51
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Adam K, Hunter T. Histidine kinases and the missing phosphoproteome from prokaryotes to eukaryotes. J Transl Med 2018; 98:233-247. [PMID: 29058706 PMCID: PMC5815933 DOI: 10.1038/labinvest.2017.118] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/16/2017] [Accepted: 08/31/2017] [Indexed: 12/20/2022] Open
Abstract
Protein phosphorylation is the most common type of post-translational modification in eukaryotes. The phosphoproteome is defined as the complete set of experimentally detectable phosphorylation sites present in a cell's proteome under various conditions. However, we are still far from identifying all the phosphorylation sites in a cell mainly due to the lack of information about phosphorylation events involving residues other than Ser, Thr and Tyr. Four types of phosphate-protein linkage exist and these generate nine different phosphoresidues-pSer, pThr, pTyr, pHis, pLys, pArg, pAsp, pGlu and pCys. Most of the effort in studying protein phosphorylation has been focused on Ser, Thr and Tyr phosphorylation. The recent development of 1- and 3-pHis monoclonal antibodies promises to increase our understanding of His phosphorylation and the kinases and phosphatases involved. Several His kinases are well defined in prokaryotes, especially those involved in two-component system (TCS) signaling. However, in higher eukaryotes, NM23, a protein originally characterized as a nucleoside diphosphate kinase, is the only characterized protein-histidine kinase. This ubiquitous and conserved His kinase autophosphorylates its active site His, and transfers this phosphate either onto a nucleoside diphosphate or onto a protein His residue. Studies of NM23 protein targets using newly developed anti-pHis antibodies will surely help illuminate the elusive His phosphorylation-based signaling pathways. This review discusses the role that the NM23/NME/NDPK phosphotransferase has, how the addition of the pHis phosphoproteome will expand the phosphoproteome and make His phosphorylation part of the global phosphorylation world. It also summarizes why our understanding of phosphorylation is still largely restricted to the acid stable phosphoproteome, and highlights the study of NM23 histidine kinase as an entrée into the world of histidine phosphorylation.
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Affiliation(s)
- Kevin Adam
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
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52
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Liu T, Zhang W, Zhang Z, Chen M, Wang J, Qian X, Qin W. Sensitive Western-Blot Analysis of Azide-Tagged Protein Post Translational Modifications Using Thermoresponsive Polymer Self-Assembly. Anal Chem 2018; 90:2186-2192. [DOI: 10.1021/acs.analchem.7b04531] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Tong Liu
- Research
Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, PR China
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Wanjun Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Zheng Zhang
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Mingli Chen
- Research
Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, PR China
| | - Jianhua Wang
- Research
Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, PR China
| | - Xiaohong Qian
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Weijie Qin
- State
Key Laboratory of Proteomics, Beijing Proteome Research Center, National
Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
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53
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Zhang JQ, Chen T, Zhang JS, Han LB. Silver-Free Direct Synthesis of Alkynylphosphine Oxides via spC–H/P(O)–H Dehydrogenative Coupling Catalyzed by Palladium. Org Lett 2017; 19:4692-4695. [DOI: 10.1021/acs.orglett.7b02389] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jian-Qiu Zhang
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Tieqiao Chen
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Ji-Shu Zhang
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Li-Biao Han
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
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54
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Hauser A, Penkert M, Hackenberger CPR. Chemical Approaches to Investigate Labile Peptide and Protein Phosphorylation. Acc Chem Res 2017; 50:1883-1893. [PMID: 28723107 DOI: 10.1021/acs.accounts.7b00170] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation is by far the most abundant and most studied post-translational modification (PTM). For a long time, phosphate monoesters of serine (pSer), threonine (pThr), and tyrosine (pTyr) have been considered as the only relevant forms of phosphorylation in organisms. Recently, several research groups have dedicated their efforts to the investigation of other, less characterized phosphoamino acids as naturally occurring PTMs. Such apparent peculiar phosphorylations include the phosphoramidates of histidine (pHis), arginine (pArg), and lysine (pLys), the phosphorothioate of cysteine (pCys), and the anhydrides of pyrophosphorylated serine (ppSer) and threonine (ppThr). Almost all of these phosphorylated amino acids show higher lability under physiological conditions than those of phosphate monoesters. Furthermore, they are prone to hydrolysis under acidic and sometimes basic conditions as well as at elevated temperatures, which renders their synthetic accessibility and proteomic analysis particularly challenging. In this Account, we illustrate recent chemical approaches to probe the occurrence and function of these labile phosphorylation events. Within these endeavors, the synthesis of site-selectively phosphorylated peptides, in particular in combination with chemoselective phosphorylation strategies, was crucial. With these well-defined standards in hand, the appropriate proteomic mass spectrometry-based analysis protocols for the characterization of labile phosphosites in biological samples could be developed. Another successful approach in this research field includes the design and synthesis of stable analogues of these labile PTMs, which were used for the generation of pHis- and pArg-specific antibodies for the detection and enrichment of endogenous phosphorylated samples. Finally, other selective enrichment techniques are described, which rely for instance on the unique chemical environment of a pyrophosphate or the selective interaction between a phosphoamino acid and its phosphatase. It is worth noting that many of those studies are still in their early stages, which is also reflected in the small number of identified phosphosites compared to that of phosphate monoesters. Thus, many challenges need to be mastered to fully understand the biological role of these poorly characterized and rather uncommon phosphorylations. Taken together, this overview exemplifies recent efforts in a flourishing field of functional proteomic analysis and furthermore manifests the power of modern peptide synthesis to address unmet questions in the life sciences.
