1
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Liao P, He C. Azole reagents enabled ligation of peptide acyl pyrazoles for chemical protein synthesis. Chem Sci 2024; 15:7965-7974. [PMID: 38817582 PMCID: PMC11134319 DOI: 10.1039/d3sc06697e] [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: 12/13/2023] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
Native chemical ligation (NCL) has been playing an increasingly important role in chemical protein synthesis (CPS). More efficient ligation methods that circumvent the requirement of a peptidyl thioester and thiol additive-which allow the following desulfurization or refolding in one pot-are urgently needed for the synthesis of more complex protein targets and in large quantities. Herein, we discover that the weak acyl donor peptidyl N-acyl pyrazole can be activated by azole reagents like 3-methylpyrazole or imidazole to facilitate its ligation directly with an N-terminal cysteine peptide. As it requires no thioester or thiol additive, this ligation strategy can be conveniently combined with metal-free desulfurization (MFD) or oxidative protein folding to allow various one-pot protocols. The utility and generality of the strategy are showcased by the total synthesis of ubiquitin via an N-to-C sequential ligation-MFD strategy, the semi-synthesis of the copper protein azurin, and the efficient assembly of a sulfated hirudin variant and the cyclotide kalata B1, all in a one-pot fashion.
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Affiliation(s)
- Peisi Liao
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
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2
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Huppelschoten Y, van der Heden van Noort GJ. State of the art in (semi-)synthesis of Ubiquitin- and Ubiquitin-like tools. Semin Cell Dev Biol 2022; 132:74-85. [PMID: 34961664 DOI: 10.1016/j.semcdb.2021.11.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/14/2022]
Abstract
Protein ubiquitination is a key post-translational modification in regulating many fundamental cellular processes and dysregulation of these processes can give rise to a vast array of diseases. Unravelling the molecular mechanisms of ubiquitination hence is an important area in current ubiquitin research with as aim to understand this enigmatic process. The complexity of ubiquitin (Ub) signaling arises from the large variety of Ub conjugates, where Ub is attached to other Ub proteins, Ub-like proteins, and protein substrates. The chemical preparation of such Ub conjugates in high homogeneity and in adequate amounts contributes greatly to the deciphering of Ub signaling. The strength of these chemically synthesized conjugates lies in the chemo-selectivity in which they can be created that are sometimes difficult to obtain using biochemical methodology. In this review, we will discuss the progress in the chemical protein synthesis of state-of-the-art Ub and Ub-like chemical probes, their unique concepts and related discoveries in the ubiquitin field.
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Affiliation(s)
- Yara Huppelschoten
- Oncode Institute and Dept. Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands; Global Research Technologies, Novo Nordisk Research Park, Måløv, Denmark
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3
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Saha A, Mandal S, Arafiles JVV, Gómez‐González J, Hackenberger CPR, Brik A. Structure-Uptake Relationship Study of DABCYL Derivatives Linked to Cyclic Cell-Penetrating Peptides for Live-Cell Delivery of Synthetic Proteins. Angew Chem Int Ed Engl 2022; 61:e202207551. [PMID: 36004945 PMCID: PMC9828537 DOI: 10.1002/anie.202207551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 01/12/2023]
Abstract
Modifying cyclic cell-penetrating deca-arginine (cR10) peptides with 4-(4-dimethylaminophenylazo)benzoic acid (DABCYL) improves the uptake efficiency of synthetic ubiquitin (Ub) cargoes into living cells. To probe the role of the DABCYL moiety, we performed time-lapse microscopy and fluorescence lifetime imaging microscopy (FLIM) of fluorescent DABCYL-R10 to evaluate the impact on cell entry by the formation of nucleation zones. Furthermore, we performed a structure-uptake relationship study with 13 DABCYL derivatives coupled to CPP to examine their effect on the cell-uptake efficiency when conjugated to mono-Ub through disulfide linkages. Our results show that through structure variations of the DABCYL moiety alone we could reach, at nanomolar concentration, an additional threefold increase in the cytosolic delivery of Ub, which will enable studies on various intracellular processes related to Ub signaling.
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Affiliation(s)
- Abhishek Saha
- Schulich Faculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
| | - Shaswati Mandal
- Schulich Faculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
| | - Jan Vincent V. Arafiles
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 10Berlin13125Germany
| | - Jacobo Gómez‐González
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 10Berlin13125Germany
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 10Berlin13125Germany
- Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Str.2Berlin12489Germany
| | - Ashraf Brik
- Schulich Faculty of ChemistryTechnion-Israel Institute of TechnologyHaifa3200008Israel
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4
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Burslem GM. The chemical biology of ubiquitin. Biochim Biophys Acta Gen Subj 2022; 1866:130079. [PMID: 34971772 PMCID: PMC10038182 DOI: 10.1016/j.bbagen.2021.130079] [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: 11/03/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
This mini-review will cover the various chemical biology approaches employed to prepare and modulate ubiquitin chains and the ubiquitin-proteasome system. Emphasis will be given to the biochemistry and chemical biology of poly-ubiquitin chain preparation as a tool to elucidate its roles in biological systems as well as the hijacking of the ubiquitin proteasome system using heterobifunctional compounds to induce intracellular ubiquitination.
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Affiliation(s)
- George M Burslem
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA.
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5
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Zhou Y, Xie Q, Wang H, Sun H. Chemical approaches for the preparation of ubiquitinated proteins via natural linkages. J Pept Sci 2021; 28:e3367. [PMID: 34514672 DOI: 10.1002/psc.3367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022]
Abstract
Ubiquitination is an important posttranslation modification (PTM) that regulates a variety of cellular processes, including protein degradation, DNA repair, and viral infections. In this process, the C-terminal carboxyl group of ubiquitin (Ub) or poly-Ub is attached to the ε-amine of lysine (Lys) side chain of an acceptor protein through an isopeptide bond. Studying a molecular mechanism of ubiquitination and deubiquitination is fundamental for unraveling its precise role in health and disease and hence crucial for drug development. Enzymatic approaches for protein ubiquitination possess limited ability to selectivity install Ub or Ub chain on the desired position of an acceptor protein and often lead to heterogeneous mixtures. In the past decades, chemical protein (semi)synthesis has been proved to be an efficient tool to facilitate site-specific protein ubiquitination, which significantly contributes to decode the Ub signal at molecular and structural levels. In this review, we summarize the synthetic strategies developed for protein ubiquitination, and the achievements to generate monoubiquitinated, di-ubiquitinated, and tetraubiquitinated proteins with native isopeptide and ester bonds.
