1
|
Arora S, Roy DS, Maiti S, Ainavarapu SRK. Phase Separation and Aggregation of a Globular Folded Protein Small Ubiquitin-like Modifier 1 (SUMO1). J Phys Chem Lett 2023; 14:9060-9068. [PMID: 37782899 DOI: 10.1021/acs.jpclett.3c02092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Liquid-liquid phase separation (LLPS) plays a crucial role in cellular organization, primarily driven by intrinsically disordered proteins (IDPs) leading to the formation of biomolecular condensates. A folded protein SUMO that post-translationally modifies cellular proteins has recently emerged as a regulator of LLPS. Given its compact structure and limited flexibility, the precise role of SUMO in condensate formation remains to be investigated. Here, we show the rapid phase separation of SUMO1 into micrometer-sized liquid-like condensates in inert crowders under physiological conditions. Subsequent time-dependent conformational changes and aggregation are probed by label-free methods (tryptophan fluorescence and Raman spectroscopy). Remarkably, experiments on a SUMO1 variant lacking the N-terminal disordered region further corroborate the role of its structured part in phase transitions. Our findings highlight the potential of folded proteins to engage in LLPS and emphasize further investigation into the influence of the SUMO tag on IDPs associated with membrane-less assemblies in cells.
Collapse
Affiliation(s)
- Simran Arora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Debsankar Saha Roy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| |
Collapse
|
2
|
Goffinont S, Coste F, Prieu-Serandon P, Mance L, Gaudon V, Garnier N, Castaing B, Suskiewicz MJ. Structural insights into the regulation of the human E2∼SUMO conjugate through analysis of its stable mimetic. J Biol Chem 2023; 299:104870. [PMID: 37247759 PMCID: PMC10404613 DOI: 10.1016/j.jbc.2023.104870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023] Open
Abstract
Protein SUMOylation is a ubiquitylation-like post-translational modification (PTM) that is synthesized through an enzymatic cascade involving an E1 (SAE1:SAE2), an E2 (UBC9), and various E3 enzymes. In the final step of this process, the small ubiquitin-like modifier (SUMO) is transferred from the UBC9∼SUMO thioester onto a lysine residue of a protein substrate. This reaction can be accelerated by an E3 ligase. As the UBC9∼SUMO thioester is chemically unstable, a stable mimetic is desirable for structural studies of UBC9∼SUMO alone and in complex with a substrate and/or an E3 ligase. Recently, a strategy for generating a mimetic of the yeast E2∼SUMO thioester by mutating alanine 129 of Ubc9 to a lysine has been reported. Here, we reproduce and further investigate this approach using the human SUMOylation system and characterize the resulting mimetic of human UBC9∼SUMO1. We show that substituting lysine for alanine 129, but not for other active-site UBC9 residues, results in a UBC9 variant that is efficiently auto-SUMOylated. The auto-modification is dependent on cysteine 93 of UBC9, suggesting that it proceeds via this residue, through the same pathway as that for SUMOylation of substrates. The process is also partially dependent on aspartate 127 of UBC9 and accelerated by high pH, highlighting the importance of the substrate lysine protonation state for efficient SUMOylation. Finally, we present the crystal structure of the UBC9-SUMO1 molecule, which reveals the mimetic in an open conformation and its polymerization via the noncovalent SUMO-binding site on UBC9. Similar interactions could regulate UBC9∼SUMO in some cellular contexts.