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Affiliation(s)
- Anett Hauser
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, 13125 Berlin, Germany
- Institute
of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße
2, 12489 Berlin, Germany
| | - Martin Penkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, 13125 Berlin, Germany
- Institute
of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße
2, 12489 Berlin, Germany
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, 13125 Berlin, Germany
- Institute
of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße
2, 12489 Berlin, Germany
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55
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Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate. Nat Chem Biol 2017; 13:1081-1087. [PMID: 28805803 PMCID: PMC5605442 DOI: 10.1038/nchembio.2453] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 07/10/2017] [Indexed: 01/16/2023]
Abstract
Lower glycolysis involves a series of reversible reactions, which interconvert intermediates that also feed anabolic pathways. 3-phosphoglycerate (3-PG) is an abundant lower glycolytic intermediate that feeds serine biosynthesis via the enzyme phosphoglycerate dehydrogenase, which is genomically amplified in several cancers. Phosphoglycerate mutase (PGAM1) catalyzes the isomerization of 3-PG into the downstream glycolytic intermediate 2-phosphoglycerate (2-PG). Catalytic activity of PGAM1 requires its histidine phosphorylation. We show that the primary PGAM1 histidine phosphate donor is 2,3-bisphosphoglycerate (2,3-BPG), which is made from the glycolytic intermediate 1,3-bisphosphoglycerate (1,3-BPG) by bisphosphoglycerate mutase (BPGM). When BPGM is knocked out, 1,3-BPG can directly phosphorylate PGAM1. In this case, PGAM1 phosphorylation and activity are decreased, but nevertheless sufficient to maintain normal glycolytic flux and cellular growth rate. 3-PG, however, accumulates, leading to increased serine synthesis. Thus, one biological function of BPGM is to control glycolytic intermediate levels and thereby serine biosynthetic flux.
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56
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Quan Q, Feng J, Lui LT, Shi T, Chu IK. Phosphoproteome of crab-eating macaque cerebral cortex characterized through multidimensional reversed-phase liquid chromatography/mass spectrometry with tandem anion/cation exchange columns. J Chromatogr A 2017; 1498:196-206. [DOI: 10.1016/j.chroma.2017.01.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 01/13/2017] [Accepted: 01/21/2017] [Indexed: 02/06/2023]
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57
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Marmelstein AM, Moreno J, Fiedler D. Chemical Approaches to Studying Labile Amino Acid Phosphorylation. Top Curr Chem (Cham) 2017; 375:22. [DOI: 10.1007/s41061-017-0111-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/23/2017] [Indexed: 12/12/2022]
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Abstract
An efficient transformation towards propynoates and propynenitriles is herein described. The practical methodology was conducted at low temperature (–78 or –60 °C) in a one-pot manner with the assistance of base rather than any transition metal catalysts. The base-induced protocol exhibits good functional group tolerance (up to 28 examples) and high efficiency (up to 92% yields) towards substituted acetylenes of great synthetic significance, which was also well demonstrated by the gram-scale reactions.
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Affiliation(s)
- Fan Shu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Qingjuan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Wanrong Dong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Zhihong Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Delie An
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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59
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Novel nucleotide analogues bearing (1 H -1,2,3-triazol-4-yl)phosphonic acid moiety as inhibitors of Plasmodium and human 6-oxopurine phosphoribosyltransferases. Tetrahedron 2017. [DOI: 10.1016/j.tet.2016.12.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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60
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Fuhs SR, Hunter T. pHisphorylation: the emergence of histidine phosphorylation as a reversible regulatory modification. Curr Opin Cell Biol 2017; 45:8-16. [PMID: 28129587 DOI: 10.1016/j.ceb.2016.12.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 12/31/2016] [Indexed: 12/30/2022]
Abstract
Histidine phosphorylation is crucial for prokaryotic signal transduction and as an intermediate for several metabolic enzymes, yet its role in mammalian cells remains largely uncharted. This is primarily caused by difficulties in studying histidine phosphorylation because of the relative instability of phosphohistidine (pHis) and lack of specific antibodies and methods to preserve and detect it. The recent synthesis of stable pHis analogs has enabled development of pHis-specific antibodies and their use has started to shed light onto this important, yet enigmatic posttranslational modification. We are beginning to understand that pHis has broader roles in protein and cellular function including; cell cycle regulation, phagocytosis, regulation of ion channel activity and metal ion coordination. Two mammalian histidine kinases (NME1 and NME2), two pHis phosphatases (PHPT1 and LHPP), and a handful of substrates were previously identified. These new tools have already led to the discovery of an additional phosphatase (PGAM5) and hundreds of putative substrates. New methodologies are also being developed to probe the pHis phosphoproteome and determine functional consequences, including negative ion mode mass spectroscopy and unnatural amino acid incorporation. These new tools and strategies have the potential to overcome the unique challenges that have been holding back our understanding of pHis in cell biology.
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Affiliation(s)
- Stephen Rush Fuhs
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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61
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62
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Johansson JR, Beke-Somfai T, Said Stålsmeden A, Kann N. Ruthenium-Catalyzed Azide Alkyne Cycloaddition Reaction: Scope, Mechanism, and Applications. Chem Rev 2016; 116:14726-14768. [DOI: 10.1021/acs.chemrev.6b00466] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Johan R. Johansson
- Cardiovascular
and Metabolic Diseases, Innovative Medicines and Early Development
Biotech Unit, AstraZeneca, Pepparedsleden 1, SE-43183 Mölndal, Sweden
| | - Tamás Beke-Somfai
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
krt. 2, H-1117 Budapest, Hungary
| | - Anna Said Stålsmeden
- Chemistry
and Biochemistry, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden
| | - Nina Kann
- Chemistry
and Biochemistry, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden
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63
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Chemoselective synthesis and analysis of naturally occurring phosphorylated cysteine peptides. Nat Commun 2016; 7:12703. [PMID: 27586301 PMCID: PMC5025809 DOI: 10.1038/ncomms12703] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/26/2016] [Indexed: 12/15/2022] Open
Abstract
In contrast to protein O-phosphorylation, studying the function of the less frequent N- and S-phosphorylation events have lagged behind because they have chemical features that prevent their manipulation through standard synthetic and analytical methods. Here we report on the development of a chemoselective synthetic method to phosphorylate Cys side-chains in unprotected peptides. This approach makes use of a reaction between nucleophilic phosphites and electrophilic disulfides accessible by standard methods. We achieve the stereochemically defined phosphorylation of a Cys residue and verify the modification using electron-transfer higher-energy dissociation (EThcD) mass spectrometry. To demonstrate the use of the approach in resolving biological questions, we identify an endogenous Cys phosphorylation site in IICB(Glc), which is known to be involved in the carbohydrate uptake from the bacterial phosphotransferase system (PTS). This new chemical and analytical approach finally allows further investigating the functions and significance of Cys phosphorylation in a wide range of crucial cellular processes.