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Affiliation(s)
- Yuhui Zhou
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qingsong Xie
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Huagui Wang
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hao Sun
- College of Sciences, Nanjing Agricultural University, Nanjing, China
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6
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Abboud SA, Amoura M, Madinier J, Renoux B, Papot S, Piller V, Aucagne V. Enzyme‐Cleavable Linkers for Protein Chemical Synthesis through Solid‐Phase Ligations. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Skander A. Abboud
- Centre de Biophysique Moléculaire CNRS UPR 4301 Rue Charles Sadron 45071 Orléans cedex 2 France
| | - Mehdi Amoura
- Centre de Biophysique Moléculaire CNRS UPR 4301 Rue Charles Sadron 45071 Orléans cedex 2 France
| | - Jean‐Baptiste Madinier
- Centre de Biophysique Moléculaire CNRS UPR 4301 Rue Charles Sadron 45071 Orléans cedex 2 France
| | - Brigitte Renoux
- Institut de Chimie des Milieux et des Matériaux de Poitiers UMR-CNRS 7285 4 rue Michel Brunet 86073 Poitiers cedex 9 France
| | - Sébastien Papot
- Institut de Chimie des Milieux et des Matériaux de Poitiers UMR-CNRS 7285 4 rue Michel Brunet 86073 Poitiers cedex 9 France
| | - Véronique Piller
- 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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7
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Abboud SA, Amoura M, Madinier JB, Renoux B, Papot S, Piller V, Aucagne V. Enzyme-Cleavable Linkers for Protein Chemical Synthesis through Solid-Phase Ligations. Angew Chem Int Ed Engl 2021; 60:18612-18618. [PMID: 34097786 DOI: 10.1002/anie.202103768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Indexed: 12/26/2022]
Abstract
The total synthesis of long proteins requires the assembly of multiple fragments through successive ligations. The need for intermediate purification steps is a strong limitation, particularly in terms of overall yield. One solution to this problem would be solid-supported chemical ligation (SPCL), for which a first peptide segment must be immobilized on a SPCL-compatible solid support through a linker that can be cleaved under very mild conditions to release the assembled protein. The cleavage of SPCL linkers has previously required chemical conditions sometimes incompatible with sensitive protein targets. Herein, we describe an alternative enzymatic approach to trigger cleavage under extremely mild and selective conditions. Optimization of the linker structure and use of a small enzyme able to diffuse into the solid support were key to the success of the strategy. We demonstrated its utility by the assembly of three peptide segments on the basis of native chemical ligation to afford a 15 kDa polypeptide.
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Affiliation(s)
- Skander A Abboud
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France
| | - Mehdi Amoura
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France
| | - Jean-Baptiste Madinier
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron, 45071, Orléans cedex 2, France
| | - Brigitte Renoux
- Institut de Chimie des Milieux et des Matériaux de Poitiers, UMR-CNRS 7285, 4 rue Michel Brunet, 86073, Poitiers cedex 9, France
| | - Sébastien Papot
- Institut de Chimie des Milieux et des Matériaux de Poitiers, UMR-CNRS 7285, 4 rue Michel Brunet, 86073, Poitiers cedex 9, France
| | - Véronique Piller
- 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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8
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General synthetic strategy for regioselective ultrafast formation of disulfide bonds in peptides and proteins. Nat Commun 2021; 12:870. [PMID: 33558523 PMCID: PMC7870662 DOI: 10.1038/s41467-021-21209-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/06/2021] [Indexed: 12/15/2022] Open
Abstract
Despite six decades of efforts to synthesize peptides and proteins bearing multiple disulfide bonds, this synthetic challenge remains an unsolved problem in most targets (e.g., knotted mini proteins). Here we show a de novo general synthetic strategy for the ultrafast, high-yielding formation of two and three disulfide bonds in peptides and proteins. We develop an approach based on the combination of a small molecule, ultraviolet-light, and palladium for chemo- and regio-selective activation of cysteine, which enables the one-pot formation of multiple disulfide bonds in various peptides and proteins. We prepare bioactive targets of high therapeutic potential, including conotoxin, RANTES, EETI-II, and plectasin peptides and the linaclotide drug. We anticipate that this strategy will be a game-changer in preparing millions of inaccessible targets for drug discovery.
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9
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Izumi M, Araki H, Tominaga M, Okamoto R, Kajihara Y. Chemical Synthesis of Ubiquitinated High-Mannose-Type N-Glycoprotein CCL1 in Different Folding States. J Org Chem 2020; 85:16024-16034. [PMID: 32985191 DOI: 10.1021/acs.joc.0c01766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Degradation of misfolded glycoproteins by the ubiquitin-proteasome system (UPS) is a very important process for protein homeostasis. To demonstrate the accessibility toward a ubiquitinated glycoprotein probe for the study of glycoprotein degradation by UPS, we synthesized ubiquitinated glycoprotein CC motif chemokine 1 (CCL1) bearing a high-mannose-type N-glycan, starting from six peptide segments. A native isopeptide linkage was constructed using δ-thiolysine (thioLys)-mediated chemical ligation. CCL1 glycopeptide with a high-mannose-type N-glycan as well as a δ-thioLys residue was synthesized chemically. The chemical ligation between δ-thioLys-containing glycopeptide and ubiquitin-α-thioester successfully yielded a ubiquitinated glycopeptide with a native isopeptide bond after desulfurization, even in the presence of a large N-glycan. In vitro folding experiments under reduced and redox conditions gave the desired two types of ubiquitinated glycosylated CCL1s, consisting of unfolded CCL1 and folded ubiquitin, and the folded form of both CCL1 as well as ubiquitin. We achieved the chemical synthesis of a complex protein molecule that contains not only the two major post-translational modifications, ubiquitination and glycosylation, but also controlled folding states of ubiquitin and CCL1. These chemical probes could have useful applications in the study of complex ubiquitin biology and glycobiology.
