101
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Garber KCA, Carlson EE. Thiol-ene enabled detection of thiophosphorylated kinase substrates. ACS Chem Biol 2013; 8:1671-6. [PMID: 23668631 DOI: 10.1021/cb400184v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein phosphorylation is a ubiquitous posttranslational modification that regulates cell signaling in both prokaryotes and eukaryotes. Although the study of phosphorylation has made great progress, several major hurdles remain, including the difficulty of the assignment of endogenous substrates to a discrete kinase and of global phosphoproteomics investigations. We have developed a novel chemical strategy for detecting phosphorylated proteins. This method utilizes adenosine 5'-O-(3-thiotriphosphate) (ATPγS), which results in the transfer of a thiophosphate moiety by a kinase to its substrate(s). This group can subsequently be employed as a nucleophilic handle to promote protein detection. To selectively label thiophosphorylated proteins, cellular thiols (e.g., cysteine-containing proteins) must first be blocked. Most common cysteine-capping strategies rely upon the nucleophilicity of the sulfur group and would therefore also modify the thiophosphate moiety. We hypothesized that the radical-mediated thiol-ene reaction, however, would be selective for cysteine over thiophosphorylated amino acids due to the differences in the electronics and pKa values between these groups. Here, we report rapid and specific tagging of thiophosphorylated proteins in vitro following chemoselective thiol capping using the thiol-ene reaction.
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Affiliation(s)
- Kathleen C. A. Garber
- Department
of Chemistry, Indiana University, 800 E.
Kirkwood Avenue, Bloomington,
Indiana 47405, United States
| | - Erin E. Carlson
- Department
of Chemistry, Indiana University, 800 E.
Kirkwood Avenue, Bloomington,
Indiana 47405, United States
- Department of Molecular and
Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, Indiana 47405, United States
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102
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Dixon EK, Castañeda CA, Kashyap T, Wang Y, Fushman D. Nonenzymatic assembly of branched polyubiquitin chains for structural and biochemical studies. Bioorg Med Chem 2013; 21:3421-9. [PMID: 23557636 PMCID: PMC3665622 DOI: 10.1016/j.bmc.2013.02.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 02/22/2013] [Accepted: 02/28/2013] [Indexed: 10/27/2022]
Abstract
Polymeric chains of a small protein ubiquitin are involved in regulation of nearly all vital processes in eukaryotic cells. Elucidating the signaling properties of polyubiquitin requires the ability to make these chains in vitro. In recent years, chemical and chemical-biology tools have been developed that produce fully natural isopeptide-linked polyUb chains with no need for linkage-specific ubiquitin-conjugating enzymes. These methods produced unbranched chains (in which no more than one lysine per ubiquitin is conjugated to another ubiquitin). Here we report a nonenzymatic method for the assembly of fully natural isopeptide-linked branched polyubiquitin chains. This method is based on the use of mutually orthogonal removable protecting groups (e.g., Boc- and Alloc-) on lysines combined with an Ag-catalyzed condensation reaction between a C-terminal thioester on one ubiquitin and a specific ε-amine on another ubiquitin, and involves genetic incorporation of more than one Lys(Boc) at the desired linkage positions in the ubiquitin sequence. We demonstrate our method by making a fully natural branched tri-ubiquitin containing isopeptide linkages via Lys11 and Lys33, and a (15)N-enriched proximal ubiquitin, which enabled monomer-specific structural and dynamical studies by NMR. Furthermore, we assayed disassembly of branched and unbranched tri-ubiquitins as well as control di-ubiquitins by the yeast proteasome-associated deubiquitinase Ubp6. Our results show that Ubp6 can recognize and disassemble a branched polyubiquitin, wherein cleavage preferences for individual linkages are retained. Our spectroscopic and functional data suggest that, at least for the chains studied here, the isopeptide linkages are effectively independent of each other. Together with our method for nonenzymatic assembly of unbranched polyubiquitin, these developments now provide tools for making fully natural polyubiquitin chains of essentially any type of linkage and length.
