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Krüger L, Albrecht CJ, Schammann HK, Stumpf FM, Niedermeier ML, Yuan Y, Stuber K, Wimmer J, Stengel F, Scheffner M, Marx A. Chemical proteomic profiling reveals protein interactors of the alarmones diadenosine triphosphate and tetraphosphate. Nat Commun 2021; 12:5808. [PMID: 34608152 PMCID: PMC8490401 DOI: 10.1038/s41467-021-26075-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/10/2021] [Indexed: 01/14/2023] Open
Abstract
The nucleotides diadenosine triphosphate (Ap3A) and diadenosine tetraphosphate (Ap4A) are formed in prokaryotic and eukaryotic cells. Since their concentrations increase significantly upon cellular stress, they are considered to be alarmones triggering stress adaptive processes. However, their cellular roles remain elusive. To elucidate the proteome-wide interactome of Ap3A and Ap4A and thereby gain insights into their cellular roles, we herein report the development of photoaffinity-labeling probes and their employment in chemical proteomics. We demonstrate that the identified ApnA interactors are involved in many fundamental cellular processes including carboxylic acid and nucleotide metabolism, gene expression, various regulatory processes and cellular response mechanisms and only around half of them are known nucleotide interactors. Our results highlight common functions of these ApnAs across the domains of life, but also identify those that are different for Ap3A or Ap4A. This study provides a rich source for further functional studies of these nucleotides and depicts useful tools for characterization of their regulatory mechanisms in cells. Diadenosine polyphosphates (ApAs) are involved in cellular stress signaling but only a few molecular targets have been characterized so far. Here, the authors develop ApnA-based photoaffinity-labeling probes and use them to identify Ap3A and Ap4A binding proteins in human cell lysates.
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Affiliation(s)
- Lena Krüger
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Christoph J Albrecht
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | | | - Florian M Stumpf
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Marie L Niedermeier
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Yizhi Yuan
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Katrin Stuber
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Josua Wimmer
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Florian Stengel
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Scheffner
- Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Research School-Chemical Biology, University of Konstanz, Konstanz, Germany.
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Hammler D, Stuber K, Offensperger F, Scheffner M, Zumbusch A, Marx A. Fluorescently Labelled ATP Analogues for Direct Monitoring of Ubiquitin Activation. Chemistry 2020; 26:6279-6284. [PMID: 32154932 PMCID: PMC7317923 DOI: 10.1002/chem.202001091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/06/2020] [Indexed: 12/18/2022]
Abstract
Simple and robust assays to monitor enzymatic ATP cleavage with high efficiency in real‐time are scarce. To address this shortcoming, we developed fluorescently labelled adenosine tri‐, tetra‐ and pentaphosphate analogues of ATP. The novel ATP analogues bear — in contrast to earlier reports — only a single acridone‐based dye at the terminal phosphate group. The dye's fluorescence is quenched by the adenine component of the ATP analogue and is restored upon cleavage of the phosphate chain and dissociation of the dye from the adenosine moiety. Thereby the activity of ATP‐cleaving enzymes can be followed in real‐time. We demonstrate this proficiency for ubiquitin activation by the ubiquitin‐activating enzymes UBA1 and UBA6 which represents the first step in an enzymatic cascade leading to the covalent attachment of ubiquitin to substrate proteins, a process that is highly conserved from yeast to humans. We found that the efficiency to serve as cofactor for UBA1/UBA6 very much depends on the length of the phosphate chain of the ATP analogue: triphosphates are used poorly while pentaphosphates are most efficiently processed. Notably, the novel pentaphosphate‐harbouring ATP analogue supersedes the efficiency of recently reported dual‐dye labelled analogues and thus, is a promising candidate for broad applications.