Collapse
Affiliation(s)
| | - Franck Coste
- Centre de Biophysique Moléculaire (CBM), CNRS UPR, Orléans, France
| | | | - Lucija Mance
- Centre de Biophysique Moléculaire (CBM), CNRS UPR, Orléans, France
| | - Virginie Gaudon
- Centre de Biophysique Moléculaire (CBM), CNRS UPR, Orléans, France
| | - Norbert Garnier
- Centre de Biophysique Moléculaire (CBM), CNRS UPR, Orléans, France
| | | | | |
Collapse
|
3
|
Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
Collapse
|
4
|
Agouridas V, Ollivier N, Vicogne J, Diemer V, Melnyk O. Redox-Controlled Chemical Protein Synthesis: Sundry Shades of Latency. Acc Chem Res 2022; 55:2685-2697. [PMID: 36083810 PMCID: PMC9494750 DOI: 10.1021/acs.accounts.2c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The last two decades have witnessed the rise in power of chemical protein synthesis to the point where it now constitutes an established corpus of synthetic methods efficiently complementing biological approaches. One factor explaining this spectacular evolution is the emergence of a new class of chemoselective reactions enabling the formation of native peptide bonds between two unprotected peptidic segments, also known as native ligation reactions. In recent years, their application has fueled the production of homogeneous batches of large and highly decorated protein targets with a control of their composition at the atomic level. In doing so, native ligation reactions have provided the means for successful applications in chemical biology, medicinal chemistry, materials science, and nanotechnology research.The native chemical ligation (NCL) reaction has had a major impact on the field by enabling the chemoselective formation of a native peptide bond between a C-terminal peptidyl thioester and an N-terminal cysteinyl peptide. Since its introduction in 1994, the NCL reaction has been made the object of significant improvements and its scope and limitations have been thoroughly investigated. Furthermore, the diversification of peptide segment assembly strategies has been essential to access proteins of increasing complexity and has had to overcome the challenge of controlling the reactivity of ligation partners.One hallmark of NCL is its dependency on thiol reactivity, including for its catalysis. While Nature constantly plays with the redox properties of biological thiols for the regulation of numerous biochemical pathways, such a control of reactivity is challenging to achieve in synthetic organic chemistry and, in particular, for those methods used for assembling peptide segments by chemical ligation. This Account covers the studies conducted by our group in this area. A leading theme of our research has been the conception of controllable acyl donors and cysteine surrogates that place the chemoselective formation of amide bonds by NCL-like reactions under the control of dichalcogenide-based redox systems. The dependency of the redox potential of dichalcogenide bonds on the nature of the chalcogenides involved (S, Se) has appeared as a powerful means for diversifying the systems, while allowing their sequential activation for protein synthesis. Such a control of reactivity mediated by the addition of harmless redox additives has greatly facilitated the modular and efficient preparation of multiple targets of biological relevance. Taken together, these endeavors provide a practical and robust set of methods to address synthetic challenges in chemical protein synthesis.
Collapse
Affiliation(s)
- Vangelis Agouridas
- Univ.
Lille, CNRS, Inserm, CHU Lille,
Institut Pasteur de Lille, U1019-UMR 9017, Center for Infection and
Immunity of Lille, F-59000 Lille, France,Centrale
Lille, F-59000 Lille, France
| | - Nathalie Ollivier
- Univ.
Lille, CNRS, Inserm, CHU Lille,
Institut Pasteur de Lille, U1019-UMR 9017, Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Jérôme Vicogne
- Univ.
Lille, CNRS, Inserm, CHU Lille,
Institut Pasteur de Lille, U1019-UMR 9017, Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Vincent Diemer
- Univ.
Lille, CNRS, Inserm, CHU Lille,
Institut Pasteur de Lille, U1019-UMR 9017, Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ.