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64
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Panda S, Srivastava S, Li Z, Vaeth M, Fuhs SR, Hunter T, Skolnik EY. Identification of PGAM5 as a Mammalian Protein Histidine Phosphatase that Plays a Central Role to Negatively Regulate CD4(+) T Cells. Mol Cell 2016; 63:457-69. [PMID: 27453048 DOI: 10.1016/j.molcel.2016.06.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/18/2016] [Accepted: 06/14/2016] [Indexed: 12/18/2022]
Abstract
Whereas phosphorylation of serine, threonine, and tyrosine is exceedingly well characterized, the role of histidine phosphorylation in mammalian signaling is largely unexplored. Here we show that phosphoglycerate mutase family 5 (PGAM5) functions as a phosphohistidine phosphatase that specifically associates with and dephosphorylates the catalytic histidine on nucleoside diphosphate kinase B (NDPK-B). By dephosphorylating NDPK-B, PGAM5 negatively regulates CD4(+) T cells by inhibiting NDPK-B-mediated histidine phosphorylation and activation of the K(+) channel KCa3.1, which is required for TCR-stimulated Ca(2+) influx and cytokine production. Using recently developed monoclonal antibodies that specifically recognize phosphorylation of nitrogens at the N1 (1-pHis) or N3 (3-pHis) positions of the imidazole ring, we detect for the first time phosphoisoform-specific regulation of histidine-phosphorylated proteins in vivo, and we link these modifications to TCR signaling. These results represent an important step forward in studying the role of histidine phosphorylation in mammalian biology and disease.
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Affiliation(s)
- Saswati Panda
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, NY 10016, USA; The Helen L. and Martin S. Kimmel Center for Biology and Medicine, New York University Langone Medical Center, New York, NY 10016, USA; Skirball Institute for Biomolecular Medicine, New York University Langone Medical Center, New York, NY 10016, USA
| | - Shekhar Srivastava
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, NY 10016, USA; The Helen L. and Martin S. Kimmel Center for Biology and Medicine, New York University Langone Medical Center, New York, NY 10016, USA; Skirball Institute for Biomolecular Medicine, New York University Langone Medical Center, New York, NY 10016, USA; Division of Nephrology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Zhai Li
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, NY 10016, USA; The Helen L. and Martin S. Kimmel Center for Biology and Medicine, New York University Langone Medical Center, New York, NY 10016, USA; Skirball Institute for Biomolecular Medicine, New York University Langone Medical Center, New York, NY 10016, USA
| | - Martin Vaeth
- Department of Pathology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Stephen R Fuhs
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Edward Y Skolnik
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, NY 10016, USA; The Helen L. and Martin S. Kimmel Center for Biology and Medicine, New York University Langone Medical Center, New York, NY 10016, USA; Skirball Institute for Biomolecular Medicine, New York University Langone Medical Center, New York, NY 10016, USA; Division of Nephrology, New York University Langone Medical Center, New York, NY 10016, USA.
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65
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Bertran-Vicente J, Schümann M, Schmieder P, Krause E, Hackenberger CPR. Direct access to site-specifically phosphorylated-lysine peptides from a solid-support. Org Biomol Chem 2016; 13:6839-43. [PMID: 26018866 DOI: 10.1039/c5ob00734h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphorylation is a key process for changing the activity and function of proteins. The impact of phospho-serine (pSer), -threonine (pThr) and -tyrosine (pTyr) is certainly understood for some proteins. Recently, peptides and proteins containing N-phosphorylated amino acids such as phosphoarginine (pArg), phosphohistidine (pHis) and phospholysine (pLys) have gained interest because of their different chemical properties and stability profiles. Due to its high intrinsic lability, pLys is the least studied within this latter group. In order to gain insight into the biological role of pLys, chemical and analytical tools, which are compatible with the labile P(=O)-N bond, are highly sought-after. We recently reported an in-solution synthetic approach to incorporate pLys residues in a site-specific manner into peptides by taking advantage of the chemoselectivity of the Staudinger-phosphite reaction. While the in-solution approach allows us to circumvent the critical TFA cleavage, it still requires several transformations and purification steps to finally deliver pLys peptides. Here we report the synthesis of site-specific pLys peptides directly from a solid support by using a base labile resin. This straightforward and highly efficient approach facilitates the synthesis of various site-specific pLys-containing peptides and lays the groundwork for future studies about this elusive protein modification.
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Affiliation(s)
- Jordi Bertran-Vicente
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, Berlin 13125, Germany.
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66
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Ouyang H, Fu C, Fu S, Ji Z, Sun Y, Deng P, Zhao Y. Development of a stable phosphoarginine analog for producing phosphoarginine antibodies. Org Biomol Chem 2016; 14:1925-9. [DOI: 10.1039/c5ob02603b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
pAIE is designed and synthesized as a stable analog and bioisostere of acid-labile pArg, to produce pArg specific antibodies, facilitating the detection of protein arginine phosphorylation.
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Affiliation(s)
- Han Ouyang
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- China
| | - Chuan Fu
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- China
| | - Songsen Fu
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- China
| | - Zhe Ji
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- China
| | - Ying Sun
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- China
| | - Peiran Deng
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- China
| | - Yufen Zhao
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- China
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67
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Behrendt R, White P, Offer J. Advances in Fmoc solid-phase peptide synthesis. J Pept Sci 2016; 22:4-27. [PMID: 26785684 PMCID: PMC4745034 DOI: 10.1002/psc.2836] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 10/20/2015] [Indexed: 12/13/2022]
Abstract
Today, Fmoc SPPS is the method of choice for peptide synthesis. Very-high-quality Fmoc building blocks are available at low cost because of the economies of scale arising from current multiton production of therapeutic peptides by Fmoc SPPS. Many modified derivatives are commercially available as Fmoc building blocks, making synthetic access to a broad range of peptide derivatives straightforward. The number of synthetic peptides entering clinical trials has grown continuously over the last decade, and recent advances in the Fmoc SPPS technology are a response to the growing demand from medicinal chemistry and pharmacology. Improvements are being continually reported for peptide quality, synthesis time and novel synthetic targets. Topical peptide research has contributed to a continuous improvement and expansion of Fmoc SPPS applications.
