1
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Park G, Wralstad EC, Faginas-Lago N, Qian K, Raines RT, Bistoni G, Cummins CC. Pentaphosphorylation via the Anhydride of Dihydrogen Pentametaphosphate: Access to Nucleoside Hexa- and Heptaphosphates and Study of Their Interaction with Ribonuclease A. ACS CENTRAL SCIENCE 2024; 10:1415-1422. [PMID: 39071052 PMCID: PMC11273453 DOI: 10.1021/acscentsci.4c00835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/30/2024]
Abstract
Pentametaphosphate is the little studied cyclic pentamer of the metaphosphate ion, [PO3]5 5-. We show that the doubly protonated form of this pentamer can be selectively dehydrated to provide the anhydride [P5O14]3- (1). This trianion is the well-defined condensed phosphate component of a novel reagent for attachment of a pentaphosphate chain to biomolecules all in one go. Here, we demonstrate by extending adenosine monophosphate (AMP) and uridine monophosphate (UMP) to their corresponding nucleoside hexaphosphates, while adenosine diphosphate (ADP) and uridine diphosphate (UDP) are phosphate chain-extended to the corresponding nucleoside heptaphosphates. Such constructs are of interest for their potential biological function with respect to RNA-processing enzymes. Thus, we go on to investigate in detail the interaction of the polyanionic constructs with ribonuclease A, a model protein containing a polycationic active site and for which X-ray crystal structures are relatively straightforward to obtain. This work presents a combined experimental and quantum chemical approach to understanding the interactions of RNase A with the new nucleoside hexa- and heptaphosphate constructs.
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Affiliation(s)
- Gyeongjin Park
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Evans C. Wralstad
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Noelia Faginas-Lago
- Department
of Chemistry, Biology,and Biotechnology, University of Perugia, 06123, Perugia, Italy
| | - Kevin Qian
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Giovanni Bistoni
- Department
of Chemistry, Biology,and Biotechnology, University of Perugia, 06123, Perugia, Italy
| | - Christopher C. Cummins
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
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2
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Celik A, Beyer I, Fiedler D. An Uncommon Phosphorylation Mode Regulates the Activity and Protein Interactions of N-Acetylglucosamine Kinase. J Am Chem Soc 2024; 146:14807-14815. [PMID: 38733353 PMCID: PMC11140747 DOI: 10.1021/jacs.4c03069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
While the function of protein phosphorylation in eukaryotic cell signaling is well established, the role of a closely related modification, protein pyrophosphorylation, is just starting to surface. A recent study has identified several targets of endogenous protein pyrophosphorylation in mammalian cell lines, including N-acetylglucosamine kinase (NAGK). Here, a detailed functional analysis of NAGK phosphorylation and pyrophosphorylation on serine 76 (S76) has been conducted. This analysis was enabled by using amber codon suppression to obtain phosphorylated pS76-NAGK, which was subsequently converted to site-specifically pyrophosphorylated NAGK (ppS76-NAGK) with a phosphorimidazolide reagent. A significant reduction in GlcNAc kinase activity was observed upon phosphorylation and near-complete inactivation upon pyrophosphorylation. The formation of ppS76-NAGK proceeded via an ATP-dependent autocatalytic process, and once formed, ppS76-NAGK displayed notable stability toward dephosphorylation in mammalian cell lysates. Proteomic examination unveiled a distinct set of protein-protein interactions for ppS76-NAGK, suggesting an alternative function, independent of its kinase activity. Overall, a significant regulatory role of pyrophosphorylation on NAGK activity was uncovered, providing a strong incentive to investigate the influence of this unusual phosphorylation mode on other kinases.
