1
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Hananya N, Koren S, Muir TW. Interrogating epigenetic mechanisms with chemically customized chromatin. Nat Rev Genet 2024; 25:255-271. [PMID: 37985791 PMCID: PMC11176933 DOI: 10.1038/s41576-023-00664-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2023] [Indexed: 11/22/2023]
Abstract
Genetic and genomic techniques have proven incredibly powerful for identifying and studying molecular players implicated in the epigenetic regulation of DNA-templated processes such as transcription. However, achieving a mechanistic understanding of how these molecules interact with chromatin to elicit a functional output is non-trivial, owing to the tremendous complexity of the biochemical networks involved. Advances in protein engineering have enabled the reconstitution of 'designer' chromatin containing customized post-translational modification patterns, which, when used in conjunction with sophisticated biochemical and biophysical methods, allow many mechanistic questions to be addressed. In this Review, we discuss how such tools complement established 'omics' techniques to answer fundamental questions on chromatin regulation, focusing on chromatin mark establishment and protein-chromatin interactions.
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Affiliation(s)
- Nir Hananya
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Shany Koren
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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2
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Moreno-Yruela C, Fierz B. Revealing chromatin-specific functions of histone deacylases. Biochem Soc Trans 2024; 52:353-365. [PMID: 38189424 DOI: 10.1042/bst20230693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024]
Abstract
Histone deacylases are erasers of Nε-acyl-lysine post-translational modifications and have been targeted for decades for the treatment of cancer, neurodegeneration and other disorders. Due to their relatively promiscuous activity on peptide substrates in vitro, it has been challenging to determine the individual targets and substrate identification mechanisms of each isozyme, and they have been considered redundant regulators. In recent years, biochemical and biophysical studies have incorporated the use of reconstituted nucleosomes, which has revealed a diverse and complex arsenal of recognition mechanisms by which histone deacylases may differentiate themselves in vivo. In this review, we first present the peptide-based tools that have helped characterize histone deacylases in vitro to date, and we discuss the new insights that nucleosome tools are providing into their recognition of histone substrates within chromatin. Then, we summarize the powerful semi-synthetic approaches that are moving forward the study of chromatin-associated factors, both in vitro by detailed single-molecule mechanistic studies, and in cells by live chromatin modification. We finally offer our perspective on how these new techniques would advance the study of histone deacylases. We envision that such studies will help elucidate the role of individual isozymes in disease and provide a platform for the development of the next generation of therapeutics.
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Affiliation(s)
- Carlos Moreno-Yruela
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Drug Design and Pharmacology (ILF), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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3
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Li M, Yu H, Li Y, Li X, Huang S, Liu X, Weng G, Xu L, Hou T, Guo DS, Wang Y. Rational design of supramolecular self-assembly sensor for living cell imaging of HDAC1 and its application in high-throughput screening. Biosens Bioelectron 2023; 242:115716. [PMID: 37820557 DOI: 10.1016/j.bios.2023.115716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023]
Abstract
Supramolecular chemistry offers new insights in bioimaging, but specific tracking of enzyme in living cells via supramolecular host-guest reporter pair remains challenging, largely due to the interference caused by the complex cellular environment on the binding between analytes and hosts. Here, by exploiting the principle of supramolecular tandem assay (STA) and the classic host-guest reporter pair (p-sulfonatocalix[4]arene (SC4A) and lucigenin (LCG)) and rationally designing artificial peptide library to screen sequence with high affinity of the target enzyme, we developed a "turn-on" fluorescent sensing system for intracellular imaging of histone deacetylase 1 (HDAC1), which is a potential therapeutic target for various diseases, including cancer, neurological, and cardiovascular diseases. Based on computational simulations and experimental validations, we verified that the deacetylated peptide by HDAC1 competed LCG, freeing it from the SC4A causing fluorescence increase. Enzyme kinetics experiments were further conducted to prove that this assay could detect HDAC1 specifically with high sensitivity (the LOD value is 0.015 μg/mL, ten times lower than the published method). This system was further applied for high-throughput screening of HDAC1 inhibitors over a natural compound library containing 147 compounds, resulting in the identification of a novel HDAC1 down-regulator (Ginsenoside RK3). Our results demonstrated the sensitivity and robustness of the assay system towards HDAC1. It should serve as a valuable tool for biochemical studies and drug screening.
