1
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Nakamura G, Nakatsu K, Hayashi G. One-pot ligation of multiple peptide segments via N-terminal thiazolidine deprotection chemistry. Methods Enzymol 2024; 698:169-194. [PMID: 38886031 DOI: 10.1016/bs.mie.2024.04.020] [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: 06/20/2024]
Abstract
Peptide ligation chemistries have revolutionized the synthesis of proteins with site-specific modifications or proteomimetics through assembly of multiple peptide segments. In order to prepare polypeptide chains consisting of 100-150 amino acid residues or larger generally assembled from three or more peptide segments, iterative purification process that decreases the product yield is usually demanded. Accordingly, methodologies for one-pot peptide ligation that omit the purification steps of intermediate peptide segments have been vigorously developed so far to improve the efficiency of chemical protein synthesis. In this chapter, we first outline the concept and recent advances of one-pot peptide ligation strategies. Then, the practical guideline for the preparation of peptide segments for one-pot peptide ligation is described with an emphasis on diketopiperazine thioester synthesis. Finally, we disclose the explicit protocols for one-pot four segment ligation via repetitive deprotection of N-terminal thiazolidine by a 2-aminobenzamide type aldehyde scavenger.
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Affiliation(s)
- Genki Nakamura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Koki Nakatsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan.
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2
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Zheng Y, Zhang B, Shi WW, Deng X, Wang TY, Han D, Ren Y, Yang Z, Zhou YK, Kuang J, Wang ZW, Tang S, Zheng JS. An Enzyme-Cleavable Solubilizing-Tag Facilitates the Chemical Synthesis of Mirror-Image Proteins. Angew Chem Int Ed Engl 2024; 63:e202318897. [PMID: 38326236 DOI: 10.1002/anie.202318897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/09/2024]
Abstract
Mirror-image proteins (D-proteins) are useful in biomedical research for purposes such as mirror-image screening for D-peptide drug discovery, but the chemical synthesis of many D-proteins is often low yielding due to the poor solubility or aggregation of their constituent peptide segments. Here, we report a Lys-C protease-cleavable solubilizing tag and its use to synthesize difficult-to-obtain D-proteins. Our tag is easily installed onto multiple amino acids such as DLys, DSer, DThr, and/or the N-terminal amino acid of hydrophobic D-peptides, is impervious to various reaction conditions, such as peptide synthesis, ligation, desulfurization, and transition metal-mediated deprotection, and yet can be completely removed by Lys-C protease under denaturing conditions to give the desired D-protein. The efficacy and practicality of the new method were exemplified in the synthesis of two challenging D-proteins: D-enantiomers of programmed cell death protein 1 IgV domain and SARS-CoV-2 envelope protein, in high yield. This work demonstrates that the enzymatic cleavage of solubilizing tags under denaturing conditions is feasible, thus paving the way for the production of more D-proteins.
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Affiliation(s)
- Yupeng Zheng
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China (USTC), MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, and Division of Life Sciences and Medicine, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Baochang Zhang
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China (USTC), MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, and Division of Life Sciences and Medicine, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Wei-Wei Shi
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Xiangyu Deng
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Tong-Yue Wang
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Dongyang Han
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yuxiang Ren
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Ziyi Yang
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yong-Kang Zhou
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Jian Kuang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Zhi-Wen Wang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Shan Tang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Ji-Shen Zheng
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China (USTC), MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, and Division of Life Sciences and Medicine, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230001, China
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3
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Li W, Jacobsen MT, Park C, Jung JU, Lin NP, Huang PS, Lal RA, Chou DHC. A cysteine-specific solubilizing tag strategy enables efficient chemical protein synthesis of difficult targets. Chem Sci 2024; 15:3214-3222. [PMID: 38425513 PMCID: PMC10901488 DOI: 10.1039/d3sc06032b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024] Open
Abstract
We developed a new cysteine-specific solubilizing tag strategy via a cysteine-conjugated succinimide. This solubilizing tag remains stable under common native chemical ligation conditions and can be efficiently removed with palladium-based catalysts. Utilizing this approach, we synthesized two proteins containing notably difficult peptide segments: interleukin-2 (IL-2) and insulin. This IL-2 chemical synthesis represents the simplest and most efficient approach to date, which is enabled by the cysteine-specific solubilizing tag to synthesize and ligate long peptide segments. Additionally, we synthesized a T8P insulin variant, previously identified in an infant with neonatal diabetes. We show that T8P insulin exhibits reduced bioactivity (a 30-fold decrease compared to standard insulin), potentially contributing to the onset of diabetes in these patients. In summary, our work provides an efficient tool to synthesize challenging proteins and opens new avenues for exploring research directions in understanding their biological functions.
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Affiliation(s)
- Wenchao Li
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Michael T Jacobsen
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Claire Park
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Jae Un Jung
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Nai-Pin Lin
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University Palo Alto CA 94305 USA
| | - Rayhan A Lal
- Division of Endocrinology, Department of Medicine, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Danny Hung-Chieh Chou
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
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4
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Saebi A, Brown JS, Marando VM, Hartrampf N, Chumbler NM, Hanna S, Poskus M, Loas A, Kiessling LL, Hung DT, Pentelute BL. Rapid Single-Shot Synthesis of the 214 Amino Acid-Long N-Terminal Domain of Pyocin S2. ACS Chem Biol 2023; 18:518-527. [PMID: 36821521 PMCID: PMC10460144 DOI: 10.1021/acschembio.2c00862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The impermeable outer membrane of Pseudomonas aeruginosa is bypassed by antibacterial proteins known as S-type pyocins. Because of their properties, pyocins are investigated as a potential new class of antimicrobials against Pseudomonas infections. Their production and modification, however, remain challenging. To address this limitation, we employed automated fast-flow peptide synthesis for the rapid production of a pyocin S2 import domain. The N-terminal domain sequence (PyS2NTD) was synthesized in under 10 h and purified to yield milligram quantities of the desired product. To our knowledge, the 214 amino acid sequence of PyS2NTD is among the longest peptides produced from a "single-shot" synthesis, i.e., made in a single stepwise route without the use of ligation techniques. Biophysical characterization of the PyS2NTD with circular dichroism was consistent with the literature reports. Fluorescently labeled PyS2NTD binds to P. aeruginosa expressing the cognate ferripyoverdine receptor and is taken up into the periplasm. This selective uptake was validated with confocal and super resolution microscopy, flow cytometry, and fluorescence recovery after photobleaching. These modified, synthetic S-type pyocin domains can be used to probe import mechanisms of P. aeruginosa and leveraged to develop selective antimicrobial agents that bypass the outer membrane.