Lille, CNRS, Inserm, CHU Lille,
Institut Pasteur de Lille, U1019-UMR 9017, Center for Infection and
Immunity of Lille, F-59000 Lille, France,
| |
Collapse
|
5
|
Mazmanian K, Chen T, Sargsyan K, Lim C. From quantum-derived principles underlying cysteine reactivity to combating the COVID-19 pandemic. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1607. [PMID: 35600063 PMCID: PMC9111396 DOI: 10.1002/wcms.1607] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 12/20/2022]
Abstract
The COVID‐19 pandemic poses a challenge in coming up with quick and effective means to counter its cause, the SARS‐CoV‐2. Here, we show how the key factors governing cysteine reactivity in proteins derived from combined quantum mechanical/continuum calculations led to a novel multi‐targeting strategy against SARS‐CoV‐2, in contrast to developing potent drugs/vaccines against a single viral target such as the spike protein. Specifically, they led to the discovery of reactive cysteines in evolutionary conserved Zn2+‐sites in several SARS‐CoV‐2 proteins that are crucial for viral polypeptide proteolysis as well as viral RNA synthesis, proofreading, and modification. These conserved, reactive cysteines, both free and Zn2+‐bound, can be targeted using the same Zn‐ejector drug (disulfiram/ebselen), which enables the use of broad‐spectrum anti‐virals that would otherwise be removed by the virus's proofreading mechanism. Our strategy of targeting multiple, conserved viral proteins that operate at different stages of the virus life cycle using a Zn‐ejector drug combined with other broad‐spectrum anti‐viral drug(s) could enhance the barrier to drug resistance and antiviral effects, as compared to each drug alone. Since these functionally important nonstructural proteins containing reactive cysteines are highly conserved among coronaviruses, our proposed strategy has the potential to tackle future coronaviruses. This article is categorized under:Structure and Mechanism > Reaction Mechanisms and Catalysis Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Density Functional Theory
Collapse
Affiliation(s)
| | - Ting Chen
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences Academia Sinica Taipei Taiwan.,Department of Chemistry National Tsing Hua University Hsinchu Taiwan
| |
Collapse
|
6
|
Abboud SA, Cisse EH, Doudeau M, Bénédetti H, Aucagne V. A straightforward methodology to overcome solubility challenges for N-terminal cysteinyl peptide segments used in native chemical ligation. Chem Sci 2021; 12:3194-3201. [PMID: 34164087 PMCID: PMC8179351 DOI: 10.1039/d0sc06001a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/10/2021] [Indexed: 02/06/2023] Open
Abstract
One of the main limitations encountered during the chemical synthesis of proteins through native chemical ligation (NCL) is the limited solubility of some of the peptide segments. The most commonly used solution to overcome this problem is to derivatize the segment with a temporary solubilizing tag. Conveniently, the tag can be introduced on the thioester segment in such a way that it is removed concomitantly with the NCL reaction. We herein describe a generalization of this approach to N-terminal cysteinyl segment counterparts, using a straightforward synthetic approach that can be easily automated from commercially available building blocks, and applied it to a well-known problematic target, SUMO-2.
Collapse
Affiliation(s)
- Skander A Abboud
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - El Hadji Cisse
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Michel Doudeau
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Hélène Bénédetti
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR 4301 Rue Charles Sadron 45071 Orléans Cedex 2 France
| |
Collapse
|
7
|
Sénéchal M, Bouchenna J, Vicogne J, Melnyk O. Comment on "N-terminal Protein Tail Acts as Aggregation Protective Entropic Bristles: The SUMO Case". Biomacromolecules 2020; 21:3480-3482. [PMID: 32702971 DOI: 10.1021/acs.biomac.0c00185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SUMO-2 protein, SUMO-2 core domain, and the tail peptide corresponding to the first 14 residues were produced by chemical synthesis, and their secondary structures were analyzed by circular dichroism. The CD spectra of SUMO-2 and SUMO-2 core domain show distinct features and α-helical contents. In particular, the presence of the disordered tail in SUMO-2 lowers the α-helical content of the protein compared with SUMO-2 core domain and also explains the shift in the position of the minimum around 208 nm.
Collapse
Affiliation(s)
- Magalie Sénéchal
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Jennifer Bouchenna
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Jérôme Vicogne
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| |
Collapse
|
8
|
The AAA+ ATPase Msp1 is a processive protein translocase with robust unfoldase activity. Proc Natl Acad Sci U S A 2020; 117:14970-14977. [PMID: 32541053 DOI: 10.1073/pnas.1920109117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Msp1 is a conserved eukaryotic AAA+ ATPase localized to the outer mitochondrial membrane, where it is thought to extract mislocalized tail-anchored proteins. Despite recent in vivo and in vitro studies supporting this function, a mechanistic understanding of how Msp1 extracts its substrates is still lacking. Msp1's ATPase activity depends on its hexameric state, and previous characterizations of the cytosolic AAA+ domain in vitro had proved challenging due to its monomeric nature in the absence of the transmembrane domain. Here, we used a hexamerization scaffold to study the substrate-processing mechanism of the soluble Msp1 motor, the functional homo-hexameric state of which was confirmed by negative-stain electron microscopy. We demonstrate that Msp1 is a robust bidirectional protein translocase that is able to unfold diverse substrates by processive threading through its central pore. This unfoldase activity is inhibited by Pex3, a membrane protein proposed to regulate Msp1 at the peroxisome.
