 residue clinically approved HIV entry inhibitor enfuvirtide and the peptide diagnostic agent somatorelin.
Collapse
Affiliation(s)
- Timothy S Chisholm
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
| | - Daniel Clayton
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
| | - Luke J Dowman
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
| | - Jessica Sayers
- 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
| |
Collapse
|
9
|
Abstract
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.
Collapse
|
10
|
Abstract
The facile rearrangement of "S-acyl isopeptides" to native peptide bonds via S,N-acyl shift is central to the success of native chemical ligation, the widely used approach for protein total synthesis. Proximity-driven amide bond formation via acyl transfer reactions in other contexts has proven generally less effective. Here, we show that under neutral aqueous conditions, "O-acyl isopeptides" derived from hydroxy-asparagine [aspartic acid-β-hydroxamic acid; Asp(β-HA)] rearrange to form native peptide bonds via an O,N-acyl shift. This process constitutes a rare example of an O,N-acyl shift that proceeds rapidly across a medium-size ring (t1/2 ∼ 15 min), and takes place in water with minimal interference from hydrolysis. In contrast to serine/threonine or tyrosine, which form O-acyl isopeptides only by the use of highly activated acyl donors and appropriate protecting groups in organic solvent, Asp(β-HA) is sufficiently reactive to form O-acyl isopeptides by treatment with an unprotected peptide-αthioester, at low mM concentration, in water. These findings were applied to an acyl transfer-based chemical ligation strategy, in which an unprotected N-terminal Asp(β-HA)-peptide and peptide-αthioester react under aqueous conditions to give a ligation product ultimately linked by a native peptide bond.
Collapse
|
11
|
Jiang YY, Liu TT, Zhang RX, Xu ZY, Sun X, Bi S. Mechanism and Rate-Determining Factors of Amide Bond Formation through Acyl Transfer of Mixed Carboxylic–Carbamic Anhydrides: A Computational Study. J Org Chem 2018; 83:2676-2685. [DOI: 10.1021/acs.joc.7b03107] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yuan-Ye Jiang
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Tian-Tian Liu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Rui-Xue Zhang
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Zhong-Yan Xu
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Xue Sun
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| | - Siwei Bi
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, People’s Republic of China
| |
Collapse
|
12
|
Qi YK, Tang S, Huang YC, Pan M, Zheng JS, Liu L. Hmb(off/on) as a switchable thiol protecting group for native chemical ligation. Org Biomol Chem 2018; 14:4194-8. [PMID: 27102373 DOI: 10.1039/c6ob00450d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new thiol protecting group Hmb(off/on) is described, which has a switchable activity that may be useful in the chemical synthesis of proteins. When placed on the side chain of Cys, Cys(Hmb(off)) is stable to trifluoroacetic acid (TFA) in the process of solid-phase peptide synthesis. When Cys(Hmb(off)) is treated with neutral aqueous buffers, it is cleanly converted to acid-labile Cys(Hmb(on)), which can later be fully deprotected by TFA to generate free Cys. The utility of Cys(Hmb(off/on)) is demonstrated by the chemical synthesis of an erythropoietin segment, EPO[Cys(98)-Arg(166)]-OH through native chemical ligation.
Collapse
Affiliation(s)
- Yun-Kun Qi
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China. and High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.
| | - Shan Tang
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Yi-Chao Huang
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Ji-Shen Zheng
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
13
|
Kent S. Chemical protein synthesis: Inventing synthetic methods to decipher how proteins work. Bioorg Med Chem 2017; 25:4926-4937. [DOI: 10.1016/j.bmc.2017.06.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/07/2017] [Accepted: 06/13/2017] [Indexed: 12/15/2022]
|
14
|
Mitchell NJ, Kulkarni SS, Malins LR, Wang S, Payne RJ. One-Pot Ligation-Oxidative Deselenization at Selenocysteine and Selenocystine. Chemistry 2016; 23:946-952. [DOI: 10.1002/chem.201604709] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Indexed: 01/27/2023]
Affiliation(s)
| | - Sameer S. Kulkarni
- School of Chemistry; The University of Sydney; Sydney, NSW 2006 Australia
| | - Lara R. Malins
- School of Chemistry; The University of Sydney; Sydney, NSW 2006 Australia
| | - Siyao Wang
- 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
| |
Collapse
|
15
|
Li YT, Huang YC, Xu Y, Pan M, Li YM. Ubiquitin 7-amino-4-carbamoylmethylcoumarin as an improved fluorogenic substrate for deubiquitinating enzymes. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.05.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
16
|
Huang Y, Chen C, Gao S, Wang Y, Xiao H, Wang F, Tian C, Li Y. Synthesis of
l
‐ and
d
‐Ubiquitin by One‐Pot Ligation and Metal‐Free Desulfurization. Chemistry 2016; 22:7623-8. [DOI: 10.1002/chem.201600101] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Yi‐Chao Huang
- School of Medical Engineering Hefei University of Technology Hefei 230009 P. R. China
- State Key Laboratory of Medicinal Chemical Biology NanKai University 94 Weijin Road Tianjin 300071 P. R. China
- Department of Chemistry School of Life Sciences Tsinghua University Beijing 100084 P. R. China
| | - Chen‐Chen Chen
- High Magnetic Field Laboratory Chinese Academy of Sciences Hefei 230026 P. R. China
| | - Shuai Gao
- Department of Chemistry School of Life Sciences Tsinghua University Beijing 100084 P. R. China
| | - Ye‐Hai Wang
- School of Medical Engineering Hefei University of Technology Hefei 230009 P. R. China
- State Key Laboratory of Medicinal Chemical Biology NanKai University 94 Weijin Road Tianjin 300071 P. R. China
| | - Hua Xiao
- School of Medical Engineering Hefei University of Technology Hefei 230009 P. R. China
- State Key Laboratory of Medicinal Chemical Biology NanKai University 94 Weijin Road Tianjin 300071 P. R. China
| | - Feng Wang
- Department of Chemistry School of Life Sciences Tsinghua University Beijing 100084 P. R. China
| | - Chang‐Lin Tian
- High Magnetic Field Laboratory Chinese Academy of Sciences Hefei 230026 P. R. China
| | - Yi‐Ming Li
- School of Medical Engineering Hefei University of Technology Hefei 230009 P. R. China
- State Key Laboratory of Medicinal Chemical Biology NanKai University 94 Weijin Road Tianjin 300071 P. R. China
| |
Collapse
|