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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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Xing Y, Wang Y, Ma D, Shen S, Song C, Zhang N, Bo T, Shi T, Huo S. N-Halosuccinimides mediated deprotection of cysteine-S protecting groups for one-pot regioselective synthesis of disulfide bonds in peptides under mild aqueous conditions. Tetrahedron Lett 2023. [DOI: 10.1016/j.tetlet.2023.154459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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3
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Nakatsu K, Okamoto A, Hayashi G, Murakami H. Repetitive Thiazolidine Deprotection Using a Thioester‐Compatible Aldehyde Scavenger for One‐Pot Multiple Peptide Ligation**. Angew Chem Int Ed Engl 2022; 61:e202206240. [DOI: 10.1002/anie.202206240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Koki Nakatsu
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology Graduate School of Engineering 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
| | - Gosuke Hayashi
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho Chikusa-ku Nagoya 464-8603 Japan
- Institute of Nano-Life-Systems Institutes of Innovation for Future Society Nagoya University Furo-cho Chikusa-ku Nagoya 464-8603 Japan
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4
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Hayashi G, Nakatsu K, Okamoto A, Murakami H. Repetitive Thiazolidine Deprotection Using a Thioester‐Compatible Aldehyde Scavenger for One‐Pot Multiple Peptide Ligation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Gosuke Hayashi
- Nagoya University Graduate School of Engineering School of Engineering: Nagoya Daigaku Kogakubu Daigakuin Kogaku Kenkyuka Biomolecular Engineering Furo-choChikusa-ku 464-8603 Nagoya JAPAN
| | - Koki Nakatsu
- Nagoya University Graduate School of Engineering School of Engineering: Nagoya Daigaku Kogakubu Daigakuin Kogaku Kenkyuka Biomolecular Engineering JAPAN
| | - Akimitsu Okamoto
- The University of Tokyo Graduate School of Engineering Faculty of Engineering: Tokyo Daigaku Daigakuin Kogakukei Kenkyuka Kogakubu Chemistry and Biotechnology JAPAN
| | - Hiroshi Murakami
- Nagoya University Graduate School of Engineering School of Engineering: Nagoya Daigaku Kogakubu Daigakuin Kogaku Kenkyuka Biomolecular Engineering JAPAN
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5
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Posttranslational Chemical Mutagenesis Methods to Insert Posttranslational Modifications into Recombinant Proteins. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144389. [PMID: 35889261 PMCID: PMC9316245 DOI: 10.3390/molecules27144389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Posttranslational modifications (PTMs) dramatically expand the functional diversity of the proteome. The precise addition and removal of PTMs appears to modulate protein structure and function and control key regulatory processes in living systems. Deciphering how particular PTMs affect protein activity is a current frontier in biology and medicine. The large number of PTMs which can appear in several distinct positions, states, and combinations makes preparing such complex analogs using conventional biological and chemical tools challenging. Strategies to access homogeneous and precisely modified proteins with desired PTMs at selected sites and in feasible quantities are critical to interpreting their molecular code. Here, we summarize recent advances in posttranslational chemical mutagenesis and late-stage functionalization chemistry to transfer novel PTM mimicry into recombinant proteins with emphasis on novel transformations.
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Jacobsen MT, Spaltenstein P, Giesler RJ, Chou DHC, Kay MS. Improved Handling of Peptide Segments Using Side Chain-Based "Helping Hand" Solubilizing Tools. Methods Mol Biol 2022; 2530:81-107. [PMID: 35761044 DOI: 10.1007/978-1-0716-2489-0_7] [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] [Indexed: 06/15/2023]
Abstract
Maintaining high, or even sufficient, solubility of every peptide segment in chemical protein synthesis (CPS) remains a critical challenge; insolubility of just a single peptide segment can thwart a total synthesis venture. Multiple approaches have been used to address this challenge, most commonly by employing a chemical tool to temporarily improve peptide solubility. In this chapter, we discuss chemical tools for introducing semipermanent solubilizing sequences (termed helping hands) at the side chains of Lys and Glu residues. We describe the synthesis, incorporation by Fmoc-SPPS, and cleavage conditions for utilizing these two tools. For Lys sites, we discuss the Fmoc-Ddap-OH dimedone-based linker, which is achiral, synthesized in one step, can be introduced directly at primary amines, and is removed using hydroxylamine (or hydrazine). For Glu sites, we detail the new Fmoc-SPPS building block, Fmoc-Glu(AlHx)-OH, which can be prepared in an efficient process over two purifications. Solubilizing sequences are introduced directly on-resin and later cleaved with palladium-catalyzed transfer under aqueous conditions to restore a native Glu side chain. These two chemical tools are straightforward to prepare and implement, and we anticipate continued usage in "difficult" peptide segments following the protocols described herein.