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Affiliation(s)
- Azin Saebi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Joseph S Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Victoria M Marando
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nina Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicole M Chumbler
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Stephanie Hanna
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mackenzie Poskus
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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5
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Wu H, Tan Y, Ngai WL, Li X. Total synthesis of interleukin-2 via a tunable backbone modification strategy. Chem Sci 2023; 14:1582-1589. [PMID: 36794182 PMCID: PMC9906654 DOI: 10.1039/d2sc05660g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/06/2023] [Indexed: 01/08/2023] Open
Abstract
Chemical synthesis of hydrophobic proteins presents a formidable task as they are often difficultly achieved via peptide synthesis, purification, and peptide ligation. Thus, peptide solubilizing strategies are needed to integrate with peptide ligation to achieve protein total synthesis. Herein, we report a tunable backbone modification strategy, taking advantage of the tunable stability of the Cys/Pen ligation intermediate, which allows for readily introducing a solubilizing tag for both peptide purification and ligation processes. The effectiveness of this strategy was demonstrated by the chemical synthesis of interleukin-2.
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Affiliation(s)
- Hongxiang Wu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Yi Tan
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Wai Lok Ngai
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology Qingdao 266237 P. R. China
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6
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Proteins through the eyes of an organic chemist. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Cui Y, Taguchi A, Shida H, Konno S, Takayama K, Taniguchi A, Hayashi Y. Chemical Synthesis of an HIV-1 Protease Analog with Some Amides in a Polypeptide Main Chain Replaced by Disulfide Bonds. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yan Cui
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Hayate Shida
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Sho Konno
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Kentaro Takayama
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
- Present address: Department of Environmental Biochemistry, Kyoto Pharmaceutical University, 5 Misasaginakauchi-cho, Yamashina, Kyoto 607-8414, Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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8
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Hanna CC, Kriegesmann J, Dowman LJ, Becker CFW, Payne RJ. Chemische Synthese und Semisynthese von lipidierten Proteinen. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202111266. [PMID: 38504765 PMCID: PMC10947004 DOI: 10.1002/ange.202111266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 11/11/2022]
Abstract
AbstractLipidierung ist eine ubiquitäre Modifikation von Peptiden und Proteinen, die entweder co‐ oder posttranslational auftreten kann. Für die Vielzahl von Lipidklassen wurde gezeigt, dass diese viele entscheidende biologische Aktivitäten, z. B. die Regulierung der Signalweiterleitung, Zell‐Zell‐Adhäsion sowie die Anlagerung von Proteinen an Lipid‐Rafts und Phospholipidmembranen, beeinflussen. Während die Natur Enzyme nutzt, um Lipidmodifikationen in Proteine einzubringen, ist ihre Nutzung für die chemoenzymatische Herstellung von lipidierten Proteinen häufig ineffizient. Eine Alternative ist die Kombination moderner synthetischer und semisynthetischer Techniken, um lipidierte Proteine in reiner und homogen modifizierter Form zu erhalten. Dieser Aufsatz erörtert Fortschritte in der Entwicklung der Lipidierungs‐ und Ligationschemie und deren Anwendung in der Synthese und Semisynthese homogen lipidierter Proteine, die es ermöglichen, den Einfluss dieser Modifikationen auf die Proteinstruktur und ‐funktion zu untersuchen.
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Affiliation(s)
- Cameron C. Hanna
- School of ChemistryThe University of SydneySydneyNSW2006Australien
| | - Julia Kriegesmann
- Institut für Biologische ChemieFakultät für ChemieUniversität WienWienÖsterreich
| | - Luke J. Dowman
- School of ChemistryThe University of SydneySydneyNSW2006Australien
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW2006Australien
| | | | - Richard J. Payne
- School of ChemistryThe University of SydneySydneyNSW2006Australien
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW2006Australien
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9
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Liu J, Wei T, Tan Y, Liu H, Li X. Enabling chemical protein (semi)synthesis via reducible solubilizing tags (RSTs). Chem Sci 2022; 13:1367-1374. [PMID: 35222920 PMCID: PMC8809390 DOI: 10.1039/d1sc06387a] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 01/11/2023] Open
Abstract
The reducible solubilizing tag strategy served as a simple and powerful method for the chemical synthesis and semi-synthesis via Ser/Thr ligation and Cys/Pen ligation of extensive self-assembly peptides, membrane proteins with poor solubility.
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Affiliation(s)
- Jiamei Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Tongyao Wei
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Yi Tan
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Heng Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
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10
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Hanna C, Kriegesmann J, Dowman L, Becker C, Payne RJ. Chemical Synthesis and Semisynthesis of Lipidated Proteins. Angew Chem Int Ed Engl 2021; 61:e202111266. [PMID: 34611966 PMCID: PMC9303669 DOI: 10.1002/anie.202111266] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 11/24/2022]
Abstract
Lipidation is a ubiquitous modification of peptides and proteins that can occur either co‐ or post‐translationally. An array of different lipid classes can adorn proteins and has been shown to influence a number of crucial biological activities, including the regulation of signaling, cell–cell adhesion events, and the anchoring of proteins to lipid rafts and phospholipid membranes. Whereas nature employs a range of enzymes to install lipid modifications onto proteins, the use of these for the chemoenzymatic generation of lipidated proteins is often inefficient or impractical. An alternative is to harness the power of modern synthetic and semisynthetic technologies to access lipid‐modified proteins in a pure and homogeneously modified form. This Review aims to highlight significant advances in the development of lipidation and ligation chemistry and their implementation in the synthesis and semisynthesis of homogeneous lipidated proteins that have enabled the influence of these modifications on protein structure and function to be uncovered.
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Affiliation(s)
- Cameron Hanna
- The University of Sydney, Chemistry, 2006, Sydney, AUSTRALIA
| | - Julia Kriegesmann
- University of Vienna: Universitat Wien, Institute of Biological Chemistry, Vienna, AUSTRIA
| | - Luke Dowman
- The University of Sydney, School of Chemistry, 2006, Sydney, AUSTRALIA
| | - Christian Becker
- University of Vienna Faculty of Chemistry: Universitat Wien Fakultat fur Chemie, Institute of Biological Chemistry, Vienna, AUSTRIA
| | - Richard James Payne
- The University of Sydney, School of Chemistry, Eastern Avenue, 2006, Sydney, AUSTRALIA
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11
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Sato K, Tanaka S, Wang J, Ishikawa K, Tsuda S, Narumi T, Yoshiya T, Mase N. Late-Stage Solubilization of Poorly Soluble Peptides Using Hydrazide Chemistry. Org Lett 2021; 23:1653-1658. [PMID: 33570416 DOI: 10.1021/acs.orglett.1c00074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel late-stage solubilization of peptides using hydrazides is described. A solubilizing tag was attached through a selective N-alkylation at a hydrazide moiety with the aid of a 2-picoline-borane complex in 50% acetic acid-hexafluoro-2-propanol. The tag, which tolerates ligation and desulfurization conditions, can be detached by a Cu-mediated selective oxidative hydrolysis of the N-alkyl hydrazide. This new method was validated through the synthesis of HIV-1 protease.