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Affiliation(s)
- Daniel Hammler
- Department of ChemistryUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Katrin Stuber
- Department of ChemistryUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
- Department of BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Fabian Offensperger
- Department of BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Martin Scheffner
- Department of BiologyUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Andreas Zumbusch
- Department of Chemistry and Center for Applied PhotonicsUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
| | - Andreas Marx
- Department of ChemistryUniversity of KonstanzUniversitätsstraße 1078457KonstanzGermany
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3
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Hammler D, Marx A, Zumbusch A. Fluorescence-Lifetime-Sensitive Probes for Monitoring ATP Cleavage. Chemistry 2018; 24:15329-15335. [PMID: 30070405 DOI: 10.1002/chem.201803234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Indexed: 12/14/2022]
Abstract
Adenosine triphosphate (ATP) probes modified with fluorescence dyes that change their fluorescence properties upon cleavage are an interesting tool for monitoring enzymatic ATP turnover. As a readout parameter, fluorescence lifetime is attractive because it is nearly independent of concentration. In our study, we synthesised and investigated fifteen different ATP analogues, in which the fluorophores were attached to the γ-phosphate of ATP. All analogues showed distinctly different fluorescence lifetimes compared to the corresponding values of the free fluorophores. Both increases and decreases in fluorescence lifetime were observed upon attachment to ATP. To shed light on the photophysical processes governing the lifetime changes, we performed photoelectron spectroscopy in air (PESA) to determine HOMO energy levels and time-resolved fluorescence spectroscopy to obtain rate constants. We present evidence that fluorescence quenching in the compounds tested is dynamic and attributed to photoinduced electron transfer (PET), whereas fluorescence lifetime increases are caused by stacking interactions between chromophore and the nucleobase reducing non-radiative relaxation. Finally, we demonstrate that enzymatic cleavage of the ATP analogues presented can be followed by continuous monitoring of fluorescence lifetime changes.
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Affiliation(s)
- Daniel Hammler
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry and Center for Applied Photonics, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
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4
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Baranowski MR, Nowicka A, Jemielity J, Kowalska J. A fluorescent HTS assay for phosphohydrolases based on nucleoside 5'-fluorophosphates: its application in screening for inhibitors of mRNA decapping scavenger and PDE-I. Org Biomol Chem 2018; 14:4595-604. [PMID: 27031609 DOI: 10.1039/c6ob00492j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Several nucleotide-specific phosphohydrolases can cleave P-F bonds in substrate analogues containing a fluorophosphate moiety to release fluoride ions. In this work, by employing a fluoride-sensitive molecular sensor, we harnessed this cleavage reaction to develop a fluorescence assay to screen for phosphohydrolase inhibitors. The assay is rapid, sensitive, and based on simple and synthetically available reagents. The assay was adapted to the high-throughput screening (HTS) format and its utility was demonstrated by screening an 'in-house' library of small nucleotides against two enzymes: DcpS, a metal-independent mRNA decapping pyrophosphatase of the histidine triad (HIT) family; and PDE-I, a divalent cation-dependent nuclease. Our screening results agreed with the known specificities of DcpS and PDE-I, and led to the selection of several inhibitors featuring low-micromolar IC50 values. For DcpS, we also verified the results by using an alternative method with the natural substrate. Notably, the assay presented here is the first fluorescence-based HTS-adaptable assay for DcpS, an established therapeutic target for spinal muscular atrophy. The assay should be useful for phosphohydrolase specificity profiling and inhibitor discovery, particularly in the context of DcpS and other HIT-family enzymes, which play key roles in maintaining cellular functions and have been linked to disease development.
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Affiliation(s)
- M R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
| | - A Nowicka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland. and Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - J Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - J Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
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5
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Ermert S, Marx A, Hacker SM. Phosphate-Modified Nucleotides for Monitoring Enzyme Activity. Top Curr Chem (Cham) 2017; 375:28. [PMID: 28251563 DOI: 10.1007/s41061-017-0117-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/30/2017] [Indexed: 02/07/2023]
Abstract
Nucleotides modified at the terminal phosphate position have been proven to be interesting entities to study the activity of a variety of different protein classes. In this chapter, we present various types of modifications that were attached as reporter molecules to the phosphate chain of nucleotides and briefly describe the chemical reactions that are frequently used to synthesize them. Furthermore, we discuss a variety of applications of these molecules. Kinase activity, for instance, was studied by transfer of a phosphate modified with a reporter group to the target proteins. This allows not only studying the activity of kinases, but also identifying their target proteins. Moreover, kinases can also be directly labeled with a reporter at a conserved lysine using acyl-phosphate probes. Another important application for phosphate-modified nucleotides is the study of RNA and DNA polymerases. In this context, single-molecule sequencing is made possible using detection in zero-mode waveguides, nanopores or by a Förster resonance energy transfer (FRET)-based mechanism between the polymerase and a fluorophore-labeled nucleotide. Additionally, fluorogenic nucleotides that utilize an intramolecular interaction between a fluorophore and the nucleobase or an intramolecular FRET effect have been successfully developed to study a variety of different enzymes. Finally, also some novel techniques applying electron paramagnetic resonance (EPR)-based detection of nucleotide cleavage or the detection of the cleavage of fluorophosphates are discussed. Taken together, nucleotides modified at the terminal phosphate position have been applied to study the activity of a large diversity of proteins and are valuable tools to enhance the knowledge of biological systems.