Collapse
|
9
|
Puszko AK, Sosnowski P, Raynaud F, Hermine O, Hopfgartner G, Lepelletier Y, Misicka A. Does Cysteine Rule (CysR) Complete the CendR Principle? Increase in Affinity of Peptide Ligands for NRP-1 Through the Presence of N-Terminal Cysteine. Biomolecules 2020; 10:biom10030448. [PMID: 32183142 PMCID: PMC7175122 DOI: 10.3390/biom10030448] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/23/2020] [Accepted: 03/05/2020] [Indexed: 01/13/2023] Open
Abstract
The structure-activity relationship of branched H-Lys(hArg)-Dab-Dhp-Arg-OH sequence analogues, modified with Cys-Asp or Cys at N-terminal amino acids (Lys, hArg), in VEGF-A165/Neuropilin-1 complex inhibition is presented. The addition of Cys residue led to a 100-fold decrease in the IC50 value, compared to the parent peptide. The change occurred regardless of coupling Cys to the free N-terminal amino group present in the main or the side chain. A few analogues extended by the attachment of Cys at the N-terminus of several potent NRP-1 peptide ligands documented in the literature are also presented. In all studied cases, the enhancement of inhibitory properties after the addition of Cys at the N-terminus is observed. It is particularly evident for the tetrapeptide derived from the C-terminus of VEGF-A165 (KPRR), suggesting that extending the K/RXXK/R motif (CendR) with the Cys moiety can significantly improve affinity to NRP-1 of CendR peptides.
Collapse
Affiliation(s)
- Anna K. Puszko
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Piotr Sosnowski
- Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211 4 Geneva, Switzerland; (P.S.); (G.H.)
| | - Françoise Raynaud
- Imagine Institute, Université de Paris, 24 boulevard Montparnasse, 75015 Paris, France; (F.R.); (O.H.)
- INSERM UMR 1163, Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications, 24 boulevard Montparnasse, 75015 Paris, France
- CNRS ERL 8254, 24 boulevard Montparnasse, 75015 Paris, France
| | - Olivier Hermine
- Imagine Institute, Université de Paris, 24 boulevard Montparnasse, 75015 Paris, France; (F.R.); (O.H.)
- INSERM UMR 1163, Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications, 24 boulevard Montparnasse, 75015 Paris, France
- CNRS ERL 8254, 24 boulevard Montparnasse, 75015 Paris, France
| | - Gérard Hopfgartner
- Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211 4 Geneva, Switzerland; (P.S.); (G.H.)
| | - Yves Lepelletier
- Imagine Institute, Université de Paris, 24 boulevard Montparnasse, 75015 Paris, France; (F.R.); (O.H.)
- INSERM UMR 1163, Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications, 24 boulevard Montparnasse, 75015 Paris, France
- CNRS ERL 8254, 24 boulevard Montparnasse, 75015 Paris, France
- Correspondence: (Y.L.); (A.M.); Tel.: +33-14275-4283 (Y.L.); +48-22-552-6424 (A.M.)