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Affiliation(s)
- Raymond Behrendt
- Novabiochem, Merck & CieIm Laternenacker 58200SchaffhausenSwitzerland
| | - Peter White
- Novabiochem, Merck Chemicals LtdPadge RoadBeestonNG9 2JRUK
| | - John Offer
- The Francis Crick Institute215 Euston RoadLondonNW1 2BEUK
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68
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Thiery E, You V, Mora AS, Abarbri M. Synthesis of 5-Substituted 1,2,3-Triazolyl-4-phosphonate through Cross-Coupling Reactions of 5-Iodo-1,2,3-triazolyl-4-phosphonate. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501266] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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69
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Fuhrmann J, Subramanian V, Thompson PR. Synthesis and Use of a Phosphonate Amidine to Generate an Anti‐Phosphoarginine‐Specific Antibody. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506737] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jakob Fuhrmann
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 (USA)
| | - Venkataraman Subramanian
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, MA 01605 (USA)
- Chemical Biology Interface Program, UMass Medical School, 364 Plantation Street, Worcester, MA 01605 (USA)
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, MA 01605 (USA)
- Chemical Biology Interface Program, UMass Medical School, 364 Plantation Street, Worcester, MA 01605 (USA)
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70
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Zhang Y, Zhang Y, Xiao J, Peng Z, Dong W, An D. Base-Induced One-Pot Preparation of N- or P-Substituted Alkynes. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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71
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Fuhrmann J, Subramanian V, Thompson PR. Synthesis and Use of a Phosphonate Amidine to Generate an Anti-Phosphoarginine-Specific Antibody. Angew Chem Int Ed Engl 2015; 54:14715-8. [PMID: 26458230 DOI: 10.1002/anie.201506737] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/08/2015] [Indexed: 01/09/2023]
Abstract
Protein arginine phosphorylation is a post-translational modification (PTM) that is important for bacterial growth and virulence. Despite its biological relevance, the intrinsic acid lability of phosphoarginine (pArg) has impaired studies of this novel PTM. Herein, we report for the first time the development of phosphonate amidines and sulfonate amidines as isosteres of pArg and then use these mimics as haptens to develop the first high-affinity sequence independent anti-pArg specific antibody. Employing this anti-pArg antibody, we further showed that arginine phosphorylation is induced in Bacillus subtilis during oxidative stress. Overall, we expect this antibody to see widespread use in analyzing the biological significance of arginine phosphorylation. Additionally, the chemistry reported here will facilitate the generation of pArg mimetics as highly potent inhibitors of the enzymes that catalyze arginine phosphorylation/dephosphorylation.
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Affiliation(s)
- Jakob Fuhrmann
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 (USA).
| | - Venkataraman Subramanian
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, MA 01605 (USA).,Chemical Biology Interface Program, UMass Medical School, 364 Plantation Street, Worcester, MA 01605 (USA)
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, MA 01605 (USA). .,Chemical Biology Interface Program, UMass Medical School, 364 Plantation Street, Worcester, MA 01605 (USA).
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72
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Fuhs SR, Meisenhelder J, Aslanian A, Ma L, Zagorska A, Stankova M, Binnie A, Al-Obeidi F, Mauger J, Lemke G, Yates JR, Hunter T. Monoclonal 1- and 3-Phosphohistidine Antibodies: New Tools to Study Histidine Phosphorylation. Cell 2015; 162:198-210. [PMID: 26140597 DOI: 10.1016/j.cell.2015.05.046] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/13/2015] [Accepted: 04/20/2015] [Indexed: 01/18/2023]
Abstract
Histidine phosphorylation (pHis) is well studied in bacteria; however, its role in mammalian signaling remains largely unexplored due to the lack of pHis-specific antibodies and the lability of the phosphoramidate (P-N) bond. Both imidazole nitrogens can be phosphorylated, forming 1-phosphohistidine (1-pHis) or 3-phosphohistidine (3-pHis). We have developed monoclonal antibodies (mAbs) that specifically recognize 1-pHis or 3-pHis; they do not cross-react with phosphotyrosine or the other pHis isomer. Assays based on the isomer-specific autophosphorylation of NME1 and phosphoglycerate mutase were used with immunoblotting and sequencing IgG variable domains to screen, select, and characterize anti-1-pHis and anti-3-pHis mAbs. Their sequence independence was determined by blotting synthetic peptide arrays, and they have been tested for immunofluorescence staining and immunoaffinity purification, leading to putative identification of pHis-containing proteins. These reagents should be broadly useful for identification of pHis substrates and functional study of pHis using a variety of immunological, proteomic, and biological assays.
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Affiliation(s)
- Stephen Rush Fuhs
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jill Meisenhelder
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Aaron Aslanian
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Li Ma
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Anna Zagorska
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Alan Binnie
- Tucson Innovation Center, Sanofi, Tucson, AZ 85755, USA
| | | | | | - Greg Lemke
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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73
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Harper B, Neumann EK, Solouki T. DNA Oligonucleotide Fragment Ion Rearrangements Upon Collision-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1404-1413. [PMID: 26041081 DOI: 10.1007/s13361-015-1153-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 03/27/2015] [Accepted: 03/30/2015] [Indexed: 06/04/2023]
Abstract
Collision-induced dissociation (CID) of m/z-isolated w type fragment ions and an intact 5' phosphorylated DNA oligonucleotide generated rearranged product ions. Of the 21 studied w ions of various nucleotide sequences, fragment ion sizes, and charge states, 18 (~86%) generated rearranged product ions upon CID in a Synapt G2-S HDMS (Waters Corporation, Manchester, England, UK) ion mobility-mass spectrometer. Mass spectrometry (MS), ion mobility spectrometry (IMS), and theoretical modeling data suggest that purine bases can attack the free 5' phosphate group in w type ions and 5' phosphorylated DNA to generate sequence permuted [phosphopurine](-) fragment ions. We propose and discuss a potential mechanism for generation of rearranged [phosphopurine](-) and complementary y-B type product ions.
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Affiliation(s)
- Brett Harper
- Institute of Biomedical Studies, Baylor University, Waco, TX, 76798, USA
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74
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John J, Thomas J, Parekh N, Dehaen W. Tandem Organocatalyzed Knoevenagel Condensation/1,3-Dipolar Cycloaddition towards Highly Functionalized Fused 1,2,3-Triazoles. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500459] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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75
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Lilley M, Mambwe B, Jackson RFW, Muimo R. 4-Phosphothiophen-2-yl alanine: a new 5-membered analogue of phosphotyrosine. Chem Commun (Camb) 2015; 50:9343-5. [PMID: 25002222 DOI: 10.1039/c4cc03393k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polyclonal antibodies raised against 4-phosphothiophen-2-yl alanine 2a, a novel five-membered ring analogue of phosphotyrosine, showed high selectivity for phosphotyrosine and no cross-reactivity with other phosphorylated amino acids. Western blots showed that the polyclonal was similarly effective, but different in selectivity, to a commercially available monoclonal antibody.