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Affiliation(s)
- Susanne Ermert
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Stephan M Hacker
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany.
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6
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Ermert S, Hacker SM, Buntru A, Scheffner M, Hauck CR, Marx A. Different Enzymatic Processing of γ-Phosphoramidate and γ-Phosphoester-Modified ATP Analogues. Chembiochem 2017; 18:378-381. [PMID: 27935244 DOI: 10.1002/cbic.201600590] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Indexed: 12/22/2022]
Abstract
Monitoring the activity of ATP-consuming enzymes provides the basis for elucidating their modes of action and regulation. Although a number of ATP analogues have been developed for this, their scope is restricted because of the limited acceptance by respective enzymes. In order to clarify which kind of phosphate-modified ATP analogues are accepted by the α-β-phosphoanhydride-cleaving ubiquitin-activating enzyme 1 (UBA1) and the β-γ-phosphoanhydride-cleaving focal adhesion kinase (FAK), we tested phosphoramidate- and phosphoester-modified ATP analogues. UBA1 and FAK were able to convert phosphoramidate-modified ATP analogues, even with a bulky modification like biotin. In contrast, a phosphoester-modified analogue was poorly accepted. These results demonstrate that minor variations in the design of ATP analogues for monitoring ATP utilization have a significant impact on enzymatic acceptance.
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Affiliation(s)
- Susanne Ermert
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Stephan M Hacker
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Alexander Buntru
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Martin Scheffner
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Christof R Hauck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
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7
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Wallrodt S, Buntz A, Wang Y, Zumbusch A, Marx A. Intrazelluläre Visualisierung der Entstehung von Poly(ADP-Ribose) mit bioorthogonal funktionalisierten NAD+-Analoga. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600464] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Sarah Wallrodt
- Fachbereich Chemie; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Annette Buntz
- Fachbereich Chemie; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Yan Wang
- Fachbereich Chemie; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Zumbusch
- Fachbereich Chemie; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Marx
- Fachbereich Chemie; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
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8
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Wallrodt S, Buntz A, Wang Y, Zumbusch A, Marx A. Bioorthogonally Functionalized NAD(+) Analogues for In-Cell Visualization of Poly(ADP-Ribose) Formation. Angew Chem Int Ed Engl 2016; 55:7660-4. [PMID: 27080423 DOI: 10.1002/anie.201600464] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/29/2016] [Indexed: 01/11/2023]
Abstract
Poly(ADP-ribos)ylation (PARylation) is a major posttranslational modification and signaling event in most eukaryotes. Fundamental processes like DNA repair and transcription are coordinated by this transient polymer and its binding to proteins. ADP-ribosyltransferases (ARTs) build complex ADP-ribose chains from NAD(+) onto various acceptor proteins. Molecular studies of PARylation thus remain challenging. Herein, we present the development of bioorthogonally functionalized NAD(+) analogues for the imaging of PARylation in vitro and in cells. Our results show that 2-modified NAD(+) analogues perform remarkably well and can be applied to the in-cell visualization of PARylation simultaneously in two colors. This tool gives insight into the substrate scope of ARTs and will help to further elucidate the biological role of PARylation by offering fast optical, multichannel read-outs.
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Affiliation(s)
- Sarah Wallrodt
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Annette Buntz
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Yan Wang
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.