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Affiliation(s)
- Emma K. Dixon
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Carlos A. Castañeda
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Tanuja Kashyap
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Yan Wang
- Proteomics Core Facility, University of Maryland, College Park, MD 20742, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
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103
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Nakasone MA, Livnat-Levanon N, Glickman MH, Cohen RE, Fushman D. Mixed-linkage ubiquitin chains send mixed messages. Structure 2013; 21:727-40. [PMID: 23562397 DOI: 10.1016/j.str.2013.02.019] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/14/2013] [Accepted: 02/17/2013] [Indexed: 02/02/2023]
Abstract
Research on ubiquitin (Ub) signaling has focused primarily on homogeneously linked polyUb. Although polyUb containing different linkages within the same chain exist, their structures and signaling properties are unknown. These mixed-linkage chains could be unbranched (i.e., no more than one lysine or methionine linkage per Ub) or branched. Here, we examined the structure, dynamics, receptor selectivity, and disassembly of branched and unbranched tri-Ub containing both K48 and K63 linkages. Each linkage was virtually indistinguishable from its counterpart in homogeneously linked polyUb. Linkage-selective receptors from hHR23A and Rap80 preferentially bound to the K48 or K63 linkages in the branched trimer. Linkage-selective deubiquitinases specifically cleaved their cognate Ub-Ub linkages in mixed-linkage chains, and the 26S proteasome recognized and processed branched tri-Ub. We conclude that mixed-linkage chains retain the distinctive signaling properties of their K48 and K63 components and that these multiple signals can be recognized by multiple linkage-specific receptors. Finally, we propose a new, comprehensive notation for Ub and Ub-like polymers.
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Affiliation(s)
- Mark A Nakasone
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
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104
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Le DD, Cortesi AT, Myers SA, Burlingame AL, Fujimori DG. Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding. J Am Chem Soc 2013; 135:2879-82. [PMID: 23398247 DOI: 10.1021/ja3108214] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Arginine methylation has emerged as a widespread post-translational modification with influence over myriad cellular processes. However, the molecular mechanisms underlying such methylarginine-dependent phenomena remain unclear. To aid in this research, a facile method was developed to install methylarginine analogues on recombinant protein for use in biochemical, biophysical, and structural studies. Through chemical conjugation of novel α,β-unsaturated amidine precursors with proteins, methylarginine mimics can be displayed with control of methylation site, extent, and regiospecificity. Analogue installation into histones using this strategy produced modified proteins that were recognized by antibodies specific to endogenous methylarginine, and these histones retained the capacity to form mononucleosomes. Moreover, a native methylarginine-specific binding domain was shown to interact with methylarginine analogue-modified substrates. This chemical conjugation method for installing methylarginine analogues provides an efficient route to produce homogeneous modified proteins for subsequent investigations of methylarginine-dependent processes.
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Affiliation(s)
- Daniel D Le
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, 600 16th Street, MC2280, San Francisco, California 94158, USA
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105
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Hemantha HP, Brik A. Non-enzymatic synthesis of ubiquitin chains: where chemistry makes a difference. Bioorg Med Chem 2013; 21:3411-20. [PMID: 23465437 DOI: 10.1016/j.bmc.2013.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 02/03/2013] [Accepted: 02/05/2013] [Indexed: 12/16/2022]
Abstract
Ubiquitination is a highly important posttranslational modification in eukaryotic cells where a target protein is conjugated to ubiquitin or a chain of ubiquitins via an isopeptide bond to trigger various cellular events such as proteasomal degradation. Rigorous investigations of the ubiquitin signal at the molecular level require homogeneous samples of ubiquitin chains in their free form or as anchored to a protein substrate in adequate quantities. The complexity of ubiquitin chains in terms of linkage types (owing to presence of seven Lys in ubiquitin) makes them difficult to prepare via enzymatic methods. Even more challenging is the attachment of these chains to a protein target at a selected site. This dearth is being filled by the recent developments of novel chemical tools that offer atomic level control over the synthesis for structural and functional studies. These emerging chemical approaches are discussed in this mini-review with focus on the preparation of ubiquitin chains to aid the ongoing efforts in understanding their role in the ubiquitin signal.
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Affiliation(s)
- Hosahalli P Hemantha
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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106
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Wojcik F, O'Brien AG, Götze S, Seeberger PH, Hartmann L. Synthesis of carbohydrate-functionalised sequence-defined oligo(amidoamine)s by photochemical thiol-ene coupling in a continuous flow reactor. Chemistry 2013; 19:3090-8. [PMID: 23325532 DOI: 10.1002/chem.201203927] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Indexed: 12/11/2022]
Abstract
Poly/oligo(amidoamine)s (PAAs) have recently been recognised for their potential as well-defined scaffolds for multiple carbohydrate presentation and as multivalent ligands. Herein, we report two complimentary strategies for the preparation of such sequence-defined carbohydrate-functionalised PAAs that use photochemical thiol-ene coupling (TEC) as an alternative to the established azide-alkyne cycloaddition ("click") reaction. In the first approach, PAAs that contained multiple olefins were synthesised on a solid support from a new building block and subsequent conjugation with unprotected thio-carbohydrates. Alternatively, a pre-functionalised building block was prepared by using TEC and assembled on a solid support to provide a carbohydrate-functionalised PAA. Both methods rely on the use of a continuous flow photoreactor for the TEC reactions. This system is highly efficient, owing to its short path length, and requires no additional radical initiator. Performing the reactions at 254 nm in Teflon AF-2400 tubing provides a highly efficient TEC procedure for carbohydrate conjugation, as demonstrated in the reactions of O-allyl glycosides with thiols. This method allowed the complete functionalisation of all of the reactive sites on the PAA backbone in a single step, thereby obtaining a defined homogeneous sequence. Furthermore, reaction at 366 nm in FEP tubing in the flow reactor enabled the large-scale synthesis of an fluorenylmethyloxycarbonyl (Fmoc)-protected glycosylated building block, which was shown to be suitable for solid-phase synthesis and will also allow heterogeneous sequence control of different carbohydrates along the oligomeric backbone. These developments enable the synthesis of sequence-defined carbohydrate-functionalised PAAs with potential biological applications.