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Affiliation(s)
- Kohei Sato
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Course of Applied Chemistry and Biochemical Engineering, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Shoko Tanaka
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Junzhen Wang
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Kenya Ishikawa
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Shugo Tsuda
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Tetsuo Narumi
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Course of Applied Chemistry and Biochemical Engineering, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Research Institute of Green Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Taku Yoshiya
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Nobuyuki Mase
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Course of Applied Chemistry and Biochemical Engineering, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan.,Research Institute of Green Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka 432-8561, Japan
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12
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Laps S, Satish G, Brik A. Harnessing the power of transition metals in solid-phase peptide synthesis and key steps in the (semi)synthesis of proteins. Chem Soc Rev 2021; 50:2367-2387. [PMID: 33432943 DOI: 10.1039/d0cs01156h] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Peptides and proteins can be either synthesized using solid-phase peptide synthesis (SPPS) or by applying a combination of SPPS and ligation approaches to address fundamental questions related to human health and disease, among others. The demand for their production either by chemical or biological methods continues to raise significant interests from the synthetic community. In this context, transition metals such as Pd, Ag, Hg, Tl, Au, Zn, Ni, and Cu have also contributed to the field of peptide and protein synthesis such as in peptide conjugation, extending native chemical ligation (NCL), and for regioselective disulfide bonds formation. In this review, we highlight, summarize, and evaluate the use of various transition metals in the chemical synthesis of peptides and proteins with emphasis on recent developments in this exciting research area.
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Affiliation(s)
- Shay Laps
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
| | - Gandhesiri Satish
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
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13
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Abboud SA, Cisse EH, Doudeau M, Bénédetti H, Aucagne V. A straightforward methodology to overcome solubility challenges for N-terminal cysteinyl peptide segments used in native chemical ligation. Chem Sci 2021; 12:3194-3201. [PMID: 34164087 PMCID: PMC8179351 DOI: 10.1039/d0sc06001a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/10/2021] [Indexed: 02/06/2023] Open
Abstract
One of the main limitations encountered during the chemical synthesis of proteins through native chemical ligation (NCL) is the limited solubility of some of the peptide segments. The most commonly used solution to overcome this problem is to derivatize the segment with a temporary solubilizing tag. Conveniently, the tag can be introduced on the thioester segment in such a way that it is removed concomitantly with the NCL reaction. We herein describe a generalization of this approach to N-terminal cysteinyl segment counterparts, using a straightforward synthetic approach that can be easily automated from commercially available building blocks, and applied it to a well-known problematic target, SUMO-2.
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Affiliation(s)
- Skander A Abboud
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - El Hadji Cisse
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Michel Doudeau
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Hélène Bénédetti
- 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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14
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Affiliation(s)
- Zachary P. Gates
- p53 Lab, Agency for Science, Technology and Research (A*STAR) Singapore Singapore
| | - Nina Hartrampf
- Department of Chemistry University of Zurich Zurich Switzerland
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15
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Hartrampf N, Saebi A, Poskus M, Gates ZP, Callahan AJ, Cowfer AE, Hanna S, Antilla S, Schissel CK, Quartararo AJ, Ye X, Mijalis AJ, Simon MD, Loas A, Liu S, Jessen C, Nielsen TE, Pentelute BL. Synthesis of proteins by automated flow chemistry. Science 2020; 368:980-987. [PMID: 32467387 DOI: 10.1126/science.abb2491] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022]
Abstract
Ribosomes can produce proteins in minutes and are largely constrained to proteinogenic amino acids. Here, we report highly efficient chemistry matched with an automated fast-flow instrument for the direct manufacturing of peptide chains up to 164 amino acids long over 327 consecutive reactions. The machine is rapid: Peptide chain elongation is complete in hours. We demonstrate the utility of this approach by the chemical synthesis of nine different protein chains that represent enzymes, structural units, and regulatory factors. After purification and folding, the synthetic materials display biophysical and enzymatic properties comparable to the biologically expressed proteins. High-fidelity automated flow chemistry is an alternative for producing single-domain proteins without the ribosome.
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Affiliation(s)
- N Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A Saebi
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - M Poskus
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Z P Gates
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A J Callahan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A E Cowfer
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - S Hanna
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - S Antilla
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - C K Schissel
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A J Quartararo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - X Ye
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A J Mijalis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - M D Simon
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A Loas
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - S Liu
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - C Jessen
- Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - T E Nielsen
- Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - B L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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16
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Mueller LK, Baumruck AC, Zhdanova H, Tietze AA. Challenges and Perspectives in Chemical Synthesis of Highly Hydrophobic Peptides. Front Bioeng Biotechnol 2020; 8:162. [PMID: 32195241 PMCID: PMC7064641 DOI: 10.3389/fbioe.2020.00162] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022] Open
Abstract
Solid phase peptide synthesis (SPPS) provides the possibility to chemically synthesize peptides and proteins. Applying the method on hydrophilic structures is usually without major drawbacks but faces extreme complications when it comes to "difficult sequences." These includes the vitally important, ubiquitously present and structurally demanding membrane proteins and their functional parts, such as ion channels, G-protein receptors, and other pore-forming structures. Standard synthetic and ligation protocols are not enough for a successful synthesis of these challenging sequences. In this review we highlight, summarize and evaluate the possibilities for synthetic production of "difficult sequences" by SPPS, native chemical ligation (NCL) and follow-up protocols.