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Affiliation(s)
- Matthew Lilley
- Department of Chemistry, The University of Sheffield, Dainton Building, Sheffield, S3 7HF, UK.
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76
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Affiliation(s)
- Manuel M. Müller
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
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77
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Yates LM, Fiedler D. Establishing the Stability and Reversibility of Protein Pyrophosphorylation with Synthetic Peptides. Chembiochem 2015; 16:415-23. [DOI: 10.1002/cbic.201402589] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Indexed: 12/24/2022]
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78
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Lilley M, Mambwe B, Thompson MJ, Jackson RFW, Muimo R. 4-Phosphopyrazol-2-yl alanine: a non-hydrolysable analogue of phosphohistidine. Chem Commun (Camb) 2015; 51:7305-8. [DOI: 10.1039/c5cc01811k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the synthesis of a stable analogue of τ-phosphohistidine: 4-phosphopyrazol-2-yl alanine (pPza).
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Affiliation(s)
- Matthew Lilley
- Department of Chemistry
- The University of Sheffield
- Sheffield
- UK
- Department of Infection and Immunity
| | - Bezaleel Mambwe
- Department of Infection and Immunity
- Academic Unit of Respiratory Medicine
- The University of Sheffield Medical School
- Sheffield
- UK
| | | | | | - Richmond Muimo
- Department of Infection and Immunity
- Academic Unit of Respiratory Medicine
- The University of Sheffield Medical School
- Sheffield
- UK
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79
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Kee JM, Oslund RC, Couvillon AD, Muir TW. A second-generation phosphohistidine analog for production of phosphohistidine antibodies. Org Lett 2014; 17:187-9. [PMID: 25531910 DOI: 10.1021/ol503320p] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein histidine phosphorylation plays a crucial role in cell signaling and central metabolism. However, its detailed functions remain elusive due to technical challenges in detecting and isolating proteins bearing phosphohistidine (pHis), a labile posttranslational modification (PTM). To address this issue, we previously developed the first pHis-specific antibodies using stable, synthetic triazole-based pHis analogs. A second-generation, pyrazole-based pHis analog that enabled the development of a pan-pHis antibody with much improved pHis specificity is now reported.
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Affiliation(s)
- Jung-Min Kee
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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80
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Schumacher D, Hackenberger CPR. More than add-on: chemoselective reactions for the synthesis of functional peptides and proteins. Curr Opin Chem Biol 2014; 22:62-9. [DOI: 10.1016/j.cbpa.2014.09.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/01/2022]
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81
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Bertran-Vicente J, Serwa RA, Schümann M, Schmieder P, Krause E, Hackenberger CPR. Site-specifically phosphorylated lysine peptides. J Am Chem Soc 2014; 136:13622-8. [PMID: 25196693 DOI: 10.1021/ja507886s] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein phosphorylation controls major processes in cells. Although phosphorylation of serine, threonine, and tyrosine and also recently histidine and arginine are well-established, the extent and biological significance of lysine phosphorylation has remained elusive. Research in this area has been particularly limited by the inaccessibility of peptides and proteins that are phosphorylated at specific lysine residues, which are incompatible with solid-phase peptide synthesis (SPPS) due to the intrinsic acid lability of the P(═O)-N phosphoramidate bond. To address this issue, we have developed a new synthetic route for the synthesis of site-specifically phospholysine (pLys)-containing peptides by employing the chemoselectivity of the Staudinger-phosphite reaction. Our synthetic approach relies on the SPPS of unprotected ε-azido lysine-containing peptides and their subsequent reaction to phosphoramidates with phosphite esters before they are converted into the natural modification via UV irradiation or basic deprotection. With these peptides in hand, we demonstrate that electron-transfer dissociation tandem mass spectrometry can be used for unambiguous assignment of phosphorylated-lysine residues within histone peptides and that these peptides can be detected in cell lysates using a bottom-up proteomic approach. This new tagging method is expected to be an essential tool for evaluating the biological relevance of lysine phosphorylation.
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Affiliation(s)
- Jordi Bertran-Vicente
- Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle Str. 10, 13125 Berlin, Germany
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82
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Oslund RC, Kee JM, Couvillon AD, Bhatia V, Perlman DH, Muir TW. A phosphohistidine proteomics strategy based on elucidation of a unique gas-phase phosphopeptide fragmentation mechanism. J Am Chem Soc 2014; 136:12899-911. [PMID: 25156620 PMCID: PMC4183637 DOI: 10.1021/ja507614f] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Indexed: 01/25/2023]
Abstract
Protein histidine phosphorylation is increasingly recognized as a critical posttranslational modification (PTM) in central metabolism and cell signaling. Still, the detection of phosphohistidine (pHis) in the proteome has remained difficult due to the scarcity of tools to enrich and identify this labile PTM. To address this, we report the first global proteomic analysis of pHis proteins, combining selective immunoenrichment of pHis peptides and a bioinformatic strategy based on mechanistic insight into pHis peptide gas-phase fragmentation during LC-MS/MS. We show that collision-induced dissociation (CID) of pHis peptides produces prominent characteristic neutral losses of 98, 80, and 116 Da. Using isotopic labeling studies, we also demonstrate that the 98 Da neutral loss occurs via gas-phase phosphoryl transfer from pHis to the peptide C-terminal α-carboxylate or to Glu/Asp side chain residues if present. To exploit this property, we developed a software tool that screens LC-MS/MS spectra for potential matches to pHis-containing peptides based on their neutral loss pattern. This tool was integrated into a proteomics workflow for the identification of endogenous pHis-containing proteins in cellular lysates. As an illustration of this strategy, we analyzed pHis peptides from glycerol-fed and mannitol-fed Escherichia coli cells. We identified known and a number of previously speculative pHis sites inferred by homology, predominantly in the phosphoenolpyruvate:sugar transferase system (PTS). Furthermore, we identified two new sites of histidine phosphorylation on aldehyde-alcohol dehydrogenase (AdhE) and pyruvate kinase (PykF) enzymes, previously not known to bear this modification. This study lays the groundwork for future pHis proteomics studies in bacteria and other organisms.