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Affiliation(s)
- Arif Celik
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut
für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Ida Beyer
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Institut
für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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3
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Mihiret YE, Schaaf G, Kamleitner M. Protein pyrophosphorylation by inositol phosphates: a novel post-translational modification in plants? FRONTIERS IN PLANT SCIENCE 2024; 15:1347922. [PMID: 38455731 PMCID: PMC10917965 DOI: 10.3389/fpls.2024.1347922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
Inositol pyrophosphates (PP-InsPs) are energy-rich molecules harboring one or more diphosphate moieties. PP-InsPs are found in all eukaryotes evaluated and their functional versatility is reflected in the various cellular events in which they take part. These include, among others, insulin signaling and intracellular trafficking in mammals, as well as innate immunity and hormone and phosphate signaling in plants. The molecular mechanisms by which PP-InsPs exert such functions are proposed to rely on the allosteric regulation via direct binding to proteins, by competing with other ligands, or by protein pyrophosphorylation. The latter is the focus of this review, where we outline a historical perspective surrounding the first findings, almost 20 years ago, that certain proteins can be phosphorylated by PP-InsPs in vitro. Strikingly, in vitro phosphorylation occurs by an apparent enzyme-independent but Mg2+-dependent transfer of the β-phosphoryl group of an inositol pyrophosphate to an already phosphorylated serine residue at Glu/Asp-rich protein regions. Ribosome biogenesis, vesicle trafficking and transcription are among the cellular events suggested to be modulated by protein pyrophosphorylation in yeast and mammals. Here we discuss the latest efforts in identifying targets of protein pyrophosphorylation, pointing out the methodological challenges that have hindered the full understanding of this unique post-translational modification, and focusing on the latest advances in mass spectrometry that finally provided convincing evidence that PP-InsP-mediated pyrophosphorylation also occurs in vivo. We also speculate about the relevance of this post-translational modification in plants in a discussion centered around the protein kinase CK2, whose activity is critical for pyrophosphorylation of animal and yeast proteins. This enzyme is widely present in plant species and several of its functions overlap with those of PP-InsPs. Until now, there is virtually no data on pyrophosphorylation of plant proteins, which is an exciting field that remains to be explored.
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Affiliation(s)
| | | | - Marília Kamleitner
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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4
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Brown NW, Schlomach SK, Marmelstein AM, Fiedler D. Chemoselective Labeling and Immobilization of Phosphopeptides with Phosphorimidazolide Reagents. Chembiochem 2023; 24:e202200407. [PMID: 36166450 DOI: 10.1002/cbic.202200407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/21/2022] [Indexed: 11/11/2022]
Abstract
Protein phosphorylation is one of the most ubiquitous post-translational modifications, regulating numerous essential processes in cells. Accordingly, the large-scale annotation of phosphorylation sites continues to provide central insight into the regulation of signaling networks. The global analysis of the phosphoproteome typically relies on mass spectrometry analysis of phosphopeptides, with an enrichment step necessary due to the sub-stoichiometric nature of phosphorylation. Several affinity-based methods and chemical modification strategies have been developed to date, but the choice of enrichment method can have a considerable impact on the results. Here, we show that a biotinylated, photo-cleavable phosphorimidazolide reagent permits the immobilization and subsequent cleavage of phosphopeptides. The method is capable of the capture and release of phosphopeptides of varying characteristics, and this mild and selective strategy expands the current repertoire for phosphopeptide chemical modification with the potential to enrich and identify new phosphorylation sites in the future.
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Affiliation(s)
- Nathaniel W Brown
- Department of Chemical Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany.,Department of Chemistry, Princeton University, Washington Rd., Princeton, NJ 08544, USA
| | - Sandra K Schlomach
- Department of Chemical Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany.,Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Alan M Marmelstein
- Department of Chemical Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany.,Department of Chemistry, Princeton University, Washington Rd., Princeton, NJ 08544, USA
| | - Dorothea Fiedler
- Department of Chemical Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany.,Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
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5
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Lin H, Leman LJ, Krishnamurthy R. One-pot chemical pyro- and tri-phosphorylation of peptides by using diamidophosphate in water. Chem Sci 2022; 13:13741-13747. [PMID: 36544739 PMCID: PMC9713773 DOI: 10.1039/d2sc04160j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/30/2022] [Indexed: 12/24/2022] Open
Abstract
Protein (pyro)phosphorylation is emerging as a post-translational modification (PTM) in signalling pathways involved in many cellular processes. However, access to synthetic pyrophosphopeptides that can serve as tools for understanding protein pyrophosphorylation is quite limited. Herein, we report a chemical phosphorylation method that enables the synthesis of pyrophosphopeptides in aqueous medium without the need for protecting groups. The strategy employs diamidophosphate (DAP) in a one-pot sequential phosphorylation-hydrolysis of mono-phosphorylated peptide precursors. This operationally simple method exploits the intrinsic nucleophilicity of a phosphate moiety installed on serine, threonine or tyrosine residues in complex peptides with excellent chemoselectivity and good yields under mild conditions. We demonstrate the installation of the pyrophosphate group within a wide range of model peptides and showcase the potential of this methodology by selectively pyrophosphorylating the highly functionalized Nopp140 peptide fragment. The potential to produce higher (poly)phosphorylated peptides was demonstrated as a proof-of-principle experiment where we synthesized the triphosphorylated peptides using this one-pot strategy.