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Affiliation(s)
- Masayuki Izumi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, 2-5-1 Akebono-cho, Kochi, Kochi 780-8520, Japan
| | - Hiroyuki Araki
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Mamiko Tominaga
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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10
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11
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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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12
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Yanase M, Nakatsu K, Cardos CJ, Konda Y, Hayashi G, Okamoto A. Cysteinylprolyl imide (CPI) peptide: a highly reactive and easily accessible crypto-thioester for chemical protein synthesis. Chem Sci 2019; 10:5967-5975. [PMID: 31360403 PMCID: PMC6566460 DOI: 10.1039/c9sc00646j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/09/2019] [Indexed: 12/21/2022] Open
Abstract
A new crypto-thioester, cysteinylprolyl imide (CPI) peptide, offers a practical synthetic pathway and reliable reaction rate to be successfully applied to chemical protein synthesis.
Native chemical ligation (NCL) between the C-terminal peptide thioester and the N-terminal cysteinyl-peptide revolutionized the field of chemical protein synthesis. The difficulty of direct synthesis of the peptide thioester in the Fmoc method has prompted the development of crypto-thioesters that can be efficiently converted into thioesters. Cysteinylprolyl ester (CPE), which is an N–S acyl shift-driven crypto-thioester that relies on an intramolecular O–N acyl shift to displace the amide-thioester equilibrium, enabled trans-thioesterification and subsequent NCL in one pot. However, the utility of CPE is limited because of the moderate thioesterification rates and the synthetic complexity introduced by the ester group. Herein, we develop a new crypto-thioester, cysteinylprolyl imide (CPI), which replaces the alcohol leaving group of CPE with other leaving groups such as benzimidazolidinone, oxazolidinone, and pyrrolidinone. CPI peptides were efficiently synthesized by using standard Fmoc solid-phase peptide synthesis (SPPS) and subsequent on-resin imide formation. Screening of the several imide structures indicated that methyloxazolidinone-t-leucine (MeOxd-Tle) showed faster conversion into thioester and higher stability against hydrolysis under NCL conditions. Finally, by using CPMeOxd-Tle peptides, we demonstrated the chemical synthesis of affibody via N-to-C sequential, three-segment ligation and histone H2A.Z via convergent four-segment ligation. This facile and straightforward method is expected to be broadly applicable to chemical protein synthesis.
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Affiliation(s)
- Masafumi Yanase
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Koki Nakatsu
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Charlane Joy Cardos
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Yoshiki Konda
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Gosuke Hayashi
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan . .,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 , 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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13
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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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14
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Friedel K, Popp MA, Matern JCJ, Gazdag EM, Thiel IV, Volkmann G, Blankenfeldt W, Mootz HD. A functional interplay between intein and extein sequences in protein splicing compensates for the essential block B histidine. Chem Sci 2018; 10:239-251. [PMID: 30713635 PMCID: PMC6333167 DOI: 10.1039/c8sc01074a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/03/2018] [Indexed: 01/28/2023] Open
Abstract
Steric bulk can compensate for a catalytically critical histidine in an intein's active site and promote the N–S acyl shift.
Inteins remove themselves from a precursor protein by protein splicing. Due to the concomitant structural changes of the host protein, this self-processing reaction has enabled many applications in protein biotechnology and chemical biology. We show that the evolved M86 mutant of the Ssp DnaB intein displays a significantly improved tolerance towards non-native amino acids at the N-terminally flanking (–1) extein position compared to the parent intein, in the form of both an artificially trans-splicing split intein and the cis-splicing mini-intein. Surprisingly, side chains with increased steric bulk compared to the native Gly(–1) residue, including d-amino acids, were found to compensate for the essential block B histidine in His73Ala mutants in the initial N–S acyl shift of the protein splicing pathway. In the case of the M86 intein, large (–1) side chains can even rescue protein splicing activity as a whole. With the comparison of three crystal structures, namely of the M86 intein as well as of its Gly(–1)Phe and Gly(–1)Phe/His73Ala mutants, our data supports a model in which the intein's active site can exert a strain by varying mechanisms on the different angles of the scissile bond at the extein–intein junction to effect a ground-state destabilization. The compensatory mechanism of the block B histidine is the first example for the direct functional role of an extein residue in protein splicing. It sheds new light on the extein–intein interplay and on possible consequences of their co-evolution as well as on the laboratory engineering of improved inteins.
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Affiliation(s)
- Kristina Friedel
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Monika A Popp
- Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 , Braunschweig , Germany
| | - Julian C J Matern
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Emerich M Gazdag
- Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 , Braunschweig , Germany
| | - Ilka V Thiel
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Gerrit Volkmann
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Wulf Blankenfeldt
- Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstraße 7 , 38124 , Braunschweig , Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics , Technische Universität Braunschweig , Spielmannstraße 7 , 38106 Braunschweig , Germany
| | - Henning D Mootz
- Institute of Biochemistry , University of Muenster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
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15
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Hou W, Liu L, Zhang X, Liu C. A new method of N to C sequential ligation using thioacid capture ligation and native chemical ligation. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172455. [PMID: 30110491 PMCID: PMC6030339 DOI: 10.1098/rsos.172455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
Sequential peptide ligation strategy becomes more and more important in large protein or long peptides chemical synthesis due to the limited peptide/protein size obtained by solid phase synthesis of individual peptides or even one-step peptide ligation. Herein, we developed an alternative method which could perform the sequential peptide ligation of several segments from N to C direction based on the combined use of thioacid capture ligation and native chemical ligation. The sweet protein monellin was produced through this strategy on a scale of multi-milligrams.