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9
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Hacker SM, Buntz A, Zumbusch A, Marx A. Direct Monitoring of Nucleotide Turnover in Human Cell Extracts and Cells by Fluorogenic ATP Analogs. ACS Chem Biol 2015; 10:2544-52. [PMID: 26274552 DOI: 10.1021/acschembio.5b00459] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleotides containing adenosine play pivotal roles in every living cell. Adenosine triphosphate (ATP), for example, is the universal energy currency, and ATP-consuming processes also contribute to posttranslational protein modifications. Nevertheless, detecting the turnover of adenosine nucleotides in the complex setting of a cell remains challenging. Here, we demonstrate the use of fluorogenic analogs of ATP and adenosine tetraphosphate to study nucleotide hydrolysis in lysates of human cell lines and in intact human cells. We found that the adenosine triphosphate analog is completely stable in lysates of human cell lines, whereas the adenosine tetraphosphate analog is rapidly turned over. The observed activity in human cell lysates can be assigned to a single enzyme, namely, the human diadenosine tetraphosphate hydrolase NudT2. Since NudT2 has been shown to be a prognostic factor for breast cancer, the adenosine tetraphosphate analog might contribute to a better understanding of its involvement in cancerogenesis and allow the straightforward screening for inhibitors. Studying hydrolysis of the analogs in intact cells, we found that electroporation is a suitable method to deliver nucleotide analogs into the cytoplasm and show that high FRET efficiencies can be detected directly after internalization. Time-dependent experiments reveal that adenosine triphosphate and tetraphosphate analogs are both processed in the cellular environment. This study demonstrates that these nucleotide analogs indeed bear the potential to be powerful tools for the exploration of nucleotide turnover in the context of whole cells.
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Affiliation(s)
- Stephan M. Hacker
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Annette Buntz
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Zumbusch
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry,
Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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10
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Hacker SM, Hintze C, Marx A, Drescher M. Monitoring enzymatic ATP hydrolysis by EPR spectroscopy. Chem Commun (Camb) 2015; 50:7262-4. [PMID: 24872080 DOI: 10.1039/c4cc02422b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An adenosine triphosphate (ATP) analogue modified with two nitroxide radicals is developed and employed to study its enzymatic hydrolysis by electron paramagnetic resonance spectroscopy. For this application, we demonstrate that EPR holds the potential to complement fluorogenic substrate analogues in monitoring enzymatic activity.
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Affiliation(s)
- Stephan M Hacker
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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11
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Iannazzo L, Laisné G, Fonvielle M, Braud E, Herbeuval JP, Arthur M, Etheve-Quelquejeu M. Synthesis of 3′-Fluoro-tRNA Analogues for Exploring Non-ribosomal Peptide Synthesis in Bacteria. Chembiochem 2015; 16:477-86. [DOI: 10.1002/cbic.201402523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 11/08/2022]
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12
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Hacker SM, Mortensen F, Scheffner M, Marx A. Selektive Beobachtung der enzymatischen Aktivität des Tumorsuppressors Fhit. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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13
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Hacker SM, Mortensen F, Scheffner M, Marx A. Selective monitoring of the enzymatic activity of the tumor suppressor Fhit. Angew Chem Int Ed Engl 2014; 53:10247-50. [PMID: 25098403 DOI: 10.1002/anie.201405259] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/25/2014] [Indexed: 11/07/2022]
Abstract
Cancer is a leading cause of death worldwide. Functional inactivation of tumor suppressor proteins, mainly by mutations in the corresponding genes, is a key event in cancer development. The fragile histidine triade protein (Fhit) is a tumor suppressor that is frequently affected in different cancer types. Fhit possesses diadenosine triphosphate hydrolase activity, but although reduction of its enzymatic activity appears to be important for exerting its tumor suppressor function, the regulation of Fhit activity is poorly understood. Here, we introduce a novel fluorogenic probe that is suited to selectively analyze the enzymatic activity of Fhit in extracts derived from human cells. This novel method will allow in-depth insight into the mechanisms involved in Fhit regulation in biologically relevant setups and, thus, into its role in the development of cancer.
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Affiliation(s)
- Stephan M Hacker
- Department of Chemistry and Department of Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany)
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14
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Gutiérrez Acosta OB, Hardt N, Hacker SM, Strittmatter T, Schink B, Marx A. Thiamine pyrophosphate stimulates acetone activation by Desulfococcus biacutus as monitored by a fluorogenic ATP analogue. ACS Chem Biol 2014; 9:1263-6. [PMID: 24779857 DOI: 10.1021/cb500152y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Acetone can be degraded by aerobic and anaerobic microorganisms. Studies with the strictly anaerobic sulfate-reducing bacterium Desulfococcus biacutus indicate that acetone degradation by these bacteria starts with an ATP-dependent carbonylation reaction leading to acetoacetaldehyde as the first reaction product. The reaction represents the second example of a carbonylation reaction in the biochemistry of strictly anaerobic bacteria, but the exact mechanism and dependence on cofactors are still unclear. Here, we use a novel fluorogenic ATP analogue to investigate its mechanism. We find that thiamine pyrophosphate is a cofactor of this ATP-dependent reaction. The products of ATP cleavage are AMP and pyrophosphate, providing first insights into the reaction mechanism by indicating that the reaction proceeds without intermediate formation of acetone enol phosphate.