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Affiliation(s)
- Huacan Lin
- Department of Chemistry, The Scripps Research InstituteLa JollaCalifornia 92037USA
| | - Luke J. Leman
- Department of Chemistry, The Scripps Research InstituteLa JollaCalifornia 92037USA
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6
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Makwana MV, Williamson MP, Jackson RFW, Muimo R. Quantitation of phosphohistidine in proteins in a mammalian cell line by 31P NMR. PLoS One 2022; 17:e0273797. [PMID: 36048825 PMCID: PMC9436146 DOI: 10.1371/journal.pone.0273797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
There is growing evidence to suggest that phosphohistidines are present at significant levels in mammalian cells and play a part in regulating cellular activity, in particular signaling pathways related to cancer. Because of the chemical instability of phosphohistidine at neutral or acid pH, it remains unclear how much phosphohistidine is present in cells. Here we describe a protocol for extracting proteins from mammalian cells in a way that avoids loss of covalent phosphates from proteins, and use it to measure phosphohistidine concentrations in human bronchial epithelial cell (16HBE14o-) lysate using 31P NMR spectroscopic analysis. Phosphohistidine is determined on average to be approximately one third as abundant as phosphoserine and phosphothreonine combined (and thus roughly 15 times more abundant than phosphotyrosine). The amount of phosphohistidine, and phosphoserine/phosphothreonine per gram of protein from a cell lysate was determined to be 23 μmol/g and 68 μmol/g respectively. The amount of phosphohistidine, and phosphoserine/phosphothreonine per cell was determined to be 1.8 fmol/cell, and 5.8 fmol/cell respectively. Phosphorylation is largely at the N3 (tele) position. Typical tryptic digest conditions result in loss of most of the phosphohistidine present, which may explain why the amounts reported here are greater than is generally seen using mass spectroscopy assays. The results further strengthen the case for a functional role of phosphohistidine in eukaryotic cells.
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Affiliation(s)
- Mehul V. Makwana
- Department of Chemistry, The University of Sheffield, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield, United Kingdom
| | - Mike P. Williamson
- School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | | | - Richmond Muimo
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield, United Kingdom
- * E-mail:
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7
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Bilbrough T, Piemontese E, Seitz O. Dissecting the role of protein phosphorylation: a chemical biology toolbox. Chem Soc Rev 2022; 51:5691-5730. [PMID: 35726784 DOI: 10.1039/d1cs00991e] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein phosphorylation is a crucial regulator of protein and cellular function, yet, despite identifying an enormous number of phosphorylation sites, the role of most is still unclear. Each phosphoform, the particular combination of phosphorylations, of a protein has distinct and diverse biological consequences. Aberrant phosphorylation is implicated in the development of many diseases. To investigate their function, access to defined protein phosphoforms is essential. Materials obtained from cells often are complex mixtures. Recombinant methods can provide access to defined phosphoforms if site-specifically acting kinases are known, but the methods fail to provide homogenous material when several amino acid side chains compete for phosphorylation. Chemical and chemoenzymatic synthesis has provided an invaluable toolbox to enable access to previously unreachable phosphoforms of proteins. In this review, we selected important tools that enable access to homogeneously phosphorylated protein and discuss examples that demonstrate how they can be applied. Firstly, we discuss the synthesis of phosphopeptides and proteins through chemical and enzymatic means and their advantages and limitations. Secondly, we showcase illustrative examples that applied these tools to answer biological questions pertaining to proteins involved in signal transduction, control of transcription, neurodegenerative diseases and aggregation, apoptosis and autophagy, and transmembrane proteins. We discuss the opportunities and challenges in the field.
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Affiliation(s)
- Tim Bilbrough
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Emanuele Piemontese
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
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8
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Shepard SM, Jessen HJ, Cummins CC. Beyond Triphosphates: Reagents and Methods for Chemical Oligophosphorylation. J Am Chem Soc 2022; 144:7517-7530. [PMID: 35471019 DOI: 10.1021/jacs.1c07990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligophosphates play essential roles in biochemistry, and considerable research has been directed toward the synthesis of both naturally occurring oligophosphates and their synthetic analogues. Greater attention has been given to mono-, di-, and triphosphates, as these are present in higher concentrations biologically and easier to synthesize. However, extended oligophosphates have potent biochemical roles, ranging from blood coagulation to HIV drug resistance. Sporadic reports have slowly built a niche body of literature related to the synthesis and study of extended oligophosphates, but newfound interests and developments have the potential to rapidly expand this field. Here we report on current methods to synthesize oligophosphates longer than triphosphates and comment on the most important future directions for this area of research. The state of the art has provided fairly robust methods for synthesizing nucleoside 5'-tetra- and pentaphosphates as well as dinucleoside 5',5'-oligophosphates. Future research should endeavor to push such syntheses to longer oligophosphates while developing synthetic methodologies for rarer morphologies such as 3'-nucleoside oligophosphates, polyphosphates, and phosphonate/thiophosphate analogues of these species.