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Affiliation(s)
- Wen Hou
- Key Laboratory for Critical Care Medicine of the Ministry of Health, Tianjin First Center Hospital, Tianjin 300192, China
- Organ Transplant Center, Tianjin First Center Hospital, Tianjin 300071, China
| | - Lei Liu
- First Center Hospital Clinic Institute, Tianjin Medical University, Tianjin 300192, China
| | - Xiaohong Zhang
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 657551, Republic of Singapore
| | - Chuanfa Liu
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 657551, Republic of Singapore
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16
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Rapid and efficient protein synthesis through expansion of the native chemical ligation concept. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0122] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Gopinath P, Ohayon S, Nawatha M, Brik A. Chemical and semisynthetic approaches to study and target deubiquitinases. Chem Soc Rev 2018; 45:4171-98. [PMID: 27049734 DOI: 10.1039/c6cs00083e] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ubiquitination is a key posttranslational modification, which affects numerous biological processes and is reversed by a class of enzymes known as deubiquitinases (DUBs). This family of enzymes cleaves mono-ubiquitin or poly-ubiquitin chains from a target protein through different mechanisms and mode of interactions with their substrates. Studying the role of DUBs in health and diseases has been a major goal for many laboratories both in academia and in industry. However, the field has been challenged by the difficulties in obtaining native substrates and novel reagents using traditional enzymatic and molecular biology approaches. Recent advancements in the synthesis and semisynthesis of proteins made it possible to prepare several unique ubiquitin conjugates to study various aspects of DUBs such as their specificities and structures. Moreover, these approaches enable the preparation of novel activity based probes and assays to monitor DUB activities in vitro and in cellular contexts. Efforts made to bring new chemical entities for the selective inhibition of DUBs based on these tools are also highlighted with selected examples.
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Affiliation(s)
- Pushparathinam Gopinath
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Shimrit Ohayon
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Mickal Nawatha
- 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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18
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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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19
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Yan B, Ye L, Xu W, Liu L. Recent advances in racemic protein crystallography. Bioorg Med Chem 2017; 25:4953-4965. [DOI: 10.1016/j.bmc.2017.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/03/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
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20
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Morimoto D, Walinda E, Sugase K, Shirakawa M. Biological and Physicochemical Functions of Ubiquitylation Revealed by Synthetic Chemistry Approaches. Int J Mol Sci 2017; 18:ijms18061145. [PMID: 28555012 PMCID: PMC5485969 DOI: 10.3390/ijms18061145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 01/08/2023] Open
Abstract
Most intracellular proteins are subjected to post-translational modification by ubiquitin. Accordingly, it is of fundamental importance to investigate the biological and physicochemical effects of ubiquitylation on substrate proteins. However, preparation of ubiquitylated proteins by an enzymatic synthesis bears limitations in terms of yield and site-specificity. Recently established chemical ubiquitylation methodologies can overcome these problems and provide a new understanding of ubiquitylation. Herein we describe the recent chemical ubiquitylation procedures with a focus on the effects of ubiquitylation on target proteins revealed by the synthetic approach.
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Affiliation(s)
- Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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21
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Bondalapati S, Eid E, Mali SM, Wolberger C, Brik A. Total chemical synthesis of SUMO-2-Lys63-linked diubiquitin hybrid chains assisted by removable solubilizing tags. Chem Sci 2017; 8:4027-4034. [PMID: 28580118 PMCID: PMC5434752 DOI: 10.1039/c7sc00488e] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/23/2017] [Indexed: 12/28/2022] Open
Abstract
We report the first total chemical synthesis of four different SUMO-2-Lys63-linked di-ubiquitin hybrid chains, in which the di-ubiquitin is linked to different lysines in SUMO.
Small ubiquitin like modifier (SUMO) proteins are known to regulate many important cellular processes such as transcription and apoptosis. Recently, hybrid SUMO-ubiquitin chains containing SUMO-2 linked to Lys63-di-ubiquitin were found to play a major role in DNA repair. Despite some progress in understanding the role of these hybrid chains in DNA repair, there are various fundamental questions remaining to be answered. To further investigate the importance of hybrid SUMO-ubiquitin chains in DNA repair, the homogenous material of these chains, and their unique analogues, are needed in workable quantities. By applying advanced chemical strategies for protein synthesis, we report the first total chemical synthesis of four different SUMO-2-Lys63-linked di-ubiquitin hybrid chains, in which the di-ubiquitin is linked to different lysines in SUMO. In these syntheses, the usefulness of removable solubilizing tags is demonstrated, and two different approaches were examined in terms of reliability and efficiency. In the first approach, a poly-Arg tag was attached to the C-terminus of SUMO via a 3,4-diaminobenzoic acid cleavable linker, whereas in the second we attached the tag via a phenylacetamidomethyl linker, which can be cleaved by PdCl2. The comparison between these different strategies offers guidelines for future scale-up preparation of these analogues and other proteins, which currently use synthetic peptide intermediates that are difficult to handle and purify. The availability of the SUMO-ubiquitin hybrid chains opens up new opportunities for studying the role of these chains in DNA repair and other cellular processes.
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Affiliation(s)
- Somasekhar Bondalapati
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Haifa 3200008 , Israel .
| | - Emad Eid
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Haifa 3200008 , Israel .
| | - Sachitanand M Mali
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Haifa 3200008 , Israel .
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Ashraf Brik
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Haifa 3200008 , Israel .
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22
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Shelton PMM, Weller CE, Chatterjee C. A Facile N-Mercaptoethoxyglycinamide (MEGA) Linker Approach to Peptide Thioesterification and Cyclization. J Am Chem Soc 2017; 139:3946-3949. [PMID: 28230996 DOI: 10.1021/jacs.6b13271] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The C-terminal electrophilic activation of peptides by α-thioesterification requires strongly acidic conditions or complex chemical manipulations, which ultimately limit functional group compatibility and broad utility. Herein, we report a readily accessible N-mercaptoethoxyglycinamide (MEGA) solid-phase linker for the facile synthesis of latent peptide α-thioesters. Incubating peptide-MEGA sequences with 2-mercaptoethanesulfonic acid at mildly acidic pH yielded α-thioesters that were directly used in NCL without purification. The MEGA linker yielded robust access to thioesters ranging in length from 4 to 35 amino acids, and greatly simplified the synthesis of cyclic peptides. Finally, the high utility of MEGA was demonstrated by the one-pot synthesis of a functional analog of the Sunflower Trypsin Inhibitor 1.