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Affiliation(s)
- Lena K. Mueller
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Darmstadt, Germany
| | - Andreas C. Baumruck
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Darmstadt University of Technology, Darmstadt, Germany
| | - Hanna Zhdanova
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Alesia A. Tietze
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
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17
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Zhao Z, Metanis N. Utilizing Copper-Mediated Deprotection of Selenazolidine for Cyclic Peptide Synthesis. J Org Chem 2019; 85:1731-1739. [DOI: 10.1021/acs.joc.9b02644] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhenguang Zhao
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Norman Metanis
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
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18
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Abstract
Chemical protein synthesis has been proved as an efficient way to afford medium-sized proteins with high homogeneity in workable quantities for various biochemical, structural, and functional studies. In particular, chemical protein synthesis has enabled access to proteins that are difficult or impossible to prepare by molecular biology approaches, such as those with post-translational modifications and mirror-image proteins. One prominent example is related to ubiquitination, a well-known modification that mediates a variety of cellular processes (e.g., proteasomal degradation). Ubiquitination is considered as a modification that is difficult to introduce into proteins in a test tube to generate ubiquitin (Ub) conjugates with high homogeneity with respect to the chain length and the anchored Lys residue in workable quantities to perform the biochemical and biophysical studies. Chemical protein synthesis has emerged as a powerful approach to prepare Ub conjugates for studies aiming to understand ubiquitination in great detail and decipher its roles in cell processes. Nevertheless, in order to answer more challenging questions in this field, it has been clear that researchers must also prepare Ub conjugates with increased size and complexity. Employing solid-phase peptide synthesis and chemoselective ligation, chemical protein synthesis offers a powerful way to furnish polypeptides composed of 100-200 residues. However, to synthesize larger proteins such as Ub conjugates, longer and more segments are required. This on the other hand leads to difficulties related to solubility, purification, ligation, and late-stage modifications. These challenges have encouraged us to explore more practical synthetic tools to facilitate the synthesis of complex Ub conjugates. In this Account, we summarize the synthetic tools that we have developed to achieve these goals. These include (1) δ-mercaptolysine-mediated isopeptide chemical ligation, (2) chemical synthesis of Ub building blocks, (3) palladium-mediated deprotection of key side chains during protein synthesis, (4) one-pot ligation and desulfurization, and (5) improving the solubility of peptide segments. The developed chemical toolbox has been a key for our successes in the synthesis of diverse and complex Ub conjugates. In this Account, we describe our approaches for generating various Ub conjugates, including (1) the K48 tetra-Ub chain composed of 304 amino acids, (2) the ubiquitinated histones and their analogues made of >200 amino acids, (3) the di-Ub-SUMO-2 hybrid chain composed of 245 amino acids, and (4) the 53 kDa tetra-Ub-α-globin composed of 472 amino acids, which represents the largest protein composed of natural amino acids ever made using chemical protein synthesis. The last target, Flag-Ub-Ub-Ub-Myc-Ub-(HA-α-globin), was prepared in the labeled form where the proximal Ub and distal Ub in the chain were labeled with Myc and Flag tags, respectively, while the α-globin was labeled with the HA tag. Applying the tetra-Ub-α-globin in proteasomal degradation studies assisted us to shed light on the proteolytic signal and the fates of the Ub moieties in the chains. Although these developments have contributed to the synthesis of interesting and challenging targets related to Ub signaling, several other targets may enforce new synthetic challenges. Hence, there is still a need to optimize the current synthetic tools and explore novel synthetic approaches to facilitate this process.
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Affiliation(s)
- Hao Sun
- Schulich Faculty of Chemistry, Technion—Israel Institute of Technology, Haifa 3200008, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion—Israel Institute of Technology, Haifa 3200008, Israel
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19
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Zhao Z, Metanis N. Copper‐Mediated Selenazolidine Deprotection Enables One‐Pot Chemical Synthesis of Challenging Proteins. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhenguang Zhao
- Institute of Chemistry The Hebrew University of Jerusalem Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Norman Metanis
- Institute of Chemistry The Hebrew University of Jerusalem Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
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20
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Zhao Z, Metanis N. Copper-Mediated Selenazolidine Deprotection Enables One-Pot Chemical Synthesis of Challenging Proteins. Angew Chem Int Ed Engl 2019; 58:14610-14614. [PMID: 31408267 DOI: 10.1002/anie.201909484] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Indexed: 12/25/2022]
Abstract
While chemical protein synthesis has granted access to challenging proteins, the synthesis of longer proteins is often limited by low abundance or non-strategic placement of cysteine residues, which are essential for native chemical ligations, as well as multiple purification and isolation steps. We describe the one-pot total synthesis of human thiosulfate:glutathione sulfurtransferase (TSTD1). WT-TSTD1 was synthesized in a C-to-N synthetic approach involving multiple NCL reactions, CuII -mediated deprotection of selenazolidine (Sez), and chemoselective deselenization. The seleno-analog Se-TSTD1, in which the active site Cys is replaced with selenocysteine, was also synthesized with a kinetically controlled ligation with an N-to-C synthetic approach. The catalytic activity of the two proteins indicated that Se-TSTD1 possessed only four-fold lower activity than WT-TSTD1, thus suggesting that selenoproteins can have physiologically comparable sulfutransferase activity to their cysteine counterparts.
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Affiliation(s)
- Zhenguang Zhao
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| | - Norman Metanis
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
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21
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Yoshiya T, Tsuda S, Masuda S. Development of Trityl Group Anchored Solubilizing Tags for Peptide and Protein Synthesis. Chembiochem 2019; 20:1906-1913. [DOI: 10.1002/cbic.201900105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Taku Yoshiya
- Peptide Institute, Inc. 7-2-9 Saito-Asagi Ibaraki-Shi Osaka 567-0085 Japan
| | - Shugo Tsuda
- Peptide Institute, Inc. 7-2-9 Saito-Asagi Ibaraki-Shi Osaka 567-0085 Japan
| | - Shun Masuda
- Peptide Institute, Inc. 7-2-9 Saito-Asagi Ibaraki-Shi Osaka 567-0085 Japan
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22
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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23
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Zhao DD, Fan XW, Hao H, Zhang HL, Guo Y. Temporary Solubilizing Tags Method for the Chemical Synthesis of Hydrophobic Proteins. CURR ORG CHEM 2019. [DOI: 10.2174/1385272822666181211121758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hydrophobic proteins, as one of the cellular protein classifications, play an essential function in maintaining the normal life cycle of living cells. Researches on the structure and function of hydrophobic proteins promote the exploration of the causes of major diseases, and development of new therapeutic agents for disease treatment. However, the poor water solubility of hydrophobic proteins creates problems for their preparation, separation, characterization and functional studies. The temporary solubilizing tags are considered a practical strategy to effectively solve the poor water solubility problem of hydrophobic proteins. This strategy can significantly improve the water solubility of hydrophobic peptides/proteins, making them like water-soluble peptides/proteins easy to be purified, characterized. More importantly, the temporary solubilizing tags can be removed after protein synthesis, so thus the structure and function of the hydrophobic proteins are not affected. At present, temporary solubilizing tags have been successfully used to prepare many important hydrophobic proteins such as membrane proteins, lipoproteins and chaperones. In this review, we summarize the recent researches and applications of temporary solubilizing tags.