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Affiliation(s)
- Scott M Shepard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg & Cluster of Excellence livMatS, FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
| | - Christopher C Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
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9
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Mou Z, Chen X, Wang C, Wang T, Yang H, Li Z. Nucleophilic 18F-fluorination of phosphorofluoridates and phosphonofluoridic acids via imidazole-activated precursors. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.152917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Ganguli S, Shah A, Hamid A, Singh A, Palakurti R, Bhandari R. A high energy phosphate jump - From pyrophospho-inositol to pyrophospho-serine. Adv Biol Regul 2020; 75:100662. [PMID: 31668836 DOI: 10.1016/j.jbior.2019.100662] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/26/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Inositol pyrophosphates (PP-IPs) are a class of energy rich metabolites present in all eukaryotic cells. The hydroxyl groups on these water soluble derivatives of inositol are substituted with diphosphate and monophosphate moieties. Since the discovery of PP-IPs in the early 1990s, enormous progress has been made in uncovering pleiotropic roles for these small molecules in cellular physiology. PP-IPs exert their effect on proteins in two ways - allosteric regulation by direct binding, or post-translational regulation by serine pyrophosphorylation, a modification unique to PP-IPs. Serine pyrophosphorylation is achieved by Mg2+-dependent, but enzyme independent transfer of a β-phosphate from a PP-IP to a pre-phosphorylated serine residue located in an acidic motif, within an intrinsically disordered protein sequence. This distinctive post-translational modification has been shown to regulate diverse cellular processes, including rRNA synthesis, glycolysis, and vesicle transport. However, our understanding of the molecular details of this phosphotransfer from pyrophospho-inositol to generate pyrophospho-serine, is still nascent. This review discusses our current knowledge of protein pyrophosphorylation, and recent advances in understanding the mechanism of this important yet overlooked post-translational modification.
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Affiliation(s)
- Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India; Manipal Academy of Higher Education, Manipal, 576104, India
| | - Akruti Shah
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India; Manipal Academy of Higher Education, Manipal, 576104, India
| | - Aisha Hamid
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Arpita Singh
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Ravichand Palakurti
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India.
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11
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Shepard SM, Windsor IW, Raines RT, Cummins CC. Nucleoside Tetra- and Pentaphosphates Prepared Using a Tetraphosphorylation Reagent Are Potent Inhibitors of Ribonuclease A. J Am Chem Soc 2019; 141:18400-18404. [PMID: 31651164 DOI: 10.1021/jacs.9b09760] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Adenosine and uridine 5'-tetra- and 5'-pentaphosphates were synthesized from an activated tetrametaphosphate ([PPN]2[P4O11], [PPN]2[1], PPN = bis(triphenylphosphine)iminium) and subsequently tested for inhibition of the enzymatic activity of ribonuclease A (RNase A). Reagent [PPN]2[1] reacts with unprotected uridine and adenosine in the presence of a base under anhydrous conditions to give nucleoside tetrametaphosphates. Ring opening of these intermediates with tetrabutylammonium hydroxide ([TBA][OH]) yields adenosine and uridine tetraphosphates (p4A, p4U) in 92% and 85% yields, respectively, from the starting nucleoside. Treatment of ([PPN]2[1]) with AMP or UMP yields nucleoside-monophosphate tetrametaphosphates (cp4pA, cp4pU) having limited aqueous stability. Ring opening of these ultraphosphates with [TBA][OH] yields p5A and p5U in 58% and 70% yield from AMP and UMP, respectively. We characterized inorganic and nucleoside-conjugated linear and cyclic oligophosphates as competitive inhibitors of RNase A. Increasing the chain length in both linear and cyclic inorganic oligophosphates resulted in improved binding affinity. Increasing the length of oligophosphates on the 5' position of adenosine beyond three had a deleterious effect on binding. Conversely, uridine nucleotides bearing 5' oligophosphates saw progressive increases in binding with chain length. We solved X-ray cocrystal structures of the highest affinity binders from several classes. The terminal phosphate of p5A binds in the P1 enzymic subsite and forces the oligophosphate to adopt a convoluted conformation, while the oligophosphate of p5U binds in several extended conformations, targeting multiple cationic regions of the active-site cleft.