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Affiliation(s)
- Patrick M M Shelton
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Caroline E Weller
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Champak Chatterjee
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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23
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Tsuda S, Mochizuki M, Sakamoto K, Denda M, Nishio H, Otaka A, Yoshiya T. N-Sulfanylethylaminooxybutyramide (SEAoxy): A Crypto-Thioester Compatible with Fmoc Solid-Phase Peptide Synthesis. Org Lett 2016; 18:5940-5943. [PMID: 27805411 DOI: 10.1021/acs.orglett.6b03055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An N-sulfanylethylaminooxybutyramide (SEAoxy) has been developed as a novel thioester equivalent for native chemical ligation. SEAoxy peptide was straightforwardly synthesized by conventional Fmoc solid-phase peptide synthesis without a problem. Moreover, SEAoxy peptide could be directly applied to native chemical ligation owing to the intramolecular N-to-S acyl shift that releases the peptide-thioester in situ. This methodology was successfully applied to the synthesis of two bioactive peptides.
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Affiliation(s)
- Shugo Tsuda
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan
| | | | - Ken Sakamoto
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan
| | - Masaya Denda
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University , Tokushima 770-8505, Japan
| | - Hideki Nishio
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University , Tokushima 770-8505, Japan
| | - Taku Yoshiya
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan
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24
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25
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Lee CL, Liu H, Wong CTT, Chow HY, Li X. Enabling N-to-C Ser/Thr Ligation for Convergent Protein Synthesis via Combining Chemical Ligation Approaches. J Am Chem Soc 2016; 138:10477-84. [DOI: 10.1021/jacs.6b04238] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Chi Lung Lee
- Department of Chemistry,
The State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Han Liu
- Department of Chemistry,
The State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Clarence T. T. Wong
- Department of Chemistry,
The State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hoi Yee Chow
- Department of Chemistry,
The State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Xuechen Li
- Department of Chemistry,
The State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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26
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van Tilburg GB, Elhebieshy AF, Ovaa H. Synthetic and semi-synthetic strategies to study ubiquitin signaling. Curr Opin Struct Biol 2016; 38:92-101. [PMID: 27315041 PMCID: PMC7125694 DOI: 10.1016/j.sbi.2016.05.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 01/30/2023]
Abstract
The post-translational modification ubiquitin can be attached to the ɛ-amino group of lysine residues or to a protein's N-terminus as a mono ubiquitin moiety. Via its seven intrinsic lysine residues and its N-terminus, it can also form ubiquitin chains on substrates in many possible ways. To study ubiquitin signals, many synthetic and semi-synthetic routes have been developed for generation of ubiquitin-derived tools and conjugates. The strength of these methods lies in their ability to introduce chemo-selective ligation handles at sites that currently cannot be enzymatically modified. Here, we review the different synthetic and semi-synthetic methods available for ubiquitin conjugate synthesis and their contribution to how they have helped investigating conformational diversity of diubiquitin signals. Next, we discuss how these methods help understanding the ubiquitin conjugation-deconjugation system by recent advances in ubiquitin ligase probes and diubiquitin-based DUB probes. Lastly, we discuss how these methods help studying post-translational modification of ubiquitin itself.
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Affiliation(s)
- Gabriëlle Ba van Tilburg
- Department of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Angela F Elhebieshy
- Department of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Huib Ovaa
- Department of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
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27
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Harmand TJ, Murar CE, Bode JW. Protein chemical synthesis by α-ketoacid–hydroxylamine ligation. Nat Protoc 2016; 11:1130-47. [DOI: 10.1038/nprot.2016.052] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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28
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Drobecq H, Boll E, Sénéchal M, Desmet R, Saliou JM, Lacapère JJ, Mougel A, Vicogne J, Melnyk O. A Central Cysteine Residue Is Essential for the Thermal Stability and Function of SUMO-1 Protein and SUMO-1 Peptide-Protein Conjugates. Bioconjug Chem 2016; 27:1540-6. [PMID: 27195426 DOI: 10.1021/acs.bioconjchem.6b00211] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
SUMOylation constitutes a major post-translational modification (PTM) used by the eukaryote cellular machinery to modulate protein interactions of the targeted proteins. The small ubiquitin-like modifier-1 (SUMO-1) features a central and conserved cysteine residue (Cys52) that is located in the hydrophobic core of the protein and in tight contact with Phe65, suggesting the occurrence of an S/π interaction. To investigate the importance of Cys52 on SUMO-1 thermal stability and biochemical properties, we produced by total chemical synthesis SUMO-1 or SUMO-1 Cys52Ala peptide-protein conjugates featuring a native isopeptidic bond between SUMO-1 and a peptide derived from p53 tumor suppressor protein. The Cys52Ala modification perturbed SUMO-1 secondary structure and resulted in a dramatic loss of protein thermal stability. Moreover, the cleavage of the isopeptidic bond by the deconjugating enzyme Upl1 was significantly less efficient than for the wild-type conjugate. Similarly, the in vitro SUMOylation of RanGap1 by E1/E2 conjugating enzymes was significantly less efficient with the SUMO-1 C52A analog compared to wild-type SUMO-1. These data demonstrate the critical role of Cys52 in maintaining SUMO-1 conformation and function and the importance of keeping this cysteine intact for the study of SUMO-1 protein conjugates.
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Affiliation(s)
- Hervé Drobecq
- M3T-Mechanisms of Tumorigenesis and Target Therapies, Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Emmanuelle Boll
- M3T-Mechanisms of Tumorigenesis and Target Therapies, Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Magalie Sénéchal
- M3T-Mechanisms of Tumorigenesis and Target Therapies, Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Rémi Desmet
- M3T-Mechanisms of Tumorigenesis and Target Therapies, Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Jean-Michel Saliou
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204, F-59000 Lille, France
| | - Jean-Jacques Lacapère
- Sorbonne Universités, UPMC Université Paris 06, École Normale Supérieure, PSL Research University, CNRS UMR 7203 LBM, F-75005, Paris, France
| | - Alexandra Mougel
- M3T-Mechanisms of Tumorigenesis and Target Therapies, Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Jérôme Vicogne
- M3T-Mechanisms of Tumorigenesis and Target Therapies, Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Oleg Melnyk
- M3T-Mechanisms of Tumorigenesis and Target Therapies, Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
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29
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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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30
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Cowper B, Shariff L, Chen W, Gibson SM, Di WL, Macmillan D. Expanding the scope of N → S acyl transfer in native peptide sequences. Org Biomol Chem 2016; 13:7469-76. [PMID: 26066020 DOI: 10.1039/c5ob01029b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the factors that influence N → S acyl transfer in native peptide sequences, and discovery of new reagents that facilitate it, will be key to expanding its scope and applicability. Here, through a study of short model peptides in thioester formation and cyclisation reactions, we demonstrate that a wider variety of Xaa-Cys motifs than originally envisaged are capable of undergoing efficient N → S acyl transfer. We present data for the relative rates of thioester formation and cyclisation for a representative set of amino acids, and show how this expanded scope can be applied to the production of the natural protease inhibitor Sunflower Trypsin Inhibitor-1 (SFTI-1).