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Affiliation(s)
- Dong-Dong Zhao
- Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia 014060, China
| | - Xiao-Wen Fan
- Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia 014060, China
| | - He Hao
- Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia 014060, China
| | - Hong-Li Zhang
- Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia 014060, China
| | - Ye Guo
- Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia 014060, China
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24
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Hayashi G, Yanase M, Nakatsuka Y, Okamoto A. Simultaneous and Traceless Ligation of Peptide Fragments on DNA Scaffold. Biomacromolecules 2019; 20:1246-1253. [PMID: 30677290 DOI: 10.1021/acs.biomac.8b01655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Peptide ligation is an indispensable step in the chemical synthesis of target peptides and proteins that are difficult to synthesize at once by a solid-phase synthesis. The ligation reaction is generally conducted with two peptide fragments at a high aqueous concentration to increase the reaction rate; however, this often causes unpredictable aggregation and precipitation of starting or resulting peptides due to their hydrophobicities. Here, we have developed a novel peptide ligation strategy harnessing the two intrinsic characteristics of oligodeoxynucleotides (ODNs), i.e., their hydrophilicity and hybridization ability, which allowed increases in the water solubility of peptides and the reaction kinetics due to the proximity effect, respectively. Peptide-ODN conjugates that can be cleaved to regenerate native peptide sequences were synthesized using novel lysine derivatives containing conjugation handles and photolabile linkers, via solid-phase peptide synthesis and subsequent conjugation to 15-mer ODNs. Two complementary conjugates were applied to carbodiimide-mediated peptide ligation on a DNA scaffold, and the subsequent DNA removal was conducted by photoirradiation in a traceless fashion. This DNA scaffold-assisted ligation resulted in a significant acceleration of the reaction kinetics and enabled ligation of a hydrophobic peptide at a micromolar concentration. On the basis of this chemistry, a simultaneous ligation of three different peptide fragments on two different DNA scaffolds has been conducted for the first time.
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Affiliation(s)
- Gosuke Hayashi
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Masafumi Yanase
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Yu Nakatsuka
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan.,Research Center for Advanced Science and Technology , The University of Tokyo , 4-6-1 Komaba, Meguro-ku , Tokyo 153-8904 , Japan
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25
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Paraskevopoulou V, Falcone FH. Polyionic Tags as Enhancers of Protein Solubility in Recombinant Protein Expression. Microorganisms 2018; 6:microorganisms6020047. [PMID: 29882886 PMCID: PMC6027335 DOI: 10.3390/microorganisms6020047] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 12/30/2022] Open
Abstract
Since the introduction of recombinant protein expression in the second half of the 1970s, the growth of the biopharmaceutical field has been rapid and protein therapeutics has come to the foreground. Biophysical and structural characterisation of recombinant proteins is the essential prerequisite for their successful development and commercialisation as therapeutics. Despite the challenges, including low protein solubility and inclusion body formation, prokaryotic host systems and particularly Escherichia coli, remain the system of choice for the initial attempt of production of previously unexpressed proteins. Several different approaches have been adopted, including optimisation of growth conditions, expression in the periplasmic space of the bacterial host or co-expression of molecular chaperones, to assist correct protein folding. A very commonly employed approach is also the use of protein fusion tags that enhance protein solubility. Here, a range of experimentally tested peptide tags, which present specific advantages compared to protein fusion tags and the concluding remarks of these experiments are reviewed. Finally, a concept to design solubility-enhancing peptide tags based on a protein’s pI is suggested.
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Affiliation(s)
- Vasiliki Paraskevopoulou
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Franco H Falcone
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK.
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26
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Brailsford JA, Stockdill JL, Axelrod AJ, Peterson MT, Vadola PA, Johnston EV, Danishefsky SJ. Total Chemical Synthesis of Human Thyroid-Stimulating Hormone (hTSH) β-Subunit: Application of Arginine-tagged Acetamidomethyl (Acm R) Protecting Groups. Tetrahedron 2018; 74:1951-1956. [PMID: 30853725 PMCID: PMC6402344 DOI: 10.1016/j.tet.2018.02.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The β-subunit of human thyroid stimulating hormone (hTSH) has been synthesized as a single glycoform bearing a chitobiose disaccharide at the native glycosylation site. Key to the successful completion of this synthesis was the introduction of an arginine-tagged acetamidomethyl group, which served to greatly facilitate handling of a glycopeptide fragment with poor aqueous solubility. This general solution to the challenge of working with intractable peptides is expected to find wide use in protein synthesis.
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Affiliation(s)
- John A Brailsford
- Laboratory for Bioorganic Chemistry, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Jennifer L Stockdill
- Laboratory for Bioorganic Chemistry, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Abram J Axelrod
- Laboratory for Bioorganic Chemistry, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Michael T Peterson
- Laboratory for Bioorganic Chemistry, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Paul A Vadola
- Laboratory for Bioorganic Chemistry, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Eric V Johnston
- Laboratory for Bioorganic Chemistry, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
| | - Samuel J Danishefsky
- Laboratory for Bioorganic Chemistry, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065
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27
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Tsuda S, Mochizuki M, Ishiba H, Yoshizawa-Kumagaye K, Nishio H, Oishi S, Yoshiya T. Easy-to-Attach/Detach Solubilizing-Tag-Aided Chemical Synthesis of an Aggregative Capsid Protein. Angew Chem Int Ed Engl 2018; 57:2105-2109. [DOI: 10.1002/anie.201711546] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/20/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Shugo Tsuda
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
| | | | - Hiroyuki Ishiba
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Kumiko Yoshizawa-Kumagaye
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Hideki Nishio
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Taku Yoshiya
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
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28
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Tsuda S, Mochizuki M, Ishiba H, Yoshizawa-Kumagaye K, Nishio H, Oishi S, Yoshiya T. Easy-to-Attach/Detach Solubilizing-Tag-Aided Chemical Synthesis of an Aggregative Capsid Protein. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shugo Tsuda
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
| | | | - Hiroyuki Ishiba
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Kumiko Yoshizawa-Kumagaye
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Hideki Nishio
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka-shi Osaka 560-0043 Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Taku Yoshiya
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
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29
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Total chemical synthesis of histones and their analogs, assisted by native chemical ligation and palladium complexes. Nat Protoc 2017; 12:2293-2322. [PMID: 28981125 DOI: 10.1038/nprot.2017.049] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chemical synthesis of histones allows precise control of the installation of post-translational modifications via the coupling of derivatized amino acids. Shortcomings of other approaches for obtaining modified histones for epigenetic studies include heterogeneity of the obtained product and difficulties in incorporating multiple modifications on the same histone. In this protocol, unprotected peptide fragments are prepared by Fmoc solid-phase synthesis and coupled in aqueous buffers via native chemical ligation (NCL; in NCL, a peptide bond is formed between a peptide with an N-terminal Cys and another peptide having a C-terminal thioester). This task is challenging, with obstacles relating to the preparation and ligation of hydrophobic peptides, as well as the requirement for multiple purification steps due to protecting-group manipulations during the polypeptide assembly process. To address this, our approach uses an easily removable solubilizing tag for the synthesis and ligation of hydrophobic peptides, as well as a more efficient and better-yielding method to remove Cys-protecting groups that uses palladium chemistry (specifically [Pd(allyl)Cl]2 and PdCl2 complexes). The utility of this approach is demonstrated in the syntheses of ubiquitinated H2B at Lys34, phosphorylated H2A at Tyr57 and unmodified H4. Each of these analogs can be prepared in milligram quantities within ∼20-30 d.
