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Xiong Y, Li M, Cao Y, Li Z, Chang Y, Zhao X, Qing G. Nanofluidic Device for Detection of Lysine Methylpeptides and Sensing of Lysine Methylation. Anal Chem 2023; 95:7761-7769. [PMID: 37140051 DOI: 10.1021/acs.analchem.3c01074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein methylation is the smallest possible yet vitally important post-translational modification (PTM). This small and chemically inert addition in proteins makes the analysis of methylation more challenging, thus calling for an efficient tool for the sake of recognition and detection. Herein, we present a nanofluidic electric sensing device based on a functionalized nanochannel that was constructed by introducing monotriazole-containing p-sulfonatocalix[4]arene (TSC) into a single asymmetric polymeric nanochannel via click chemistry. The device can selectively detect lysine methylpeptides with subpicomole sensitivity, distinguish between different lysine methylation states, and monitor the lysine methylation process by methyltransferase at the peptide level in real time. The introduced TSC molecule, with its confined asymmetric configuration, presents the remarkable ability to selectively bind to lysine methylpeptides, which, coupled with the release of the complexed Cu ions, allows the device to transform the molecular-level recognition to the discernible change in ionic current of the nanofluidic electric device, thus enabling detection. This work could serve as a stepping stone to the development of a new methyltransferase assay and the chemical that specifically targets lysine methylation in PTM proteomics.
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Affiliation(s)
- Yuting Xiong
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, College of Chemistry and Materials Science, East China University of Technology, Nanchang 330013, P. R. China
| | - Minmin Li
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, College of Chemistry and Materials Science, East China University of Technology, Nanchang 330013, P. R. China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yuchen Cao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Zan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yongxin Chang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xinjia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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Kauerhof D, Niemeyer J. Functionalized Macrocycles in Supramolecular Organocatalysis. Chempluschem 2020; 85:889-899. [PMID: 32391655 DOI: 10.1002/cplu.202000152] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/26/2020] [Indexed: 01/18/2023]
Abstract
Supramolecular organocatalysis has emerged as a novel research field in the context of homogeneous catalysis. In particular, the use of functionalized macrocycles as supramolecular catalysts is highly promising, as these systems are oftentimes easily accessible and offer distinct advantages in catalysis. Macrocyclic catalysts can provide defined binding pockets, such as hydrophobic cavities, and can thus create a reaction microenvironment for catalysis. In addition, macrocycles can offer a preorganized arrangement of functional groups, such as binding sites or catalytically active groups, thus enabling a defined and possibly multivalent binding and activation of substrates. The aim of this Minireview is to provide an overview of recent advances in the area of supramolecular organocatalysis based on functionalized macrocycles (including cyclodextrins, calixarenes, and resorcinarenes), with a focus on those examples where certain catalytically active groups (such as hydrogen bond donors/acceptors, Brønsted acid or base groups, or nucleophilic units) are present in or have been installed on the macrocycles.
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Affiliation(s)
- Dana Kauerhof
- Faculty of Chemistry (Organic Chemistry) and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstr. 7, 45141, Essen, Germany
| | - Jochen Niemeyer
- Faculty of Chemistry (Organic Chemistry) and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstr. 7, 45141, Essen, Germany
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Mullins AG, St. Louis LE, Waters ML. Using changes in speciation in a dynamic combinatorial library as a fingerprint to differentiate the methylation states of arginine. Chem Commun (Camb) 2020; 56:3947-3950. [DOI: 10.1039/d0cc00415d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A dynamic combinatorial library was shown to provide a direct method of sensing methylated arginine and lysine due to differences in speciation. This provides the first sensor array for all the methylation states of arginine.
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Affiliation(s)
- Alexandria G. Mullins
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Lauren E. St. Louis
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Marcey L. Waters
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
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Gruber T. Synthetic Receptors for the Recognition and Discrimination of Post-Translationally Methylated Lysines. Chembiochem 2018; 19:2324-2340. [DOI: 10.1002/cbic.201800398] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Tobias Gruber
- School of Pharmacy; University of Lincoln; Joseph Banks Laboratories; Green Lane Lincoln LN6 7DL UK
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Finbloom JA, Francis MB. Supramolecular strategies for protein immobilization and modification. Curr Opin Chem Biol 2018; 46:91-98. [DOI: 10.1016/j.cbpa.2018.05.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/19/2018] [Accepted: 05/29/2018] [Indexed: 02/03/2023]
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Hanauer T, Hopkinson RJ, Patel K, Li Y, Correddu D, Kawamura A, Sarojini V, Leung IKH, Gruber T. Selective recognition of the di/trimethylammonium motif by an artificial carboxycalixarene receptor. Org Biomol Chem 2017; 15:1100-1105. [PMID: 28091667 DOI: 10.1039/c6ob02616h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Chemical tools that recognise post-translational modifications have promising applications in biochemistry and in therapy. We report a simple carboxycalixarene that selectively binds molecules containing di/trimethylammonium moieties in isolation, in cell lysates and when incorporated in histone peptides. Our findings reveal the potential of using carboxycalixarene-based receptors to study epigenetic regulation.
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Affiliation(s)
- Thomas Hanauer
- Institute of Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, Freiberg, Sachsen, Germany.
| | - Richard J Hopkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Kamal Patel
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Yu Li
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Danilo Correddu
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Ivanhoe K H Leung
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Tobias Gruber
- Institute of Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, Freiberg, Sachsen, Germany.
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Gober IN, Waters ML. Optimization of a synthetic receptor for dimethyllysine using a biphenyl-2,6-dicarboxylic acid scaffold: insights into selective recognition of hydrophilic guests in water. Org Biomol Chem 2017; 15:7789-7795. [DOI: 10.1039/c7ob01921a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Introduction of an endo-carboxylate in a building block for dynamic combinatorial chemistry resulted in amplification of a new host with a Kd of 200 nM for dimethyllysine, a biologically important post-translational modification.
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Affiliation(s)
- Isaiah N. Gober
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Marcey L. Waters
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
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Liu Y, Perez L, Mettry M, Easley CJ, Hooley RJ, Zhong W. Self-Aggregating Deep Cavitand Acts as a Fluorescence Displacement Sensor for Lysine Methylation. J Am Chem Soc 2016; 138:10746-9. [DOI: 10.1021/jacs.6b05897] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yang Liu
- Department of Chemistry and ‡Environmental Toxicology Program, University of California-Riverside, Riverside, California 92521, United States
| | - Lizeth Perez
- Department of Chemistry and ‡Environmental Toxicology Program, University of California-Riverside, Riverside, California 92521, United States
| | - Magi Mettry
- Department of Chemistry and ‡Environmental Toxicology Program, University of California-Riverside, Riverside, California 92521, United States
| | - Connor J. Easley
- Department of Chemistry and ‡Environmental Toxicology Program, University of California-Riverside, Riverside, California 92521, United States
| | - Richard J. Hooley
- Department of Chemistry and ‡Environmental Toxicology Program, University of California-Riverside, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry and ‡Environmental Toxicology Program, University of California-Riverside, Riverside, California 92521, United States
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Peacock H, Thinnes CC, Kawamura A, Hamilton AD. Tetracyanoresorcin[4]arene selectively recognises trimethyllysine and inhibits its enzyme-catalysed demethylation. Supramol Chem 2016. [DOI: 10.1080/10610278.2016.1140898] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Hayden Peacock
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Cyrille C. Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andrew D. Hamilton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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