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Affiliation(s)
- Scott M Shepard
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
| | - Ian W Windsor
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
| | - Ronald T Raines
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
| | - Christopher C Cummins
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
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12
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Penkert M, Hauser A, Harmel R, Fiedler D, Hackenberger CPR, Krause E. Electron Transfer/Higher Energy Collisional Dissociation of Doubly Charged Peptide Ions: Identification of Labile Protein Phosphorylations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1578-1585. [PMID: 31111417 DOI: 10.1007/s13361-019-02240-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/07/2019] [Accepted: 03/16/2019] [Indexed: 06/09/2023]
Abstract
In recent years, labile phosphorylation sites on arginine, histidine, cysteine, and lysine as well as pyrophosphorylation of serine and threonine have gained more attention in phosphoproteomic studies. However, the analysis of these delicate posttranslational modifications via tandem mass spectrometry remains a challenge. Common fragmentation techniques such as collision-induced dissociation (CID) and higher energy collisional dissociation (HCD) are limited due to extensive phosphate-related neutral loss. Electron transfer dissociation (ETD) has shown to preserve labile modifications, but is restricted to higher charge states, missing the most prevalent doubly charged peptides. Here, we report the ability of electron transfer/higher energy collisional dissociation (EThcD) to fragment doubly charged phosphorylated peptides without losing the labile modifications. Using synthetic peptides that contain phosphorylated arginine, histidine, cysteine, and lysine as well as pyrophosphorylated serine residues, we evaluated the optimal fragmentation conditions, demonstrating that EThcD is the method of choice for unambiguous assignment of tryptic, labile phosphorylated peptides. Graphical Abstract.
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Affiliation(s)
- Martin Penkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany.
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany.
| | - Anett Hauser
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Robert Harmel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Christian P R Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Eberhard Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Str. 10, 13125, Berlin, Germany
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13
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Marmelstein AM, Morgan JAM, Penkert M, Rogerson DT, Chin JW, Krause E, Fiedler D. Pyrophosphorylation via selective phosphoprotein derivatization. Chem Sci 2018; 9:5929-5936. [PMID: 30079207 PMCID: PMC6050540 DOI: 10.1039/c8sc01233d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/08/2018] [Indexed: 01/13/2023] Open
Abstract
An important step in elucidating the function of protein post-translational modifications (PTMs) is gaining access to site-specifically modified, homogeneous samples for biochemical characterization. Protein pyrophosphorylation is a poorly characterized PTM, and here a chemical approach to obtain pyrophosphoproteins is reported. Photo-labile phosphorimidazolide reagents were developed for selective pyrophosphorylation, affinity-capture, and release of pyrophosphoproteins. Kinetic analysis of the reaction revealed rate constants between 9.2 × 10-3 to 0.58 M-1 s-1, as well as a striking proclivity of the phosphorimidazolides to preferentially react with phosphate monoesters over other nucleophilic side chains. Besides enabling the characterization of pyrophosphorylation on protein function, this work highlights the utility of phosphoryl groups as handles for selective protein modification for a variety of applications, such as phosphoprotein bioconjugation and enrichment.
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Affiliation(s)
- Alan M Marmelstein
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
- Department of Chemistry , Princeton University , Washington Road , Princeton , New Jersey 08544 , USA
| | - Jeremy A M Morgan
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
| | - Martin Penkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
- Institut für Chemie , Humboldt Universität zu Berlin , Brook-Taylor-Str. 2 , 12489 Berlin , Germany
| | - Daniel T Rogerson
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , UK
| | - Eberhard Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
- Institut für Chemie , Humboldt Universität zu Berlin , Brook-Taylor-Str. 2 , 12489 Berlin , Germany
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14
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Brown NW, Marmelstein AM, Fiedler D. Chemical tools for interrogating inositol pyrophosphate structure and function. Chem Soc Rev 2018; 45:6311-6326. [PMID: 27462803 DOI: 10.1039/c6cs00193a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The inositol pyrophosphates (PP-InsPs) are a unique group of intracellular messengers that represent some of the most highly phosphorylated molecules in nature. Genetic perturbation of the PP-InsP biosynthetic network indicates a central role for these metabolites in maintaining cellular energy homeostasis and in controlling signal transduction networks. However, despite their discovery over two decades ago, elucidating their physiologically relevant isomers, the biochemical pathways connecting these molecules to their associated phenotypes, and their modes of signal transduction has often been stymied by technical challenges. Many of the advances in understanding these molecules to date have been facilitated by the total synthesis of the various PP-InsP isomers and by the development of new methods that are capable of identifying their downstream signalling partners. Chemical tools have also been developed to distinguish between the proposed PP-InsP signal transduction mechanisms: protein binding, and a covalent modification of proteins termed protein pyrophosphorylation. In this article, we review these recent developments, discuss how they have helped to illuminate PP-InsP structure and function, and highlight opportunities for future discovery.