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30
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Harmand TJ, Pattabiraman VR, Bode JW. Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane-Associated Protein IFITM3 and Modified Variants. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 129:12813-12817. [PMID: 32313320 PMCID: PMC7159699 DOI: 10.1002/ange.201707554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Indexed: 12/18/2022]
Abstract
Interferon-induced transmembrane protein 3 (IFITM3) is an antiviral transmembrane protein that is thought to serve as the primary factor for inhibiting the replication of a large number of viruses, including West Nile virus, Dengue virus, Ebola virus, and Zika virus. Production of this 14.5 kDa, 133-residue transmembrane protein, especially with essential posttranslational modifications, by recombinant expression is challenging. In this report, we document the chemical synthesis of IFTIM3 in multi-milligram quantities (>15 mg) and the preparation of phosphorylated and fluorescent variants. The synthesis was accomplished by using KAHA ligations, which operate under acidic aqueous/organic mixtures that excel at solubilizing even the exceptionally hydrophobic C-terminal region of IFITM3. The synthetic material is readily incorporated into model vesicles and forms the basis for using synthetic, homogenous IFITM3 and its derivatives for further studying its structure and biological mode of action.
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Affiliation(s)
- Thibault J. Harmand
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied BiosciencesETH ZürichWolfgang Pauli Strasse 108093ZürichSwitzerland
| | - Vijaya R. Pattabiraman
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied BiosciencesETH ZürichWolfgang Pauli Strasse 108093ZürichSwitzerland
| | - Jeffrey W. Bode
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied BiosciencesETH ZürichWolfgang Pauli Strasse 108093ZürichSwitzerland
- Institue of Transformative Bio-Molecules (WPI-ITbM)Nagoya UniversityChisukaNagoya464-8602Japan
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Harmand TJ, Pattabiraman VR, Bode JW. Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane-Associated Protein IFITM3 and Modified Variants. Angew Chem Int Ed Engl 2017; 56:12639-12643. [PMID: 28834009 PMCID: PMC5658968 DOI: 10.1002/anie.201707554] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Indexed: 12/12/2022]
Abstract
Interferon‐induced transmembrane protein 3 (IFITM3) is an antiviral transmembrane protein that is thought to serve as the primary factor for inhibiting the replication of a large number of viruses, including West Nile virus, Dengue virus, Ebola virus, and Zika virus. Production of this 14.5 kDa, 133‐residue transmembrane protein, especially with essential posttranslational modifications, by recombinant expression is challenging. In this report, we document the chemical synthesis of IFTIM3 in multi‐milligram quantities (>15 mg) and the preparation of phosphorylated and fluorescent variants. The synthesis was accomplished by using KAHA ligations, which operate under acidic aqueous/organic mixtures that excel at solubilizing even the exceptionally hydrophobic C‐terminal region of IFITM3. The synthetic material is readily incorporated into model vesicles and forms the basis for using synthetic, homogenous IFITM3 and its derivatives for further studying its structure and biological mode of action.
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Affiliation(s)
- Thibault J Harmand
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang Pauli Strasse 10, 8093, Zürich, Switzerland
| | - Vijaya R Pattabiraman
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang Pauli Strasse 10, 8093, Zürich, Switzerland
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang Pauli Strasse 10, 8093, Zürich, Switzerland.,Institue of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chisuka, Nagoya, 464-8602, Japan
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Li JB, Tang S, Zheng JS, Tian CL, Liu L. Removable Backbone Modification Method for the Chemical Synthesis of Membrane Proteins. Acc Chem Res 2017; 50:1143-1153. [PMID: 28374993 DOI: 10.1021/acs.accounts.7b00001] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chemical synthesis can produce water-soluble globular proteins bearing specifically designed modifications. These synthetic molecules have been used to study the biological functions of proteins and to improve the pharmacological properties of protein drugs. However, the above advances notwithstanding, membrane proteins (MPs), which comprise 20-30% of all proteins in the proteomes of most eukaryotic cells, remain elusive with regard to chemical synthesis. This difficulty stems from the strong hydrophobic character of MPs, which can cause considerable handling issues during ligation, purification, and characterization steps. Considerable efforts have been made to improve the solubility of transmembrane peptides for chemical ligation. These methods can be classified into two main categories: the manipulation of external factors and chemical modification of the peptide. This Account summarizes our research advances in the development of chemical modification especially the two generations of removable backbone modification (RBM) strategy for the chemical synthesis of MPs. In the first RBM generation, we install a removable modification group at the backbone amide of Gly within the transmembrane peptides. In the second RBM generation, the RBM group can be installed into all primary amino acid residues. The second RBM strategy combines the activated intramolecular O-to-N acyl transfer reaction, in which a phenyl group remains unprotected during the coupling process, which can play a catalytic role to generate the activated phenyl ester to assist in the formation of amide. The key feature of the RBM group is its switchable stability in trifluoroacetic acid. The stability of these backbone amide N-modifications toward TFA can be modified by regulating the electronic effects of phenol groups. The free phenol group is acylated to survive the TFA deprotection step, while the acyl phenyl ester will be quantitatively hydrolyzed in a neutral aqueous solution, and the free phenol group increases the electron density of the benzene ring to make the RBM labile to TFA. The transmembrane peptide segment bearing RBM groups behaves like a water-soluble peptide during fluorenylmethyloxycarbonyl based solid-phase peptide synthesis (Fmoc SPPS), ligation, purification, and characterization. The quantitative removal of the RBM group can be performed to obtain full-length MPs. The RBM strategy was used to prepare the core transmembrane domain Kir5.1[64-179] not readily accessible by recombinant protein expression, the influenza A virus M2 proton channel with phosphorylation, the cation-specific ion channel p7 from the hepatitis C virus with site-specific NMR isotope labels, and so on. The RBM method enables the practical engineering of small- to medium-sized MPs or membrane protein domains to address fundamental questions in the biochemical, biophysical, and pharmaceutical sciences.