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
- Correspondence: (Y.L.); (A.M.); Tel.: +33-14275-4283 (Y.L.); +48-22-552-6424 (A.M.)
| |
Collapse
|
10
|
Bouchenna J, Sénéchal M, Drobecq H, Vicogne J, Melnyk O. Total Chemical Synthesis of All SUMO-2/3 Dimer Combinations. Bioconjug Chem 2019; 30:2967-2973. [PMID: 31702897 DOI: 10.1021/acs.bioconjchem.9b00661] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
One hallmark of protein chemical synthesis is its capacity to access proteins that living systems can hardly produce. This is typically the case for proteins harboring post-translational modifications such as ubiquitin or ubiquitin-like modifiers. Various methods have been developed for accessing polyubiquitin conjugates by semi- or total synthesis. Comparatively, the preparation of small-ubiquitin-like modifier (SUMO) conjugates, and more particularly of polySUMO scaffolds, is much less developed. We describe hereinafter a synthetic strategy for accessing all SUMO-2/3 dimer combinations.
Collapse
Affiliation(s)
- Jennifer Bouchenna
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille , F-59000 Lille , France
| | - Magalie Sénéchal
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille , F-59000 Lille , France
| | - Hervé Drobecq
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille , F-59000 Lille , France
| | - Jérôme Vicogne
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille , F-59000 Lille , France
| | - Oleg Melnyk
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille , F-59000 Lille , France
| |
Collapse
|
11
|
Bouchenna J, Sénéchal M, Drobecq H, Stankovic-Valentin N, Vicogne J, Melnyk O. The Role of the Conserved SUMO-2/3 Cysteine Residue on Domain Structure Investigated Using Protein Chemical Synthesis. Bioconjug Chem 2019; 30:2684-2696. [PMID: 31532181 DOI: 10.1021/acs.bioconjchem.9b00598] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
While the semi or total synthesis of ubiquitin or polyubiquitin conjugates has attracted a lot of attention the past decade, the preparation of small ubiquitin-like modifier (SUMO) conjugates is much less developed. We describe hereinafter some important molecular features to consider when preparing SUMO-2/3 conjugates by chemical synthesis using the native chemical ligation and extended methods. In particular, we clarify the role of the conserved cysteine residue on SUMO-2/3 domain stability and properties. Our data reveal that SUMO-2 and -3 proteins behave differently from the Cys → Ala modification with SUMO-2 being less impacted than SUMO-3, likely due to a stabilizing interaction occurring in SUMO-2 between its tail and the SUMO core domain. While the Cys → Ala modification has no effect on the enzyme-catalyzed conjugation, it shows a deleterious effect on the enzyme-catalyzed deconjugation process, especially with the SUMO-3 conjugate. Whereas it is often stated that SUMO-2 and SUMO-3 are structurally and functionally indistinguishable, here we show that these proteins have specific structural and biochemical properties. This information is important to consider when designing and preparing SUMO-2/3 conjugates, and should help in making progress in the understanding of the specific role of SUMO-2 and/or SUMO-3 modifications on protein structure and function.
Collapse
Affiliation(s)
- Jennifer Bouchenna
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Magalie Sénéchal
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Hervé Drobecq
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Nicolas Stankovic-Valentin
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH) , DKFZ - ZMBH Alliance, 69120 , Heidelberg , Germany
| | - Jérôme Vicogne
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| | - Oleg Melnyk
- University of Lille , CNRS, Institut Pasteur de Lille, INSERM U1019, UMR CNRS 8204, Centre d'Immunité et d'Infection de Lille, F-59000 Lille , France
| |
Collapse
|
12
|
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
| |
Collapse
|
13
|
Hewings DS, Heideker J, Ma TP, AhYoung AP, El Oualid F, Amore A, Costakes GT, Kirchhofer D, Brasher B, Pillow T, Popovych N, Maurer T, Schwerdtfeger C, Forrest WF, Yu K, Flygare J, Bogyo M, Wertz IE. Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes. Nat Commun 2018; 9:1162. [PMID: 29563501 PMCID: PMC5862848 DOI: 10.1038/s41467-018-03511-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/20/2018] [Indexed: 11/25/2022] Open
Abstract
Activity-based probes (ABPs) are widely used to monitor the activity of enzyme families in biological systems. Inferring enzyme activity from probe reactivity requires that the probe reacts with the enzyme at its active site; however, probe-labeling sites are rarely verified. Here we present an enhanced chemoproteomic approach to evaluate the activity and probe reactivity of deubiquitinase enzymes, using bioorthogonally tagged ABPs and a sequential on-bead digestion protocol to enhance the identification of probe-labeling sites. We confirm probe labeling of deubiquitinase catalytic Cys residues and reveal unexpected labeling of deubiquitinases on non-catalytic Cys residues and of non-deubiquitinase proteins. In doing so, we identify ZUFSP (ZUP1) as a previously unannotated deubiquitinase with high selectivity toward cleaving K63-linked chains. ZUFSP interacts with and modulates ubiquitination of the replication protein A (RPA) complex. Our reactive-site-centric chemoproteomics method is broadly applicable for identifying the reaction sites of covalent molecules, which may expand our understanding of enzymatic mechanisms. Deubiquitinases are proteases that cleave after the C-terminus of ubiquitin to hydrolyze ubiquitin chains and cleave ubiquitin from substrates. Here the authors describe a reactive-site-centric chemoproteomics approach to studying deubiquitinase activity, and expand the repertoire of known deubiquitinases.