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Affiliation(s)
- Rob C. Oslund
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jung-Min Kee
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | | | - Vivek
N. Bhatia
- Heartflow,
Inc., 1400 Seaport Boulevard,
Building B, Redwood City, California 94063, United States
| | - David H. Perlman
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Lewis-Sigler
Institute for Integrative Genomics and the Princeton Collaborative
Proteomics Mass Spectrometry Center, Princeton
University, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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83
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Gurard-Levin ZA, Almouzni G. Histone modifications and a choice of variant: a language that helps the genome express itself. F1000PRIME REPORTS 2014; 6:76. [PMID: 25343033 PMCID: PMC4166940 DOI: 10.12703/p6-76] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covalent post-translational modifications on histones impact chromatin structure and function. Their misfunction, along with perturbations or mutations in genes that regulate their dynamic status, has been observed in several diseases. Thus, targeting histone modifications represents attractive opportunities for therapeutic intervention and biomarker discovery. The best approach to address this challenge is to paint a comprehensive picture integrating the growing number of modifications on individual residues and their combinatorial association, the corresponding modifying enzymes, and effector proteins that bind modifications. Furthermore, how they are imposed in a distinct manner during the cell cycle and on specific histone variants are important dimensions to consider. Firstly, this report highlights innovative technologies used to characterize histone modifications, and the corresponding enzymes and effector proteins. Secondly, we examine the recent progress made in understanding the dynamics and maintenance of histone modifications on distinct variants. We also discuss their roles as potential carriers of epigenetic information. Finally, we provide examples of initiatives to exploit histone modifications in cancer management, with the potential for new therapeutic opportunities.
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Affiliation(s)
- Zachary A. Gurard-Levin
- Institut Curie, Centre de RechercheParis, F-75248France
- CNRS, UMR3664Paris, F-75248France
- Équipe Labellisée Ligue contre le Cancer, UMR3664Paris, F-75248France
- UPMC, UMR3664Paris, F-75248France
- Sorbonne University, PSLParisFrance
| | - Geneviève Almouzni
- Institut Curie, Centre de RechercheParis, F-75248France
- CNRS, UMR3664Paris, F-75248France
- Équipe Labellisée Ligue contre le Cancer, UMR3664Paris, F-75248France
- UPMC, UMR3664Paris, F-75248France
- Sorbonne University, PSLParisFrance
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84
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Oakdale JS, Sit RK, Fokin VV. Ruthenium-catalyzed cycloadditions of 1-haloalkynes with nitrile oxides and organic azides: synthesis of 4-haloisoxazoles and 5-halotriazoles. Chemistry 2014; 20:11101-10. [PMID: 25059647 PMCID: PMC4442801 DOI: 10.1002/chem.201402559] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Indexed: 01/22/2023]
Abstract
(Cyclopentadienyl)(cyclooctadiene) ruthenium(II) chloride [CpRuCl(cod)] catalyzes the reaction between nitrile oxides and electronically deficient 1-choro-, 1-bromo-, and 1-iodoalkynes leading to 4-haloisoxazoles. Organic azides are also suitable 1,3-dipoles, resulting in 5-halo-1,2,3-triazoles. These air-tolerant reactions can be performed at room temperature with 1.25 equivalents of the respective 1,3-dipole relative to the alkyne component. Reactive 1-haloalkynes include propiolic amides, esters, ketones, and phosphonates. Post-functionalization of the halogenated azole products can be accomplished by using palladium-catalyzed cross-coupling reactions and by manipulation of reactive amide groups. The lack of catalysis observed with [Cp*RuCl(cod)] (Cp* = pentamethylcyclopentadienyl) is attributed to steric demands of the Cp* (η(5)-C5Me5) ligand in comparison to the parent Cp (η(5)-C5H5). This hypothesis is supported by the poor reactivity of [(η(5)-C5Me4CF3)RuCl(cod)], which serves as a an isosteric mimic of Cp* and as an isoelectronic analogue of Cp.
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Affiliation(s)
- James S. Oakdale
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-7562
| | - Rakesh K. Sit
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-7562
| | - Valery V. Fokin
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA), Fax: (+1) 858-784-7562
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85
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Thomas J, John J, Parekh N, Dehaen W. A Metal-Free Three-Component Reaction for the Regioselective Synthesis of 1,4,5-Trisubstituted 1,2,3-Triazoles. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403453] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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86
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Thomas J, John J, Parekh N, Dehaen W. A metal-free three-component reaction for the regioselective synthesis of 1,4,5-trisubstituted 1,2,3-triazoles. Angew Chem Int Ed Engl 2014; 53:10155-9. [PMID: 24989456 DOI: 10.1002/anie.201403453] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/12/2014] [Indexed: 01/05/2023]
Abstract
A metal-free three-component reaction to synthesize 1,4,5-trisubstituted 1,2,3-triazoles from readily available building blocks, such as aldehydes, nitroalkanes, and organic azides, is described. The process is enabled by an organocatalyzed Knoevenagel condensation of the formyl group with the nitro compound, which is followed by the 1,3-dipolar cycloaddition of the azide to the activated alkene. The reaction features an excellent substrate scope, and the products are obtained with high yield and regioselectivity. This method can be utilized for the synthesis of fused triazole heterocycles and materials with several triazole moieties.
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Affiliation(s)
- Joice Thomas
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven (Belgium)
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87
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Sadu VS, Roy HN, Arigala P, Hwang IT, Lee KI. Entry to Highly Hindered Chiral β-Amino Triazoles Bearing a gem-Diaryl Group by Azide-alkyne Click Chemistry. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.6.1605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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88
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McAllister TE, Horner KA, Webb ME. Evaluation of the interaction between phosphohistidine analogues and phosphotyrosine binding domains. Chembiochem 2014; 15:1088-91. [PMID: 24771713 PMCID: PMC4159583 DOI: 10.1002/cbic.201402090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Indexed: 12/16/2022]
Abstract
We have investigated the interaction of peptides containing phosphohistidine analogues and their homologues with the prototypical phosphotyrosine binding SH2 domain from the eukaryotic cell signalling protein Grb2 by using a combination of isothermal titration calorimetry and a fluorescence anisotropy competition assay. These investigations demonstrated that the triazole class of phosphohistidine analogues are capable of binding too, suggesting that phosphohistidine could potentially be detected by this class of proteins in vivo.