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Affiliation(s)
- Jia-Bin Li
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
- 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
| | - 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
| | - Ji-Shen Zheng
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, China
| | - Chang-Lin Tian
- School of Life Sciences, University of Science and Technology of China , Hefei 230027, 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
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Jacobsen MT, Petersen ME, Ye X, Galibert M, Lorimer GH, Aucagne V, Kay MS. A Helping Hand to Overcome Solubility Challenges in Chemical Protein Synthesis. J Am Chem Soc 2016; 138:11775-82. [PMID: 27532670 DOI: 10.1021/jacs.6b05719] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Although native chemical ligation (NCL) and related chemoselective ligation approaches provide an elegant method to stitch together unprotected peptides, the handling and purification of insoluble and aggregation-prone peptides and assembly intermediates create a bottleneck to routinely preparing large proteins by completely synthetic means. In this work, we introduce a new general tool, Fmoc-Ddae-OH, N-Fmoc-1-(4,4-dimethyl-2,6-dioxocyclo-hexylidene)-3-[2-(2-aminoethoxy)ethoxy]-propan-1-ol, a heterobifunctional traceless linker for temporarily attaching highly solubilizing peptide sequences ("helping hands") onto insoluble peptides. This tool is implemented in three simple and nearly quantitative steps: (i) on-resin incorporation of the linker at a Lys residue ε-amine, (ii) Fmoc-SPPS elongation of a desired solubilizing sequence, and (iii) in-solution removal of the solubilizing sequence using mild aqueous hydrazine to cleave the Ddae linker after NCL-based assembly. Successful introduction and removal of a Lys6 helping hand is first demonstrated in two model systems (Ebola virus C20 peptide and the 70-residue ribosomal protein L31). It is then applied to the challenging chemical synthesis of the 97-residue co-chaperonin GroES, which contains a highly insoluble C-terminal segment that is rescued by a helping hand. Importantly, the Ddae linker can be cleaved in one pot following NCL or desulfurization. The purity, structure, and chaperone activity of synthetic l-GroES were validated with respect to a recombinant control. Additionally, the helping hand enabled synthesis of d-GroES, which was inactive in a heterochiral mixture with recombinant GroEL, providing additional insight into chaperone specificity. Ultimately, this simple, robust, and easy-to-use tool is expected to be broadly applicable for the synthesis of challenging peptides and proteins.
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Affiliation(s)
- Michael T Jacobsen
- Department of Biochemistry, University of Utah School of Medicine , 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112-5650, United States
| | - Mark E Petersen
- Department of Biochemistry, University of Utah School of Medicine , 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112-5650, United States
| | - Xiang Ye
- Department of Chemistry & Biochemistry, 8051 Regents Drive, University of Maryland , College Park, Maryland 20742-4454, United States
| | - Mathieu Galibert
- Centre de Biophysique Moléculaire, CNRS UPR4301 , Rue Charles Sadron, Orléans CEDEX 2 45071, France
| | - George H Lorimer
- Department of Chemistry & Biochemistry, 8051 Regents Drive, University of Maryland , College Park, Maryland 20742-4454, United States
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR4301 , Rue Charles Sadron, Orléans CEDEX 2 45071, France
| | - Michael S Kay
- Department of Biochemistry, University of Utah School of Medicine , 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112-5650, United States
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Qi YK, Chang HN, Pan KM, Tian CL, Zheng JS. Total chemical synthesis of the site-selective azide-labeled [I66A]HIV-1 protease. Chem Commun (Camb) 2016; 51:14632-5. [PMID: 26289550 DOI: 10.1039/c5cc04846j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The first total chemical synthesis of the site-selective azide-labeled [I66A]HIV-1 protease is described by native chemical ligation. Chemical synthesis of azide-labeled proteins would provide useful protein tools for biochemical, biophysical or medical studies.
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Affiliation(s)
- Yun-Kun Qi
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.
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35
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Bondalapati S, Jbara M, Brik A. Expanding the chemical toolbox for the synthesis of large and uniquely modified proteins. Nat Chem 2016; 8:407-18. [DOI: 10.1038/nchem.2476] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 02/04/2016] [Indexed: 12/18/2022]
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Jbara M, Maity SK, Seenaiah M, Brik A. Palladium Mediated Rapid Deprotection of N-Terminal Cysteine under Native Chemical Ligation Conditions for the Efficient Preparation of Synthetically Challenging Proteins. J Am Chem Soc 2016; 138:5069-75. [DOI: 10.1021/jacs.5b13580] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Mallikanti Seenaiah
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
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37
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Jbara M, Maity SK, Morgan M, Wolberger C, Brik A. Chemical Synthesis of Phosphorylated Histone H2A at Tyr57 Reveals Insight into the Inhibition Mode of the SAGA Deubiquitinating Module. Angew Chem Int Ed Engl 2016; 55:4972-6. [PMID: 26960207 DOI: 10.1002/anie.201600638] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Indexed: 11/06/2022]
Abstract
Monoubiquitination of histone H2B plays a central role in transcription activation and is required for downstream histone-methylation events. Deubiquitination of H2B by the Spt-Ada-Gcn5 acetyltransferase (SAGA) coactivator complex is regulated by a recently discovered histone mark, phosphorylated H2AY57 (H2AY57p), which inhibits deubiquitination of H2B by the SAGA complex as well as restricting demethylation of H3 and increasing its acetylation. Evidence for the effect of H2AY57p, however, was indirect and was investigated in vivo by monitoring the effects of chemical inhibition of Tyr kinase CK2 or by mutating the phosphorylation site. We applied the total chemical synthesis of proteins to prepare H2AY57p efficiently and study the molecular details of this regulation. This analogue, together with semisynthetically prepared ubiquitinated H2B, enabled us to provide direct evidence for the cross-talk between those two marks and the inhibition of SAGA activity by H2AY57p.
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Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel
| | - Michael Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205-2185, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD, 21205-2185, USA.
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 3200008, Israel.
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38
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Jbara M, Maity SK, Morgan M, Wolberger C, Brik A. Chemical Synthesis of Phosphorylated Histone H2A at Tyr57 Reveals Insight into the Inhibition Mode of the SAGA Deubiquitinating Module. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600638] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Michael Morgan
- Department of Biophysics and Biophysical Chemistry; Johns Hopkins University School of Medicine; 725 North Wolfe Street Baltimore MD 21205-2185 USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry; Johns Hopkins University School of Medicine; 725 North Wolfe Street Baltimore MD 21205-2185 USA
| | - Ashraf Brik
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
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39
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Zheng JS, He Y, Zuo C, Cai XY, Tang S, Wang ZA, Zhang LH, Tian CL, Liu L. Robust Chemical Synthesis of Membrane Proteins through a General Method of Removable Backbone Modification. J Am Chem Soc 2016; 138:3553-61. [PMID: 26943264 DOI: 10.1021/jacs.6b00515] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemical protein synthesis can provide access to proteins with post-translational modifications or site-specific labelings. Although this technology is finding increasing applications in the studies of water-soluble globular proteins, chemical synthesis of membrane proteins remains elusive. In this report, a general and robust removable backbone modification (RBM) method is developed for the chemical synthesis of membrane proteins. This method uses an activated O-to-N acyl transfer auxiliary to install in the Fmoc solid-phase peptide synthesis process a RBM group with switchable reactivity toward trifluoroacetic acid. The method can be applied to versatile membrane proteins because the RBM group can be placed at any primary amino acid. With RBM, the membrane proteins and their segments behave almost as if they were water-soluble peptides and can be easily handled in the process of ligation, purification, and mass characterizations. After the full-length protein is assembled, the RBM group can be readily removed by trifluoroacetic acid. The efficiency and usefulness of the new method has been demonstrated by the successful synthesis of a two-transmembrane-domain protein (HCV p7 ion channel) with site-specific isotopic labeling and a four-transmembrane-domain protein (multidrug resistance transporter EmrE). This method enables practical synthesis of small- to medium-sized membrane proteins or membrane protein domains for biochemical and biophysical studies.