Collapse
Affiliation(s)
- David S Hewings
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA.,Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Johanna Heideker
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Taylur P Ma
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, 94080, USA
| | - Andrew P AhYoung
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Farid El Oualid
- UbiQ Bio BV, Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Alessia Amore
- UbiQ Bio BV, Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Gregory T Costakes
- Boston Biochem Inc., 840 Memorial Drive, Cambridge, Massachussetts, 02139, USA
| | - Daniel Kirchhofer
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Bradley Brasher
- Boston Biochem Inc., 840 Memorial Drive, Cambridge, Massachussetts, 02139, USA
| | - Thomas Pillow
- Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA
| | - Nataliya Popovych
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Till Maurer
- Structural Biology, Genentech, South San Francisco, California, 94080, USA
| | | | - William F Forrest
- Bioinformatics, Genentech, South San Francisco, California, 94080, USA
| | - Kebing Yu
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, 94080, USA
| | - John Flygare
- Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA.,Merck, 630 Gateway Boulevard, South San Francisco, California, 94080, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Ingrid E Wertz
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA. .,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA.
| |
Collapse
|
14
|
Kost LJ, Mootz HD. A FRET Sensor to Monitor Bivalent SUMO-SIM Interactions in SUMO Chain Binding. Chembiochem 2017; 19:177-184. [DOI: 10.1002/cbic.201700507] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Lisa J. Kost
- Department of Chemistry and Pharmacy; Institute of Biochemistry; Westfälische Wilhelms-Universität Münster; Wilhelm-Klemm-Strasse 2 48149 Münster Germany
| | - Henning D. Mootz
- Department of Chemistry and Pharmacy; Institute of Biochemistry; Westfälische Wilhelms-Universität Münster; Wilhelm-Klemm-Strasse 2 48149 Münster Germany
| |
Collapse
|
15
|
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.
Collapse
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 .
| |
Collapse
|
16
|
Bacchi M, Fould B, Jullian M, Kreiter A, Maurras A, Nosjean O, Coursindel T, Puget K, Ferry G, Boutin JA. Screening ubiquitin specific protease activities using chemically synthesized ubiquitin and ubiquitinated peptides. Anal Biochem 2017; 519:57-70. [PMID: 27993553 DOI: 10.1016/j.ab.2016.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 12/12/2022]
Abstract
Ubiquitin, a 76 amino acid protein, is a key component that contributes to cellular protein homeostasis. The specificity of this modification is due to a series of enzymes: ligases, attaching the ubiquitin to a lysine, and deubiquitinases, which remove it. More than a hundred of such proteins are implicated in the regulation of protein turnover. Their specificities are only partially understood. We chemically synthesized ubiquitin, attached it to lysines belonging to the protein sequences known to be ubiquitinated. We chose the model protein "murine double minute 2" (mdm2), a ubiquitin ligase, itself ubiquitinated and deubiquitinated. We folded the ubiquitinated peptides and checked their tridimensional conformation. We assessed the use of these substrates with a series of fifteen deubiquitinases to show the potentiality of such an enzymological technique. By manipulating the sequence of the peptide on which ubiquitin is attached, we were able to detect differences in the enzyme/substrate recognition, and to determine that these differences are deubiquitinase-dependent. This approach could be used to understand the substrate/protein relationship between the protagonists of this reaction. The methodology could be customized for a given substrate and used to advance our understanding of the key amino acids responsible for the deubiquitinase specificities.