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Affiliation(s)
- Felix Wojcik
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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107
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Tanaka K, Nakamoto Y, Siwu ERO, Pradipta AR, Morimoto K, Fujiwara T, Yoshida S, Hosoya T, Tamura Y, Hirai G, Sodeoka M, Fukase K. Development of bis-unsaturated ester aldehydes as amino-glue probes: sequential double azaelectrocyclization as a promising strategy for bioconjugation. Org Biomol Chem 2013; 11:7326-33. [DOI: 10.1039/c3ob41507d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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108
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Dresselhaus T, Weikart ND, Mootz HD, Waller MP. Naturally and synthetically linked lys48 diubiquitin: a QM/MM study. RSC Adv 2013. [DOI: 10.1039/c3ra42649a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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109
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Trang VH, Valkevich EM, Minami S, Chen YC, Ge Y, Strieter ER. Nonenzymatic polymerization of ubiquitin: single-step synthesis and isolation of discrete ubiquitin oligomers. Angew Chem Int Ed Engl 2012; 51:13085-8. [PMID: 23161800 PMCID: PMC4083817 DOI: 10.1002/anie.201207171] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/26/2012] [Indexed: 11/05/2022]
Abstract
Linked: a method based on thiol-ene chemistry enables the synthesis and purification of ubiquitin oligomers with ≥4 units. This approach, which employs free-radical polymerization, can be applied towards the synthesis of homogeneous Lys6-linked ubiquitin oligomers currently inaccessible by enzymatic methods. By using these chains, one can study their roles in the ubiquitin proteasome system and the DNA damage response pathway.
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Affiliation(s)
- Vivian H. Trang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
| | - Ellen M. Valkevich
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
| | - Shoko Minami
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
| | - Yi-Chen Chen
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, 1300 University Ave. Madison, WI 53706
| | - Ying Ge
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, 1300 University Ave. Madison, WI 53706
| | - Eric R. Strieter
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, Wi 53706
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110
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Trang VH, Valkevich EM, Minami S, Chen YC, Ge Y, Strieter ER. Nonenzymatic Polymerization of Ubiquitin: Single-Step Synthesis and Isolation of Discrete Ubiquitin Oligomers. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207171] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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111
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Moyal T, Bavikar SN, Karthikeyan SV, Hemantha HP, Brik A. Polymerization behavior of a bifunctional ubiquitin monomer as a function of the nucleophile site and folding conditions. J Am Chem Soc 2012; 134:16085-92. [PMID: 22963682 DOI: 10.1021/ja3078736] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Biopolymers with repeating modules composed of either folded peptides or tertiary protein domains are considered some of the basic biomaterials that nature has evolved to optimize for energy efficient synthesis and unique functions. Such biomaterials continue to inspire scientists to mimic their exceptional properties and the ways that nature adopts to prepare them. Ubiquitin chains represent another example of nature's approach to use a protein-repeating module to prepare functionally important biopolymers. In the current work, we utilize a novel synthetic strategy to prepare bifunctional ubiquitin monomers having a C-terminal thioester and a nucleophilic 1,2-aminothiol at a desired position to examine their polymerization products under different conditions. Our study reveals that such analogues, when subjected to polymerization conditions under different folding states, afford distinct patterns of polymerization products where both the dynamic and the tertiary structures of the chains play important roles in such processes. Moreover, we also show that the presence of a specific ubiquitin-binding domain, which binds specifically to some of these chains, could interfere selectively with the polymerization outcome. Our study represents the first example of examining the polymerization of designed and synthetic repeating modules based on tertiary protein domains and affords early lessons in the design and synthesis of biomaterial. In regards to the ubiquitin system, our study may have implications on the ease of synthesis of ubiquitin chains with varying lengths and types for structural and functional analyses. Importantly, such an approach could also assist in understanding the enzymatic machinery and the factors controlling the assembly of these chains with a desired length.
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Affiliation(s)
- Tal Moyal
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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