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Affiliation(s)
- Tom E McAllister
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsWoodhouse Lane, Leeds, LS2 9JT (UK) E-mail: Homepage: http://www.chem.leeds.ac.uk/MEW/
| | - Katherine A Horner
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsWoodhouse Lane, Leeds, LS2 9JT (UK) E-mail: Homepage: http://www.chem.leeds.ac.uk/MEW/
| | - Michael E Webb
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsWoodhouse Lane, Leeds, LS2 9JT (UK) E-mail: Homepage: http://www.chem.leeds.ac.uk/MEW/
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89
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Pick H, Kilic S, Fierz B. Engineering chromatin states: chemical and synthetic biology approaches to investigate histone modification function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:644-56. [PMID: 24768924 DOI: 10.1016/j.bbagrm.2014.04.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/26/2014] [Accepted: 04/16/2014] [Indexed: 01/11/2023]
Abstract
Patterns of histone post-translational modifications (PTMs) and DNA modifications establish a landscape of chromatin states with regulatory impact on gene expression, cell differentiation and development. These diverse modifications are read out by effector protein complexes, which ultimately determine their functional outcome by modulating the activity state of underlying genes. From genome-wide studies employing high-throughput ChIP-Seq methods as well as proteomic mass spectrometry studies, a large number of PTMs are known and their coexistence patterns and associations with genomic regions have been mapped in a large number of different cell types. Conversely, the molecular interplay between chromatin effector proteins and modified chromatin regions as well as their resulting biological output is less well understood on a molecular level. Within the last decade a host of chemical approaches has been developed with the goal to produce synthetic chromatin with a defined arrangement of PTMs. These methods now permit systematic functional studies of individual histone and DNA modifications, and additionally provide a discovery platform to identify further interacting nuclear proteins. Complementary chemical- and synthetic-biology methods have emerged to directly observe and modulate the modification landscape in living cells and to readily probe the effect of altered PTM patterns on biological processes. Herein, we review current methodologies allowing chemical and synthetic biological engineering of distinct chromatin states in vitro and in vivo with the aim of obtaining a molecular understanding of histone and DNA modification function. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Horst Pick
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Sinan Kilic
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Beat Fierz
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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90
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Wang Y, Gan J, Liu LL, Yuan H, Gao Y, Liu Y, Zhao Y. Cs2CO3-Promoted One-Pot Synthesis of Alkynylphosphonates, -phosphinates, and -phosphine Oxides. J Org Chem 2014; 79:3678-83. [DOI: 10.1021/jo500312n] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yulei Wang
- Department of Chemistry, College of Chemistry and Chemical Engineering, and the Key Laboratory for Chemical Biology of Fujian Province and ‡Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, China
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91
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Fierz B. Synthetic chromatin approaches to probe the writing and erasing of histone modifications. ChemMedChem 2014; 9:495-504. [PMID: 24497444 DOI: 10.1002/cmdc.201300487] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/18/2014] [Indexed: 11/11/2022]
Abstract
Posttranslational modifications (PTMs) of chromatin are involved in gene regulation, thereby contributing to cell differentiation, lineage determination, and organism development. Discrete chromatin states are established by the action of a large set of enzymes that catalyze the deposition, propagation, and removal of histone PTMs, thereby modulating gene expression. Given their central role in determining and maintaining cellular phenotype, as well as in controlling chromatin processes such as DNA repair, the dysregulation of these enzymes can have serious consequences, and can result in cancer and neurodegenerative diseases. Thus, such chromatin regulator proteins are promising drug targets. However, they are often present in large, modular protein complexes that specifically recognize target chromatin regions and exhibit intricate regulation through preexisting histone marks. This renders the study of their enzymatic mechanisms complex. Recent developments in the chemical production of defined chromatin substrates show great promise for improving our understanding of the activity of chromatin regulator complexes at the molecular level. Herein I discuss examples highlighting the application of synthetic chromatin to study the enzymatic mechanisms and regulatory pathways of these crucial protein complexes in detail, with potential implications for assay development in pharmacological research.
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Affiliation(s)
- Beat Fierz
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland)
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92
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Li J, Li Y, He Q, Li Y, Li H, Liu L. One-pot native chemical ligation of peptide hydrazides enables total synthesis of modified histones. Org Biomol Chem 2014; 12:5435-41. [DOI: 10.1039/c4ob00715h] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
One of the rising demands in the field of protein chemical synthesis is the development of facile strategies that yield the protein in workable quantities and homogeneity, with fewer handling steps.
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Affiliation(s)
- Jiabin Li
- Tsinghua-Peking Center for Life Sciences
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)
- Department of Chemistry
- MOE Key Laboratory of Protein Sciences
- Center for Structural Biology
| | - Yuanyuan Li
- Tsinghua-Peking Center for Life Sciences
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)
- Department of Chemistry
- MOE Key Laboratory of Protein Sciences
- Center for Structural Biology
| | - Qiaoqiao He
- Tsinghua-Peking Center for Life Sciences
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)
- Department of Chemistry
- MOE Key Laboratory of Protein Sciences
- Center for Structural Biology
| | - Yiming Li
- Tsinghua-Peking Center for Life Sciences
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)
- Department of Chemistry
- MOE Key Laboratory of Protein Sciences
- Center for Structural Biology
| | - Haitao Li
- Tsinghua-Peking Center for Life Sciences
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)
- Department of Chemistry
- MOE Key Laboratory of Protein Sciences
- Center for Structural Biology
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education)
- Department of Chemistry
- MOE Key Laboratory of Protein Sciences
- Center for Structural Biology
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93
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Chen CC, Waser J. Room temperature alkynylation of H-phosphi(na)tes and secondary phosphine oxides with ethynylbenziodoxolone (EBX) reagents. Chem Commun (Camb) 2014; 50:12923-6. [DOI: 10.1039/c4cc06851c] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We report the alkynylation of H-phosphi(na)tes and secondary phosphine oxides at room temperature using ethynylbenziodoxolone (EBX) reagents.