Collapse
Affiliation(s)
- Marine Bacchi
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Benjamin Fould
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Magali Jullian
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Aude Kreiter
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Amélie Maurras
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Olivier Nosjean
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | | | - Karine Puget
- Genepep S.A., 12 Rue du Fer à Cheval, 34430 Saint-Jean-de-Védas, France
| | - Gilles Ferry
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Jean A Boutin
- Pôle d'Expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France.
| |
Collapse
|
17
|
Taupitz KF, Dörner W, Mootz HD. Covalent Capturing of Transient SUMO-SIM Interactions Using Unnatural Amino Acid Mutagenesis and Photocrosslinking. Chemistry 2017; 23:5978-5982. [PMID: 28121373 DOI: 10.1002/chem.201605619] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Indexed: 11/09/2022]
Abstract
The weak interaction between the post-translational modifier SUMO (small ubiquitin-like modifier) and proteins containing the SUMO-interacting motif (SIM) poses limitations to the identification of interaction partners of SUMOylated proteins and to the mapping of the interfaces. To overcome these limitations, genetically encoded photocrosslinker amino acids were incorporated close to the SIM-interaction groove in human SUMO1. UV irradiation resulted in the desired covalent crosslinks both in a purified protein environment and in cell extracts.
Collapse
Affiliation(s)
- Kim F Taupitz
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
| | - Wolfgang Dörner
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
| | - Henning D Mootz
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
| |
Collapse
|
18
|
Forbes CR, Sinha SK, Ganguly HK, Bai S, Yap GPA, Patel S, Zondlo NJ. Insights into Thiol-Aromatic Interactions: A Stereoelectronic Basis for S-H/π Interactions. J Am Chem Soc 2017; 139:1842-1855. [PMID: 28080040 PMCID: PMC5890429 DOI: 10.1021/jacs.6b08415] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thiols can engage favorably with aromatic rings in S-H/π interactions, within abiological systems and within proteins. However, the underlying bases for S-H/π interactions are not well understood. The crystal structure of Boc-l-4-thiolphenylalanine tert-butyl ester revealed crystal organization centered on the interaction of the thiol S-H with the aromatic ring of an adjacent molecule, with a through-space Hthiol···Caromatic distance of 2.71 Å, below the 2.90 Å sum of the van der Waals radii of H and C. The nature of this interaction was further examined by DFT calculations, IR spectroscopy, solid-state NMR spectroscopy, and analysis of the Cambridge Structural Database. The S-H/π interaction was found to be driven significantly by favorable molecular orbital interactions, between an aromatic π donor orbital and the S-H σ* acceptor orbital (a π → σ* interaction). For comparison, a structural analysis of O-H/π interactions and of cation/π interactions of alkali metal cations with aromatic rings was conducted. Na+ and K+ exhibit a significant preference for the centroid of the aromatic ring and distances near the sum of the van der Waals and ionic radii, as expected for predominantly electrostatic interactions. Li+ deviates substantially from Na+ and K+. The S-H/π interaction differs from classical cation/π interactions by the preferential alignment of the S-H σ* toward the ring carbons and an aromatic π orbital rather than toward the aromatic centroid. These results describe a potentially broadly applicable approach to understanding the interactions of weakly polar bonds with π systems.