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Affiliation(s)
- Nathaniel W Brown
- Princeton University, Frick Chemistry Laboratory, Washington Road, Princeton, NJ 08544, USA and Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str 10, 13125 Berlin, Berlin, Germany.
| | - Alan M Marmelstein
- Princeton University, Frick Chemistry Laboratory, Washington Road, Princeton, NJ 08544, USA and Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str 10, 13125 Berlin, Berlin, Germany.
| | - Dorothea Fiedler
- Princeton University, Frick Chemistry Laboratory, Washington Road, Princeton, NJ 08544, USA and Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str 10, 13125 Berlin, Berlin, Germany.
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15
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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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16
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Tasnádi G, Zechner M, Hall M, Baldenius K, Ditrich K, Faber K. Investigation of acid phosphatase variants for the synthesis of phosphate monoesters. Biotechnol Bioeng 2017; 114:2187-2195. [DOI: 10.1002/bit.26352] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/18/2017] [Accepted: 06/05/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Gábor Tasnádi
- Austrian Centre of Industrial Biotechnology, c/o
- Department of Chemistry; Organic & Bioorganic Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
| | - Michaela Zechner
- Department of Chemistry; Organic & Bioorganic Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
| | - Mélanie Hall
- Department of Chemistry; Organic & Bioorganic Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
| | - Kai Baldenius
- White Biotechnology Research Biocatalysis; BASF SE; Ludwigshafen 67056 Germany
| | - Klaus Ditrich
- White Biotechnology Research Biocatalysis; BASF SE; Ludwigshafen 67056 Germany
| | - Kurt Faber
- Department of Chemistry; Organic & Bioorganic Chemistry; University of Graz; Heinrichstrasse 28 8010 Graz Austria
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17
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Penkert M, Yates LM, Schümann M, Perlman D, Fiedler D, Krause E. Unambiguous Identification of Serine and Threonine Pyrophosphorylation Using Neutral-Loss-Triggered Electron-Transfer/Higher-Energy Collision Dissociation. Anal Chem 2017; 89:3672-3680. [DOI: 10.1021/acs.analchem.6b05095] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Martin Penkert
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
- Humboldt Universität zu Berlin, Department
of Chemistry, Brook-Taylor-Straße
2, 12489 Berlin, Germany
| | - Lisa M. Yates
- Princeton University, Department of Chemistry, Frick Chemistry Building, Washington
Road, Princeton, New Jersey 08544, United States
| | - Michael Schümann
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
| | - David Perlman
- Princeton University, Department of Molecular Biology, 119 Lewis Thomas Laboratory, Washington
Road, Princeton, New Jersey 08544, United States
| | - Dorothea Fiedler
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
- Humboldt Universität zu Berlin, Department
of Chemistry, Brook-Taylor-Straße
2, 12489 Berlin, Germany
| | - Eberhard Krause
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125 Berlin, Germany
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18
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Shah A, Ganguli S, Sen J, Bhandari R. Inositol Pyrophosphates: Energetic, Omnipresent and Versatile Signalling Molecules. J Indian Inst Sci 2017; 97:23-40. [PMID: 32214696 PMCID: PMC7081659 DOI: 10.1007/s41745-016-0011-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 11/16/2016] [Indexed: 12/21/2022]
Abstract
Inositol pyrophosphates (PP-IPs) are a class of energy-rich signalling molecules found in all eukaryotic cells. These are derivatives of inositol that contain one or more diphosphate (or pyrophosphate) groups in addition to monophosphates. The more abundant and best studied PP-IPs are diphosphoinositol pentakisphosphate (IP7) and bis-diphosphoinositol tetrakisphosphate (IP8). These molecules can influence protein function by two mechanisms: binding and pyrophosphorylation. The former involves the specific interaction of a particular inositol pyrophosphate with a binding site on a protein, while the latter is a unique attribute of inositol pyrophosphates, wherein the β-phosphate moiety is transferred from a PP-IP to a pre-phosphorylated serine residue in a protein to generate pyrophosphoserine. Both these events can result in changes in the target protein’s activity, localisation or its interaction with other partners. As a consequence of their ubiquitous presence in all eukaryotic organisms and all cell types examined till date, and their ability to modify protein function, PP-IPs have been found to participate in a wide range of metabolic, developmental, and signalling pathways. This review highlights
many of the known functions of PP-IPs in the context of their temporal and spatial distribution in eukaryotic cells.