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Affiliation(s)
- Ben Cowper
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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31
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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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32
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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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33
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Maity SK, Jbara M, Brik A. Chemical and semisynthesis of modified histones. J Pept Sci 2016; 22:252-9. [DOI: 10.1002/psc.2848] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 12/06/2015] [Accepted: 12/07/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Suman Kumar Maity
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 3200008 Israel
| | - Muhammad Jbara
- 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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34
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Hemantha HP, Bondalapati S, Singh SK, Brik A. Chemical Synthesis of Ubiquitin Chains. ACTA ACUST UNITED AC 2015; 7:229-248. [DOI: 10.1002/9780470559277.ch150099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hosahalli P. Hemantha
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology; Haifa Israel
| | | | - Sumeet K. Singh
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology; Haifa Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology; Haifa Israel
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35
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Meledin R, Mali SM, Brik A. Pushing the Boundaries of Chemical Protein Synthesis: The Case of Ubiquitin Chains and Polyubiquitinated Peptides and Proteins. CHEM REC 2015; 16:509-19. [DOI: 10.1002/tcr.201500209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Roman Meledin
- Schulich Department of Chemistry; Israel Institute of Technology - Technion; Haifa Israel
| | - Sachitanand M. Mali
- Schulich Department of Chemistry; Israel Institute of Technology - Technion; Haifa Israel
| | - Ashraf Brik
- Schulich Department of Chemistry; Israel Institute of Technology - Technion; Haifa Israel
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36
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Terrier VP, Adihou H, Arnould M, Delmas AF, Aucagne V. A straightforward method for automated Fmoc-based synthesis of bio-inspired peptide crypto-thioesters. Chem Sci 2015; 7:339-345. [PMID: 29861986 PMCID: PMC5952550 DOI: 10.1039/c5sc02630j] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/22/2015] [Indexed: 01/19/2023] Open
Abstract
A bio-inspired method for the synthesis of peptide thioester surrogates for native chemical ligation was developed. The process can be fully automated and does not require postsynthetic steps.
Despite recent advances, the direct Fmoc-based solid phase synthesis of peptide α-thioesters for the convergent synthesis of proteins via native chemical ligation (NCL) remains a challenge in the field. We herein report a simple and general methodology, enabling access to peptide thioester surrogates. A novel C-terminal N-(2-hydroxybenzyl)cysteine thioesterification device based on an amide-to-thioester rearrangement was developed, and the resulting peptide crypto-thioesters can be directly used in NCL reactions with fast N → S shift kinetics at neutral pH. These fast kinetics arise from our bio-inspired design, via intein-like intramolecular catalysis. Due to a well-positioned phenol moiety, an impressive >50 fold increase in the kinetic rate is observed compared to an O-methylated derivative. Importantly, the synthesis of this new device can be fully automated using inexpensive commercially available materials and does not require any post-synthetic steps prior to NCL. We successfully applied this new method to the synthesis of two long naturally-occurring cysteine-rich peptide sequences.
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Affiliation(s)
- Victor P Terrier
- Centre de Biophysique Moléculaire , CNRS UPR 4301 , Rue Charles Sadron , 45071 Orléans Cedex 2 , France .
| | - Hélène Adihou
- Centre de Biophysique Moléculaire , CNRS UPR 4301 , Rue Charles Sadron , 45071 Orléans Cedex 2 , France .
| | - Mathieu Arnould
- Centre de Biophysique Moléculaire , CNRS UPR 4301 , Rue Charles Sadron , 45071 Orléans Cedex 2 , France .
| | - Agnès F Delmas
- Centre de Biophysique Moléculaire , CNRS UPR 4301 , Rue Charles Sadron , 45071 Orléans Cedex 2 , France .
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire , CNRS UPR 4301 , Rue Charles Sadron , 45071 Orléans Cedex 2 , France .
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37
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Han C, Pao KC, Kazlauskaite A, Muqit MMK, Virdee S. A Versatile Strategy for the Semisynthetic Production of Ser65 Phosphorylated Ubiquitin and Its Biochemical and Structural Characterisation. Chembiochem 2015; 16:1574-9. [PMID: 26010437 PMCID: PMC4581463 DOI: 10.1002/cbic.201500185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/22/2015] [Indexed: 11/10/2022]
Abstract
Ubiquitin phosphorylation is emerging as an important regulatory layer in the ubiquitin system. This is exemplified by the phosphorylation of ubiquitin on Ser65 by the Parkinson's disease-associated kinase PINK1, which mediates the activation of the E3 ligase Parkin. Additional phosphorylation sites on ubiquitin might also have important cellular roles. Here we report a versatile strategy for preparing phosphorylated ubiquitin. We biochemically and structurally characterise semisynthetic phospho-Ser65-ubiquitin. Unexpectedly, we observed disulfide bond formation between ubiquitin molecules, and hence a novel crystal form. The method outlined provides a direct approach to study the combinatorial effects of phosphorylation on ubiquitin function. Our analysis also suggests that disulfide engineering of ubiquitin could be a useful strategy for obtaining alternative crystal forms of ubiquitin species thereby facilitating structural validation.
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Affiliation(s)
- Cong Han
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK)
| | - Kuan-Chuan Pao
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK)
| | - Agne Kazlauskaite
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK)
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK)
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK).
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38
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Koniev O, Wagner A. Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation. Chem Soc Rev 2015; 44:5495-551. [PMID: 26000775 DOI: 10.1039/c5cs00048c] [Citation(s) in RCA: 390] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.
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Affiliation(s)
- Oleksandr Koniev
- Laboratory of Functional Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg, 74 Route du Rhin, 67401 Illkirch-Graffenstaden, France.