Collapse
Affiliation(s)
- Christina R. Forbes
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, United States
| | | | | | - Shi Bai
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, United States
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716, United States
| |
Collapse
|
19
|
Lin D, Jing X, Chen Y, Liang Y, Lei M, Peng S, Zhou T, Zheng D, Zeng Z, Wu X, Yang L, Xiao S, Liu J, Tao E. Rifampicin pre-treatment inhibits the toxicity of rotenone-induced PC12 cells by enhancing sumoylation modification of α-synuclein. Biochem Biophys Res Commun 2017; 485:23-29. [PMID: 28132806 DOI: 10.1016/j.bbrc.2017.01.100] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 01/19/2017] [Indexed: 11/26/2022]
Abstract
Our previous research revealed that rifampicin could protect PC12 (pheochromocytoma 12) cells from rotenone-induced cytotoxicity by reversing the aggregation of α-synuclein. Furthermore, increasing evidence indicated that the misfolded α-synuclein with SUMOylation, an important protein posttranslational modification, was easier to solubilize and was less toxic. Here, we investigated whether rifampicin could stabilize α-synuclein and prevent rotenone-induced PC12 cells from undergoing apoptosis by enhancing SUMOylation of α-synuclein. The expression of SUMO1 and SUMO2/3, the two main proteins responsible for the SUMOylation modification in PC12 cells, were detected by western blotting. Co-immunoprecipitation was performed to compare qualitatively the SUMOylation modification of α-synuclein. The cell viability and apoptosis rate were measured by a CCK-8 assay kit and flow cytometry, respectively. We targeted Ubc9 as a key enzyme in the SUMOylation modification pathway and knocked down the UBC9 gene using a short interfering RNA. Treatment with 150 μmol/L rifampicin, increased the expressions of SUMO1 and SUMO2/3 in cells by 1.5 times compared with the control group; meanwhile, the cell viability of rotenone-induced cells increased from 20 to 80% (P < 0.05). In addition, the increased SUMOylation activity in the cells stimulated by rifampicin was observed 18 h earlier compared with cells treated by rotenone alone. SUMOylation of α-synuclein was more significant in rifampicin-treated cells and Ubc9 upregulated cells. However, the same phenomenon and the protective effect of rifampicin were reversed after UBC9 knockout. In conclusion, rifampicin might reduce the cytotoxicity of rotenone-induced PC12 cells by promoting SUMOylation of α-synuclein.
Collapse
Affiliation(s)
- D Lin
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - X Jing
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - Y Chen
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - Y Liang
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - M Lei
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - S Peng
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - T Zhou
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - D Zheng
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - Z Zeng
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - X Wu
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - L Yang
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - S Xiao
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - J Liu
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China
| | - E Tao
- Department of Neurology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou 510080, China; Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou 510080, China.
| |
Collapse
|
20
|
|
21
|
|
22
|
Boll E, Drobecq H, Lissy E, Cantrelle FX, Melnyk O. Kinetically Controlled Chemoselective Cyclization Simplifies the Access to Cyclic and Branched Peptides. Org Lett 2016; 18:3842-5. [DOI: 10.1021/acs.orglett.6b01847] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Emmanuelle Boll
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Hervé Drobecq
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Elizabeth Lissy
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - François-Xavier Cantrelle
- Université de Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Oleg Melnyk
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| |
Collapse
|
23
|
Eisenhardt N, Chaugule VK, Pichler A. A Fluorescent In Vitro Assay to Investigate Paralog-Specific SUMO Conjugation. Methods Mol Biol 2016; 1475:67-78. [PMID: 27631798 DOI: 10.1007/978-1-4939-6358-4_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Protein modification with the small ubiquitin-related modifier SUMO is a potent regulatory mechanism implicated in a variety of biological pathways. In vitro sumoylation reactions have emerged as a versatile tool to identify and characterize novel SUMO enzymes as well as their substrates. Here, we present detailed protocols for the purification and fluorescent labeling of mammalian SUMO paralogs for their application in sumoylation assays. These assays provide a fast readout for in vitro SUMO chain formation activity of E3 ligases in a paralog-specific manner. Finally, we critically analyze the application of fluorescent SUMO proteins to study substrate modification in vitro revealing also the drawbacks of the system.
Collapse
Affiliation(s)
- Nathalie Eisenhardt
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Viduth K Chaugule
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.
| |
Collapse
|