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Affiliation(s)
- Akruti Shah
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Shubhra Ganguli
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Jayraj Sen
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
- Graduate Studies, Manipal University, Manipal, Karnataka India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana India
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19
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Engelsma SB, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Combined Phosphoramidite-Phosphodiester Reagents for the Synthesis of Methylene Bisphosphonates. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611878] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sander B. Engelsma
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. van der Marel
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
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20
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Engelsma SB, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Combined Phosphoramidite-Phosphodiester Reagents for the Synthesis of Methylene Bisphosphonates. Angew Chem Int Ed Engl 2017; 56:2955-2959. [DOI: 10.1002/anie.201611878] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Sander B. Engelsma
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. van der Marel
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
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21
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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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22
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Depaix A, Peyrottes S, Roy B. One-Pot Synthesis of Nucleotides and Conjugates in Aqueous Medium. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
| | - Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; ENSCM, Université de Montpellier; Campus Triolet, cc 1705, Place Eugène Bataillon 34095 Montpellier cedex 5 France
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23
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Abstract
To help define the molecular basis of cellular signalling cascades, and their biological functions, there is considerable value in utilizing a high-quality chemical 'probe' that has a well-defined interaction with a specific cellular protein. Such reagents include inhibitors of protein kinases and small molecule kinases, as well as mimics or antagonists of intracellular signals. The purpose of this review is to consider recent progress and promising future directions for the development of novel molecules that can interrogate and manipulate the cellular actions of inositol pyrophosphates (PP-IPs)--a specialized, 'energetic' group of cell-signalling molecules in which multiple phosphate and diphosphate groups are crammed around a cyclohexane polyol scaffold.
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24
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Komatsu T, Virdee S. ICBS and ECBS Chemical Biology Meeting 2015 - Let Them Come to Berlin! ACS Chem Biol 2016; 11:1159-66. [PMID: 27198933 DOI: 10.1021/acschembio.6b00268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Toru Komatsu
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- JST PRESTO, Tokyo, Japan
| | - Satpal Virdee
- MRC
Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
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25
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Yates LM, Fiedler D. A Stable Pyrophosphoserine Analog for Incorporation into Peptides and Proteins. ACS Chem Biol 2016; 11:1066-73. [PMID: 26760216 DOI: 10.1021/acschembio.5b00972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein pyrophosphorylation is a covalent modification of proteins, mediated by the inositol pyrophosphate messengers. Although the inositol pyrophosphates have been linked to a range of cellular processes, the role of protein pyrophosphorylation remains minimally characterized in vivo. The inherent instability of the phosphoanhydride bond has hampered the development of useful bioanalytical techniques to interrogate this novel signaling mechanism. Here, we describe the preparation of a pyrophosphoserine analog containing a stable methylene-bisphosphonate group that is compatible with solid-phase peptide synthesis. The resulting peptides demonstrate enhanced stability in Eukaryotic cell lysates and mammalian plasma and display resistance toward chemical degradation, when compared to the corresponding pyrophosphopeptides. In addition, the peptides containing the stable pyrophosphoserine analog are highly compatible with common ligation methods, such as native chemical ligation, maleimide conjugation, and glutaraldehyde ligation. The bisphosphonate-containing peptides will, therefore, be well-suited for future pyrophosphoserine antibody generation and affinity capture of pyrophosphoprotein binding partners and provide a key entry point to study the regulatory role of protein pyrophosphorylation.
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Affiliation(s)
- Lisa M. Yates
- Department
of Chemistry, Princeton University, Washington Rd, Princeton, New Jersey 08544, United States
| | - Dorothea Fiedler
- Department
of Chemistry, Princeton University, Washington Rd, Princeton, New Jersey 08544, United States
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
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26
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Vibhute AM, Konieczny V, Taylor CW, Sureshan KM. Triazolophostins: a library of novel and potent agonists of IP3 receptors. Org Biomol Chem 2016; 13:6698-710. [PMID: 25869535 PMCID: PMC4533600 DOI: 10.1039/c5ob00440c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IP3R initiate most cellular Ca2+ signaling. AdA is the most potent agonist of IP3R. The structural complexity of AdA makes synthesis of its analogs cumbersome. We report an easy method for generating a library of potent triazole-based analogs of AdA, triazolophostins, which are the most potent AdA analogs devoid of a nucleobase.