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39
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Bondalapati S, Mansour W, Nakasone MA, Maity SK, Glickman MH, Brik A. Chemical synthesis of phosphorylated ubiquitin and diubiquitin exposes positional sensitivities of e1-e2 enzymes and deubiquitinases. Chemistry 2015; 21:7360-4. [PMID: 25829361 DOI: 10.1002/chem.201500540] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Indexed: 12/22/2022]
Abstract
Modification of ubiquitin by phosphorylation extends the signaling possibilities of this dynamic signal, as it could affect the activity of ligases and the processing of ubiquitin chains by deubiquitinases. The first chemical synthesis of phosphorylated ubiquitin and of Lys63-linked diubiquitin at the proximal, distal or both ubiquitins is reported. This enabled the examination of how such a modification alters E1-E2 activities of the ubiquitination machinery. It is found that E1 charging was not affected, while the assembly of phosphorylated ubiquitin chains was differentially inhibited with E2 enzymes tested. Moreover, this study shows that phosphorylation interferes with the recognition of linkage specific antibodies and the activities of several deubiquitinases. Notably, phosphorylation in the proximal or distal ubiquitin unit has differential effects on specific deubiquitinases. These results support a unique role of phosphorylation in the dynamics of the ubiquitin signal.
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Affiliation(s)
- Somasekhar Bondalapati
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653 Beer-Sheva 8410501 (Israel); Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, 3200008 Haifa (Israel)
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40
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Boll E, Drobecq H, Ollivier N, Blanpain A, Raibaut L, Desmet R, Vicogne J, Melnyk O. One-pot chemical synthesis of small ubiquitin-like modifier protein-peptide conjugates using bis(2-sulfanylethyl)amido peptide latent thioester surrogates. Nat Protoc 2015; 10:269-92. [PMID: 25591010 DOI: 10.1038/nprot.2015.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Small ubiquitin-like modifier (SUMO) post-translational modification (PTM) of proteins has a crucial role in the regulation of important cellular processes. This protocol describes the chemical synthesis of functional SUMO-peptide conjugates. The two crucial stages of this protocol are the solid-phase synthesis of peptide segments derivatized by thioester or bis(2-sulfanylethyl)amido (SEA) latent thioester functionalities and the one-pot assembly of the SUMO-peptide conjugate by a sequential native chemical ligation (NCL)/SEA native peptide ligation reaction sequence. This protocol also enables the isolation of a SUMO SEA latent thioester, which can be attached to a target peptide or protein in a subsequent step. It is compatible with 9-fluorenylmethoxycarbonyl (Fmoc) chemistry, and it gives access to homogeneous, reversible and functional SUMO conjugates that are not easily produced using living systems. The synthesis of SUMO-peptide conjugates on a milligram scale takes 20 working days.
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Affiliation(s)
- Emmanuelle Boll
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Hervé Drobecq
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Nathalie Ollivier
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Annick Blanpain
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Laurent Raibaut
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Rémi Desmet
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Jérôme Vicogne
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Oleg Melnyk
- Centre National de la Recherche Scientifique, Lille Institute of Biology, Institut Pasteur de Lille, University of Lille, Lille, France
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41
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Murar CE, Thuaud F, Bode JW. KAHA Ligations That Form Aspartyl Aldehyde Residues as Synthetic Handles for Protein Modification and Purification. J Am Chem Soc 2014; 136:18140-8. [DOI: 10.1021/ja511231f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Claudia E. Murar
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH−Zürich, 8093 Zürich, Switzerland
| | - Frédéric Thuaud
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH−Zürich, 8093 Zürich, Switzerland
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Jeffrey W. Bode
- Laboratorium
für Organische Chemie, Department of Chemistry and Applied
Biosciences, ETH−Zürich, 8093 Zürich, Switzerland
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
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42
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Abeywardana T, Pratt MR. Using Chemistry to Investigate the Molecular Consequences of Protein Ubiquitylation. Chembiochem 2014; 15:1547-54. [DOI: 10.1002/cbic.201402117] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Indexed: 12/21/2022]
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43
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Karas JA, Scanlon DB, Forbes BE, Vetter I, Lewis RJ, Gardiner J, Separovic F, Wade JD, Hossain MA. 2-Nitroveratryl as a Photocleavable Thiol-Protecting Group for Directed Disulfide Bond Formation in the Chemical Synthesis of Insulin. Chemistry 2014; 20:9549-52. [DOI: 10.1002/chem.201403574] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Indexed: 12/20/2022]
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44
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Weller CE, Huang W, Chatterjee C. Facile synthesis of native and protease-resistant ubiquitylated peptides. Chembiochem 2014; 15:1263-7. [PMID: 24838693 PMCID: PMC4085112 DOI: 10.1002/cbic.201402135] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Indexed: 12/13/2022]
Abstract
The reversible post-translational modification of eukaryotic proteins by ubiquitin regulates key cellular processes including protein degradation and gene transcription. Studies of the mechanistic roles for protein ubiquitylation require quantities of homogenously modified substrates that are typically inaccessible from natural sources or by enzymatic ubiquitylation in vitro. Therefore, we developed a facile and scalable methodology for site-specific chemical ubiquitylation. Our semisynthetic strategy utilized a temporary ligation auxiliary, 2-(aminooxy)ethanethiol, to direct ubiquitylation to specific lysine residues in peptide substrates. Mild reductive removal of the auxiliary after ligation yielded ubiquitylated peptides with the native isopeptide linkage. Alternatively, retention of the ligation auxiliary yielded protease-resistant analogues of ubiquitylated peptides. Importantly, our strategy was fully compatible with the presence of protein thiol groups, as demonstrated by the synthesis of peptides modified by the human small ubiquitin-related modifier 3 protein.