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Affiliation(s)
- Olga B. Gutiérrez Acosta
- Department of Biology and ‡Department of Chemistry, Konstanz Research
School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Norman Hardt
- Department of Biology and ‡Department of Chemistry, Konstanz Research
School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Stephan M. Hacker
- Department of Biology and ‡Department of Chemistry, Konstanz Research
School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Tobias Strittmatter
- Department of Biology and ‡Department of Chemistry, Konstanz Research
School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Bernhard Schink
- Department of Biology and ‡Department of Chemistry, Konstanz Research
School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Biology and ‡Department of Chemistry, Konstanz Research
School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
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15
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Fechner P, Bleher O, Ewald M, Freudenberger K, Furin D, Hilbig U, Kolarov F, Krieg K, Leidner L, Markovic G, Proll G, Pröll F, Rau S, Riedt J, Schwarz B, Weber P, Widmaier J. Size does matter! Label-free detection of small molecule-protein interaction. Anal Bioanal Chem 2014; 406:4033-51. [PMID: 24817356 DOI: 10.1007/s00216-014-7834-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/07/2014] [Accepted: 04/11/2014] [Indexed: 11/28/2022]
Abstract
This review is focused on methods for detecting small molecules and, in particular, the characterisation of their interaction with natural proteins (e.g. receptors, ion channels). Because there are intrinsic advantages to using label-free methods over labelled methods (e.g. fluorescence, radioactivity), this review only covers label-free techniques. We briefly discuss available techniques and their advantages and disadvantages, especially as related to investigating the interaction between small molecules and proteins. The reviewed techniques include well-known and widely used standard analytical methods (e.g. HPLC-MS, NMR, calorimetry, and X-ray diffraction), newer and more specialised analytical methods (e.g. biosensors), biological systems (e.g. cell lines and animal models), and in-silico approaches.
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Affiliation(s)
- Peter Fechner
- Biametrics GmbH, Auf der Morgenstelle 18, 72076, Tübingen, Germany,
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16
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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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17
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Hardt N, Hacker SM, Marx A. Synthesis and fluorescence characteristics of ATP-based FRET probes. Org Biomol Chem 2013; 11:8298-305. [PMID: 24173528 DOI: 10.1039/c3ob41751d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Adenosine triphosphate (ATP) analogues labelled with two dyes suitable for undergoing Förster Resonance Energy Transfer (FRET) have the potential to be valuable tools to continuously study the enzymatic activity of ATP consuming enzymes. Here, we present a synthesis strategy that allows obtaining these ATP analogues in a straight-forward manner. Earlier studies indicate that modifying ATP at the O2'- and the γ-position is a very promising starting point for the design of these probes. We synthesized probes modified with five different combinations of dyes attached to these positions and investigated their fluorescence characteristics in the non-cleaved state as well as after enzymatic hydrolysis. All presented probes largely change their fluorescence characteristics upon cleavage. They include ratiometric FRET probes as well as dark quenched analogues. For typical in vitro applications a combination of the sulfonated polymethine dyes Sulfo-Cy3 and Sulfo-Cy5 seems to be most promising due to their excellent solubility in aqueous buffer and a large change of fluorescence characteristics upon cleavage. For this combination of dyes we also synthesized analogues modified at the γ- and the C2- or the O3'-position, respectively, as these attachment sites are also well accepted by certain ATP consuming enzymes. These analogues show comparably large changes in fluorescence characteristics. Overall, we present new ATP-based FRET probes that have the potential to enable monitoring the enzymatic activity of ATP consuming enzymes.
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Affiliation(s)
- Norman Hardt
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany.
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Hacker SM, Pagliarini D, Tischer T, Hardt N, Schneider D, Mex M, Mayer TU, Scheffner M, Marx A. Fluorogene ATP-Analoga zur Detektion von ATP-Verbrauch: Beobachtung der Aktivierung von Ubiquitin in Echtzeit. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304723] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Hacker SM, Pagliarini D, Tischer T, Hardt N, Schneider D, Mex M, Mayer TU, Scheffner M, Marx A. Fluorogenic ATP analogues for online monitoring of ATP consumption: observing ubiquitin activation in real time. Angew Chem Int Ed Engl 2013; 52:11916-9. [PMID: 24105922 DOI: 10.1002/anie.201304723] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/19/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Stephan M Hacker
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany)
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