IP3 receptors are channels that mediate the release of Ca2+ from the intracellular stores of cells stimulated by hormones or neurotransmitters. Adenophostin A (AdA) is the most potent agonist of IP3 receptors, with the β-anomeric adenine contributing to the increased potency. The potency of AdA and its stability towards the enzymes that degrade IP3 have aroused interest in AdA analogs for biological studies. The complex structure of AdA poses problems that have necessitated optimization of synthetic conditions for each analog. Such lengthy one-at-a-time syntheses limit access to AdA analogs. We have addressed this problem by synthesizing a library of triazole-based AdA analogs, triazolophostins, by employing click chemistry. An advanced intermediate having all the necessary phosphates and a β-azide at the anomeric position was reacted with various alkynes under Cu(i) catalysis to yield triazoles, which upon deprotection gave triazolophostins. All eleven triazolophostins synthesized are more potent than IP3 and some are equipotent with AdA in functional analyses of IP3 receptors. We show that a triazole ring can replace adenine without compromising the potency of AdA and provide facile routes to novel AdA analogs.
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Affiliation(s)
- Amol M Vibhute
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala-695016, India.
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27
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Hofer A, Cremosnik GS, Müller AC, Giambruno R, Trefzer C, Superti-Furga G, Bennett KL, Jessen HJ. A Modular Synthesis of Modified Phosphoanhydrides. Chemistry 2015; 21:10116-22. [PMID: 26033174 DOI: 10.1002/chem.201500838] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/11/2022]
Abstract
Phosphoanhydrides (P-anhydrides) are ubiquitously occurring modifications in nature. Nucleotides and their conjugates, for example, are among the most important building blocks and signaling molecules in cell biology. To study and manipulate their biological functions, a diverse range of analogues have been developed. Phosphate-modified analogues have been successfully applied to study proteins that depend on these abundant cellular building blocks, but very often both the preparation and purification of these molecules are challenging. This study discloses a general access to P-anhydrides, including different nucleotide probes, that greatly facilitates their preparation and isolation. The convenient and scalable synthesis of, for example, (18) O labeled nucleoside triphosphates holds promise for future applications in phosphoproteomics.
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Affiliation(s)
- Alexandre Hofer
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland)
| | - Gregor S Cremosnik
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA (UK)
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Roberto Giambruno
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Claudia Trefzer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna (Austria)
| | - Henning J Jessen
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland).
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28
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Conway JH, Fiedler D. An Affinity Reagent for the Recognition of Pyrophosphorylated Peptides. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Conway JH, Fiedler D. An affinity reagent for the recognition of pyrophosphorylated peptides. Angew Chem Int Ed Engl 2015; 54:3941-5. [PMID: 25651128 DOI: 10.1002/anie.201411232] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Indexed: 11/05/2022]
Abstract
A resin-bound dinuclear zinc(II) complex for the selective capture of pyrophosphopeptides is reported. The metal complex binds diphosphate esters over other anionic groups, such as monophosphate esters, sulfate esters, and carboxylic acids, with high specificity. Immobilization of the compound provided a reagent capable of binding and retaining nanomolar quantities of pyrophosphopeptide in the presence of cell lysate. The high affinity and specificity of the reagent makes it an attractive tool for the study of in vivo pyrophosphorylation.
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Affiliation(s)
- John H Conway
- Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544 (USA)
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30
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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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31
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Sohail M, Zhang Y, Liu W, Chen Q, Wang L, Zhao ZK. Four-component α-bromo-β-phosphoalkoxylation of aromatic α,β-unsaturated carbonyl compounds. RSC Adv 2015. [DOI: 10.1039/c4ra12417k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Novel α-bromo-β-phosphoalkoxylated carbonyl compounds were produced in moderate to excellent yields via highly selective four-component reaction involving NBS, a cyclic ether, an organic phosphate and an aromatic α,β-unsaturated carbonyl compound.
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Affiliation(s)
- Muhammad Sohail
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- CAS
- Dalian 116032
- China
| | - Yixin Zhang
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- CAS
- Dalian 116032
- China
| | - Wujun Liu
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- CAS
- Dalian 116032
- China
| | - Qin Chen
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- CAS
- Dalian 116032
- China
| | - Lei Wang
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- CAS
- Dalian 116032
- China
| | - Zongbao K. Zhao
- Division of Biotechnology
- Dalian Institute of Chemical Physics
- CAS
- Dalian 116032
- China
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32
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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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33
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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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Jessen HJ, Ahmed N, Hofer A. Phosphate esters and anhydrides--recent strategies targeting nature's favoured modifications. Org Biomol Chem 2014; 12:3526-30. [PMID: 24781815 DOI: 10.1039/c4ob00478g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Esters and anhydrides of phosphoric acid are essential in biology. It is very difficult to identify processes in life that do not involve these modifications and their transformation at some point. Consequently, phosphorylation chemistry is an essential methodology with significant impact on the biological sciences. This perspective gives an overview of some very recent achievements in synthetic phosphorylation chemistry and aims at identifying challenges that lie ahead.
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Affiliation(s)
- Henning J Jessen
- University of Zürich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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