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Affiliation(s)
- C. Chun Chen
- Laboratory of Catalysis and Organic Synthesis
- Ecole Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCSO
- 1015 Lausanne (CH), Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis
- Ecole Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCSO
- 1015 Lausanne (CH), Switzerland
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94
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Li L, Hao G, Zhu A, Fan X, Zhang G, Zhang L. A copper(I)-catalyzed three-component domino process: assembly of complex 1,2,3-triazolyl-5-phosphonates from azides, alkynes, and H-phosphates. Chemistry 2013; 19:14403-6. [PMID: 24114953 DOI: 10.1002/chem.201303324] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Indexed: 11/09/2022]
Abstract
Three is better than one! A new copper-catalyzed tricomponent reaction of a terminal alkyne, organic azide, and H-phosphate (CuAA[P]C) leads to a structurally diverse polysubstituted 1,2,3-triazolyl-5-phosphonate, which provides an efficient tool for the direct introduction of phosphonic acid groups by a "click reaction".
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Affiliation(s)
- Lingjun Li
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007 (P. R. China), Fax: (+86) 3733325250.
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95
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Kazancioglu EA, Kazancioglu MZ, Fistikci M, Secen H, Altundas R. Photooxygenation of Azidoalkyl Furans: Catalyst-Free Triazole and New Endoperoxide Rearrangement. Org Lett 2013; 15:4790-3. [DOI: 10.1021/ol402163u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | | | - Meryem Fistikci
- Department of Chemistry, Ataturk University, 25240 Erzurum, Turkey
| | - Hasan Secen
- Department of Chemistry, Ataturk University, 25240 Erzurum, Turkey
| | - Ramazan Altundas
- Department of Chemistry, Ataturk University, 25240 Erzurum, Turkey
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96
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Attempting to rewrite History: challenges with the analysis of histidine-phosphorylated peptides. Biochem Soc Trans 2013; 41:1089-95. [DOI: 10.1042/bst20130072] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A significant number of proteins in both eukaryotes and prokaryotes are known to be post-translationally modified by the addition of phosphate, serving as a means of rapidly regulating protein function. Phosphorylation of the amino acids serine, threonine and tyrosine are the focus of the vast majority of studies aimed at elucidating the extent and roles of such modification, yet other amino acids, including histidine and aspartate, are also phosphorylated. Although histidine phosphorylation is known to play extensive roles in signalling in eukaryotes, plants and fungi, roles for phosphohistidine are poorly defined in higher eukaryotes. Characterization of histidine phosphorylation aimed at elucidating such information is problematic due to the acid-labile nature of the phosphoramidate bond, essential for many of its biological functions. Although MS-based strategies have proven extremely useful in the analysis of other types of phosphorylated peptides, the chromatographic procedures essential for such approaches promote rapid hydrolysis of phosphohistidine-containing peptides. Phosphate transfer to non-biologically relevant aspartate residues during MS analysis further complicates the scenario.
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97
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Abstract
It is more than 50 years since protein histidine phosphorylation was first discovered in 1962 by Boyer and co-workers; however, histidine kinases are still much less well recognized than the serine/threonine and tyrosine kinases. The best-known histidine kinases are the two-component signalling kinases that occur in bacteria, fungi and plants. The mechanisms and functions of these kinases, their cognate response regulators and associated phosphorelay proteins are becoming increasingly well understood. When genomes of higher eukaryotes began to be sequenced, it did not appear that they contained two-component histidine kinase system homologues, apart from a couple of related mitochondrial enzymes that were later shown not to function as histidine kinases. However, as a result of the burgeoning sequencing of genomes from a wide variety of eukaryotic organisms, it is clear that there are proteins that correspond to components of the two-component histidine kinase systems in higher eukaryotes and that operational two-component kinase systems are likely to occur in these organisms. There is unequivocal direct evidence that protein histidine phosphorylation does occur in mammals. So far, only nucleoside diphosphate kinases have been shown to be involved in protein histidine phosphorylation, but their mechanisms of action are not well understood. It is clear that other, yet to be identified, histidine kinases also exist in mammals and that protein histidine phosphorylation may play important roles in higher eukaryotes.
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98
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Abstract
Phosphorylation is a ubiquitous protein post-translational modification, and the importance of phosphorylation of serine, threonine and tyrosine is well established. What is lesser known is that almost all heteroatom-containing amino acids can be phosphorylated and, among these, histidine, aspartate and cysteine have well established roles in bacterial signalling pathways. The first of these, phosphohistidine, is the most unusual in that it is labile under many conditions used to study proteins in vitro and can exist as two different isomers. In the present short review, we highlight the chemical challenges that this modification presents and the manner in which chemical synthesis has been used to identify and mimic the modification in proteins.
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99
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Černý M, Skalák J, Cerna H, Brzobohatý B. Advances in purification and separation of posttranslationally modified proteins. J Proteomics 2013; 92:2-27. [PMID: 23777897 DOI: 10.1016/j.jprot.2013.05.040] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 05/27/2013] [Accepted: 05/29/2013] [Indexed: 11/25/2022]
Abstract
Posttranslational modifications (PTMs) of proteins represent fascinating extensions of the dynamic complexity of living cells' proteomes. The results of enzymatically catalyzed or spontaneous chemical reactions, PTMs form a fourth tier in the gene - transcript - protein cascade, and contribute not only to proteins' biological functions, but also to challenges in their analysis. There have been tremendous advances in proteomics during the last decade. Identification and mapping of PTMs in proteins have improved dramatically, mainly due to constant increases in the sensitivity, speed, accuracy and resolution of mass spectrometry (MS). However, it is also becoming increasingly evident that simple gel-free shotgun MS profiling is unlikely to suffice for comprehensive detection and characterization of proteins and/or protein modifications present in low amounts. Here, we review current approaches for enriching and separating posttranslationally modified proteins, and their MS-independent detection. First, we discuss general approaches for proteome separation, fractionation and enrichment. We then consider the commonest forms of PTMs (phosphorylation, glycosylation and glycation, lipidation, methylation, acetylation, deamidation, ubiquitination and various redox modifications), and the best available methods for detecting and purifying proteins carrying these PTMs. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Martin Černý
- Department of Molecular Biology and Radiobiology, Mendel University in Brno & CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
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100
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Piggott MJ, Attwood PV. Post-translational modifications: Panning for phosphohistidine. Nat Chem Biol 2013; 9:411-2. [PMID: 23708075 DOI: 10.1038/nchembio.1273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew J Piggott
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, Australia.
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