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Affiliation(s)
- Michael T Jacobsen
- Division of Diabetes and Endocrinology, Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Paul Spaltenstein
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Riley J Giesler
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Danny Hung-Chieh Chou
- Division of Diabetes and Endocrinology, Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Michael S Kay
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
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7
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Giesler RJ, Spaltenstein P, Jacobsen MT, Xu W, Maqueda M, Kay MS. A glutamic acid-based traceless linker to address challenging chemical protein syntheses. Org Biomol Chem 2021; 19:8821-8829. [PMID: 34585207 PMCID: PMC8604549 DOI: 10.1039/d1ob01611c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Native chemical ligation (NCL) enables the total chemical synthesis of proteins. However, poor peptide segment solubility remains a frequently encountered challenge. Here we introduce a traceless linker that can be temporarily attached to Glu side chains to overcome this problem. This strategy employs a new tool, Fmoc-Glu(AlHx)-OH, which can be directly installed using standard Fmoc-based solid-phase peptide synthesis. The incorporated residue, Glu(AlHx), is stable to a wide range of chemical protein synthesis conditions and is removed through palladium-catalyzed transfer under aqueous conditions. General handling characteristics, such as efficient incorporation, stability and rapid removal were demonstrated through a model peptide modified with Glu(AlHx) and a Lys6 solubilizing tag. Glu(AlHx) was incorporated into a highly insoluble peptide segment during the total synthesis of the bacteriocin AS-48. This challenging peptide was successfully synthesized and folded, and it has comparable antimicrobial activity to the native AS-48. We anticipate widespread use of this easy-to-use, robust linker for the preparation of challenging synthetic peptides and proteins.
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Affiliation(s)
- Riley J Giesler
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112-5650, USA.
| | - Paul Spaltenstein
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112-5650, USA.
| | - Michael T Jacobsen
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, CA 94304, USA
| | - Weiliang Xu
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112-5650, USA.
| | - Mercedes Maqueda
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain
| | - 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, USA.
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Spears RJ, McMahon C, Chudasama V. Cysteine protecting groups: applications in peptide and protein science. Chem Soc Rev 2021; 50:11098-11155. [PMID: 34605832 DOI: 10.1039/d1cs00271f] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protecting group chemistry for the cysteine thiol group has enabled a vast array of peptide and protein chemistry over the last several decades. Increasingly sophisticated strategies for the protection, and subsequent deprotection, of cysteine have been developed, facilitating synthesis of complex disulfide-rich peptides, semisynthesis of proteins, and peptide/protein labelling in vitro and in vivo. In this review, we analyse and discuss the 60+ individual protecting groups reported for cysteine, highlighting their applications in peptide synthesis and protein science.
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Affiliation(s)
| | - Clíona McMahon
- Department of Chemistry, University College London, London, UK.
| | - Vijay Chudasama
- Department of Chemistry, University College London, London, UK.