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Affiliation(s)
- Ji-Shen Zheng
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Yao He
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Chao Zuo
- 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
| | - Xiao-Ying Cai
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , 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
| | - Zhipeng A Wang
- 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
| | - Long-Hua Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , Hefei 230031, China
| | - Chang-Lin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China , 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
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40
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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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41
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Hojo H. A strategy for the synthesis of hydrophobic proteins and glycoproteins. Org Biomol Chem 2016; 14:6368-74. [DOI: 10.1039/c6ob00827e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrophobic glycoprotein was successfully synthesized by the reverse polarity protection strategy combined with the O-acylisopeptide method, which will be useful for the synthesis of various hydrophobic (glyco)proteins.
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Affiliation(s)
- Hironobu Hojo
- Institute for Protein Research
- Osaka University
- Suita
- Japan
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42
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Tian Y, Wang L, Shi J, Yu HZ. Desulfurization Mechanism of Cysteine in Synthesis of Polypeptides. CHINESE J CHEM PHYS 2015. [DOI: 10.1063/1674-0068/28/cjcp1501009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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43
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Zhao J, Zhou Y, Li Y, Pan X, Zhang W, Zhou N, Zhang K, Zhang Z, Zhu X. Modular construction of macrocycle-based topological polymers via high-efficient thiol chemistry. Polym Chem 2015. [DOI: 10.1039/c5py00174a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tadpole-, spiro-shaped, fused-dicyclic tadpole and other complex macrocycle-based topological polymers were modularly constructed via thiol-X chemistry.
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Affiliation(s)
- Junfei Zhao
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
| | - Yanyan Zhou
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
| | - Yiwen Li
- Department of Chemistry and Biochemistry
- University of California
- La Jolla
- USA
| | - Xiangqiang Pan
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
| | - Wei Zhang
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
| | - Nianchen Zhou
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
| | - Ke Zhang
- State Key Laboratory of Polymer Physics and Chemistry
- Institute of Chemistry
- The Chinese Academy of Sciences
- Beijing 100190
- China
| | - Zhengbiao Zhang
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
| | - Xiulin Zhu
- Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
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Zheng JS, Yu M, Qi YK, Tang S, Shen F, Wang ZP, Xiao L, Zhang L, Tian CL, Liu L. Expedient total synthesis of small to medium-sized membrane proteins via Fmoc chemistry. J Am Chem Soc 2014; 136:3695-704. [PMID: 24559202 DOI: 10.1021/ja500222u] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Total chemical synthesis provides a unique approach for the access to uncontaminated, monodisperse, and more importantly, post-translationally modified membrane proteins. In the present study we report a practical procedure for expedient and cost-effective synthesis of small to medium-sized membrane proteins in multimilligram scale through the use of automated Fmoc chemistry. The key finding of our study is that after the attachment of a removable arginine-tagged backbone modification group, the membrane protein segments behave almost the same as ordinary water-soluble peptides in terms of Fmoc solid-phase synthesis, ligation, purification, and mass spectrometry characterization. The efficiency and practicality of the new method is demonstrated by the successful preparation of Ser64-phosphorylated M2 proton channel from influenza A virus and the membrane-embedded domain of an inward rectifier K(+) channel protein Kir5.1. Functional characterizations of these chemically synthesized membrane proteins indicate that they provide useful and otherwise-difficult-to-access materials for biochemistry and biophysics studies.
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Affiliation(s)
- Ji-Shen Zheng
- 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
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45
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Liu F, Mayer JP. Protein Chemical Synthesis in Drug Discovery. PROTEIN LIGATION AND TOTAL SYNTHESIS I 2014; 362:183-228. [DOI: 10.1007/128_2014_598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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46
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Modern Extensions of Native Chemical Ligation for Chemical Protein Synthesis. PROTEIN LIGATION AND TOTAL SYNTHESIS I 2014; 362:27-87. [DOI: 10.1007/128_2014_584] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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47
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Huang YC, Li YM, Chen Y, Pan M, Li YT, Yu L, Guo QX, Liu L. Synthesis of Autophagosomal Marker Protein LC3-II under Detergent-Free Conditions. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209523] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Huang YC, Li YM, Chen Y, Pan M, Li YT, Yu L, Guo QX, Liu L. Synthesis of Autophagosomal Marker Protein LC3-II under Detergent-Free Conditions. Angew Chem Int Ed Engl 2013; 52:4858-62. [DOI: 10.1002/anie.201209523] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/06/2013] [Indexed: 11/10/2022]
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49
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Li KK, Luo C, Wang D, Jiang H, Zheng YG. Chemical and biochemical approaches in the study of histone methylation and demethylation. Med Res Rev 2012; 32:815-67. [PMID: 22777714 DOI: 10.1002/mrr.20228] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Histone methylation represents one of the most critical epigenetic events in DNA function regulation in eukaryotic organisms. Classic molecular biology and genetics tools provide significant knowledge about mechanisms and physiological roles of histone methyltransferases and demethylases in various cellular processes. In addition to this stream line, development and application of chemistry and chemistry-related techniques are increasingly involved in biological study, and offer information otherwise difficult to obtain by standard molecular biology methods. Herein, we review recent achievements and progress in developing and applying chemical and biochemical approaches in the study of histone methylation, including chromatin immunoprecipitation, chemical ligation, mass spectrometry, biochemical methylation and demethylation assays, and inhibitor development. These technological advances allow histone methylation to be studied from genome-wide level to molecular and atomic levels. With ChIP technology, information can be obtained about precise mapping of histone methylation patterns at specific promoters, genes, or other genomic regions. MS is particularly useful in detecting and analyzing methylation marks in histone and nonhistone protein substrates. Chemical approaches that permit site-specific incorporation of methyl groups into histone proteins greatly facilitate the investigation of biological impacts of methylation at individual modification sites. Discovery and design of selective organic inhibitors of histone methyltransferases and demethylases provide chemical probes to interrogate methylation-mediated cellular pathways. Overall, these chemistry-related technological advances have greatly improved our understanding of the biological functions of histone methylation in normal physiology and diseased states, and also are of great potential to translate basic epigenetics research into diagnostic and therapeutic applications in the clinic.
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Affiliation(s)
- Keqin Kathy Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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50
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Shen F, Huang YC, Tang S, Chen YX, Liu L. Chemical Synthesis of Integral Membrane Proteins: Methods and Applications. Isr J Chem 2011. [DOI: 10.1002/ijch.201100076] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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