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Affiliation(s)
| | - Wei Huang
- Department of Chemistry, University of Washington, Seattle, WA 98195
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45
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Ruff Y, Garavini V, Giuseppone N. Reversible native chemical ligation: a facile access to dynamic covalent peptides. J Am Chem Soc 2014; 136:6333-9. [PMID: 24717128 DOI: 10.1021/ja4129845] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The broad interest of using reversible covalent bonds in chemistry, in particular at its interfaces with biology and materials science, has been recently established through numerous examples in the literature. However, the challenging exchange of peptide fragments using a dynamic covalent peptide bond has not yet been achieved without enzymatic catalysis because of its high thermodynamic stability. Here we show that peptide fragments can be exchanged by a chemoselective and reversible native chemical ligation (NCL) which can take place at N-(methyl)-cysteine residues. This very mild reaction is efficient in aqueous solution, is buffered at physiological pH in the presence of dithiothreitol (DTT), and shows typical half-times of equilibration in the 10 h range.
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Affiliation(s)
- Yves Ruff
- SAMS Research Group, University of Strasbourg, Institut Charles Sadron, CNRS, 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2, France
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46
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Boll E, Drobecq H, Ollivier N, Raibaut L, Desmet R, Vicogne J, Melnyk O. A novel PEG-based solid support enables the synthesis of >50 amino-acid peptide thioesters and the total synthesis of a functional SUMO-1 peptide conjugate. Chem Sci 2014. [DOI: 10.1039/c3sc53509f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bis(2-sulfanylethyl)amino PEG resin gives access to large peptide thioester segments and to functional SUMO-1 conjugates.
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Affiliation(s)
- Emmanuelle Boll
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Hervé Drobecq
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Nathalie Ollivier
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Laurent Raibaut
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Rémi Desmet
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Jérome Vicogne
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
| | - Oleg Melnyk
- UMR CNRS 8161
- Université Lille Nord de France
- Institut Pasteur de Lille
- 59021 Lille, France
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47
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Chemical synthesis of proteins using N-sulfanylethylanilide peptides, based on N-S acyl transfer chemistry. Top Curr Chem (Cham) 2014; 363:33-56. [PMID: 25467538 DOI: 10.1007/128_2014_586] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Native chemical ligation (NCL), which features the use of peptide thioesters, is among the most reliable ligation protocols in chemical protein synthesis. Thioesters have conventionally been synthesized using tert-butyloxycarbonyl (Boc)-based solid-phase peptide synthesis (SPPS); however, the increasing use of 9-fluorenylmethyloxycarbonyl (Fmoc) SPPS requires an efficient preparative protocol for thioesters which is fully compatible with Fmoc chemistry. We have addressed this issue by mimicking the naturally occurring thioester-forming step seen in intein-mediated protein splicing of the intein-extein system, using an appropriate chemical device to induce N-S acyl transfer reaction, avoiding the problems associated with Fmoc strategies. We have developed N-sulfanylethylanilide (SEAlide) peptides, which can be synthesized by standard Fmoc SPPS and converted to the corresponding thioesters through treatment under acidic conditions. Extensive examination of SEAlide peptides showed that the amide-type SEAlide peptides can be directly and efficiently involved in NCL via thioester species in the presence of phosphate salts, even under neutral conditions. The presence or absence of phosphate salts provided kinetically controllable chemoselectivity in NCL for SEAlide peptides. This allowed SEAlide peptides to be used in both one-pot/N-to-C-directed sequential NCL under kinetically controlled conditions, and the convergent coupling of large peptide fragments, which facilitated the chemical synthesis of proteins over about 100 residues. The use of SEAlide peptides, enabling sequential NCL operated under kinetically controlled conditions, and the convergent coupling, were used for the total chemical synthesis of a 162-residue monoglycosylated GM2-activator protein (GM2AP) analog.
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48
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Guan X, Chaffey PK, Zeng C, Tan Z. New Methods for Chemical Protein Synthesis. Top Curr Chem (Cham) 2014; 363:155-92. [DOI: 10.1007/128_2014_599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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49
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Takenouchi T, Katayama H, Nakahara Y, Nakahara Y, Hojo H. A novel post-ligation thioesterification device enables peptide ligation in the N to C direction: synthetic study of human glycodelin. J Pept Sci 2013; 20:55-61. [PMID: 24357164 DOI: 10.1002/psc.2592] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 11/08/2022]
Abstract
Human glycodelin consists of 162 amino acid residues and two N-linked glycans at Asn(28) and Asn(63) . In this study, we synthesized it by a fully convergent strategy using native chemical ligation (NCL) in N to C direction. The four peptide segments corresponding to 1-31, 32-65, 66-105 and 106-162 sequences were synthesized by 9-fluorenylmethoxycarbonyl based solid-phase peptide synthesis. At the C-terminus of the second segment, N-ethyl-S-acetamidomethyl-cysteine was attached as a post-ligation thioesterification device. The N-terminal two segments were condensed by the homocysteine-mediated NCL at Leu-Met site, and the product was methylated to convert homocysteine to methionine. After deprotection of acetamidomethyl group on the N-ethylcysteine residue, the peptide was thioesterified by N-alkylcysteine-assisted method. The product was then ligated with the C-terminal half, which was obtained by the NCL of third and fourth segments, to give the full-length glycodelin.
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Affiliation(s)
- Takaomi Takenouchi
- Department of Applied Biochemistry, Faculty of Engineering, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa, 259-1292, Japan
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50
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Synthetic polyubiquitinated α-Synuclein reveals important insights into the roles of the ubiquitin chain in regulating its pathophysiology. Proc Natl Acad Sci U S A 2013; 110:17726-31. [PMID: 24043770 DOI: 10.1073/pnas.1315654110] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Ubiquitination regulates, via different modes of modifications, a variety of biological processes, and aberrations in the process have been implicated in the pathogenesis of several neurodegenerative diseases. However, our ability to dissect the pathophysiological relevance of the ubiquitination code has been hampered due to the lack of methods that allow site-specific introduction of ubiquitin (Ub) chains to a specific substrate. Here, we describe chemical and semisynthetic strategies for site-specific incorporation of K48-linked di- or tetra-Ub chains onto the side chain of Lys12 of α-Synuclein (α-Syn). These advances provided unique opportunities to elucidate the role of ubiquitination and Ub chain length in regulating α-Syn stability, aggregation, phosphorylation, and clearance. In addition, we investigated the cross-talk between phosphorylation and ubiquitination, the two most common α-Syn pathological modifications identified within Lewy bodies and Parkinson disease. Our results suggest that α-Syn functions under complex regulatory mechanisms involving cross-talk among different posttranslational modifications.
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