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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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Kamo N, Kujirai T, Kurumizaka H, Murakami H, Hayashi G, Okamoto A. Organoruthenium-catalyzed chemical protein synthesis to elucidate the functions of epigenetic modifications on heterochromatin factors. Chem Sci 2021; 12:5926-5937. [PMID: 35342540 PMCID: PMC8872386 DOI: 10.1039/d1sc00731a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/21/2021] [Indexed: 12/21/2022] Open
Abstract
The application of organometallic compounds for protein science has received attention. Recently, total chemical protein synthesis using transition metal complexes has been developed to produce various proteins bearing site-specific posttranslational modifications (PTMs). However, in general, significant amounts of metal complexes were required to achieve chemical reactions of proteins bearing a large number of nucleophilic functional groups. Moreover, syntheses of medium-size proteins (>20 kDa) were plagued by time-consuming procedures due to cumbersome purification and isolation steps, which prevented access to variously decorated proteins. Here, we report a one-pot multiple peptide ligation strategy assisted by an air-tolerant organoruthenium catalyst that showed more than 50-fold activity over previous palladium complexes, leading to rapid and quantitative deprotection on a protein with a catalytic amount (20 mol%) of the metal complex even in the presence of excess thiol moieties. Utilizing the organoruthenium catalyst, heterochromatin factors above 20 kDa, such as linker histone H1.2 and heterochromatin protein 1α (HP1α), bearing site-specific PTMs including phosphorylation, ubiquitination, citrullination, and acetylation have been synthesized. The biochemical assays using synthetic proteins revealed that the citrullination at R53 in H1.2 resulted in the reduced electrostatic interaction with DNA and the reduced binding affinity to nucleosomes. Furthermore, we identified a key phosphorylation region in HP1α to control its DNA-binding ability. The ruthenium chemistry developed here will facilitate the preparation of a variety of biologically and medically significant proteins containing PTMs and non-natural amino acids. Chemical protein synthesis assisted by an organoruthenium catalyst streamlined the production of heterochromatin factors bearing various patterns of epigenetic modifications, and their biological significance was elucidated.![]()
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Affiliation(s)
- Naoki Kamo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, 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, Meguro-ku, Tokyo 153-8904, Japan
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Kobayashi D, Naruse N, Denda M, Shigenaga A, Otaka A. Deprotection of S-acetamidomethyl cysteine with copper(ii) and 1,2-aminothiols under aerobic conditions. Org Biomol Chem 2020; 18:8638-8645. [PMID: 32856682 DOI: 10.1039/d0ob01475c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Ring-opening by CuSO4 of a 1,3-thiazolidine carbonyl structure (Thz) as an N-terminal cysteine (Cys) residue revealed that an intramolecular S-acetamidomethyl cysteine (Cys(Acm)) can also be deprotected with concomitant formation of a disulphide bond connecting the two Cys residues. A mechanistic study on the disulphide formation led to a general protocol for deprotection of the S-Acm group by CuSO4 and a 1,2-aminothiol under aerobic conditions. Application of this new deprotection reaction allowed for the synthesis of Apamin, a peptide with two-disulphides in a one-pot/stepwise disulphide-bridging procedure.
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Affiliation(s)
- Daishiro Kobayashi
- Insutitute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima 770-8505, Japan.
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Nakatsu K, Hayashi G, Okamoto A. Toolbox for chemically synthesized histone proteins. Curr Opin Chem Biol 2020; 58:10-19. [DOI: 10.1016/j.cbpa.2020.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 01/28/2023]
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Abstract
Abstract
Site-specific protein conjugation is a critical step in the generation of unique protein analogs for a range of basic research and therapeutic developments. Protein transformations must target a precise residue in the presence of a plethora of functional groups to obtain a well-characterized homogeneous product. Competing reactive residues on natural proteins render rapid and selective conjugation a challenging task. Organometallic reagents have recently emerged as a powerful strategy to achieve site-specific labeling of a diverse set of biopolymers, due to advances in water-soluble ligand design, high reaction rate, and selectivity. The thiophilic nature of various transition metals, especially soft metals, makes cysteine an ideal target for these reagents. The distinctive reactivity and selectivity of organometallic-based reactions, along with the unique reactivity and abundancy of cysteine within the human proteome, provide a powerful platform to modify native proteins in aqueous media. These reactions often provide the modified proteins with a stable linkage made from irreversible cross-coupling steps. Additionally, transition metal reagents have recently been applied for the decaging of cysteine residues in the context of chemical protein synthesis. Orthogonal cysteine protecting groups and functional tags are often necessary for the synthesis of challenging proteins, and organometallic reagents are powerful tools for selective, rapid, and water-compatible removal of those moieties. This review examines transition metal-based reactions of cysteine residues for the synthesis and modification of natural peptides and proteins.
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Affiliation(s)
- Muhammad Jbara
- Massachusetts Institute of Technology , Department of Chemistry , 77 Massachusetts Avenue , Cambridge , MA , 02139, USA
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Nakatsu K, Yanase M, Hayashi G, Okamoto A. Fmoc-Compatible and C-terminal-Sequence-Independent Peptide Alkyl Thioester Formation Using Cysteinylprolyl Imide. Org Lett 2020; 22:4670-4674. [PMID: 32484687 DOI: 10.1021/acs.orglett.0c01450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report an Fmoc-compatible and external-thiol-free method of peptide C-terminus thioesterification with cysteinylprolyl imide. The newly synthesized structure, i.e., cysteinylprolyl-thiazolidinone, provided high conversion and sequence-independent fast kinetics (90 min) in the diketopiperazine thioester formation under relatively mild conditions: pH 6.0, 37 °C. Employing this thioesterification method, we synthesized histone H3.2 bearing K56 acetylation.
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Affiliation(s)
- Koki Nakatsu
- 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
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, 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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