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Affiliation(s)
- Min Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huijuan Yu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yiran Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shiqing Huang
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road 487372, Singapore
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road 487372, Singapore
| | - Gaoqi Weng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dong-Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China
| | - Yi Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Future Health Laboratory Innovation Center of Yangtze River Delta Zhejiang University, Jiaxing 314100, China.
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4
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Bolding JE, Nielsen AL, Jensen I, Hansen TN, Ryberg LA, Jameson ST, Harris P, Peters GHJ, Denu JM, Rogers JM, Olsen CA. Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7. Angew Chem Int Ed Engl 2023; 62:e202314597. [PMID: 37873919 DOI: 10.1002/anie.202314597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
The sirtuins are NAD+ -dependent lysine deacylases, comprising seven isoforms (SIRT1-7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.
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Affiliation(s)
- Julie E Bolding
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Alexander L Nielsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
- Current address: Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Iben Jensen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Line A Ryberg
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Current address: Department of Immunology and Microbiology, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Samuel T Jameson
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Current address: Department of Chemistry, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Joseph M Rogers
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
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5
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Nagata R, Nishiyama M, Kuzuyama T. Substrate Recognition Mechanism of a Trichostatin A-Forming Hydroxyamidotransferase. Biochemistry 2023. [PMID: 37167424 DOI: 10.1021/acs.biochem.3c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The hydroxyamidotransferase TsnB9 catalyzes hydroxylamine transfer from l-glutamic acid γ-monohydroxamate to the carboxyl group of trichostatic acid to produce the terminal hydroxamic acid group of trichostatin A, which is a potent inhibitor of histone deacetylase (HDAC). The reaction catalyzed by TsnB9 is similar to that catalyzed by glutamine-dependent asparagine synthetase, but the trichostatic acid recognition mechanism remains unclear. Here, we determine the crystal structure of TsnB9 composed of the N-terminal glutaminase domain and the C-terminal synthetase domain. Two consecutive phenylalanine residues, which are not found in glutamine-dependent asparagine synthetase, in the N-terminal glutaminase domain structurally form the bottom of the hydrophobic pocket in the C-terminal synthetase domain. Mutational and computational analyses of TsnB9 suggest five aromatic residues, including the two consecutive phenylalanine residues, in the hydrophobic pocket are important for the recognition of the dimethylaniline moiety of trichostatic acid. These insights lead us to the discovery of hydroxyamidotransferase to produce terminal hydroxamic acid group-containing HDAC inhibitors different from trichostatin A.
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Affiliation(s)
- Ryuhei Nagata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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6
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Zecha J, Bayer FP, Wiechmann S, Woortman J, Berner N, Müller J, Schneider A, Kramer K, Abril-Gil M, Hopf T, Reichart L, Chen L, Hansen FM, Lechner S, Samaras P, Eckert S, Lautenbacher L, Reinecke M, Hamood F, Prokofeva P, Vornholz L, Falcomatà C, Dorsch M, Schröder A, Venhuizen A, Wilhelm S, Médard G, Stoehr G, Ruland J, Grüner BM, Saur D, Buchner M, Ruprecht B, Hahne H, The M, Wilhelm M, Kuster B. Decrypting drug actions and protein modifications by dose- and time-resolved proteomics. Science 2023; 380:93-101. [PMID: 36926954 PMCID: PMC7615311 DOI: 10.1126/science.ade3925] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 02/21/2023] [Indexed: 03/18/2023]
Abstract
Although most cancer drugs modulate the activities of cellular pathways by changing posttranslational modifications (PTMs), little is known regarding the extent and the time- and dose-response characteristics of drug-regulated PTMs. In this work, we introduce a proteomic assay called decryptM that quantifies drug-PTM modulation for thousands of PTMs in cells to shed light on target engagement and drug mechanism of action. Examples range from detecting DNA damage by chemotherapeutics, to identifying drug-specific PTM signatures of kinase inhibitors, to demonstrating that rituximab kills CD20-positive B cells by overactivating B cell receptor signaling. DecryptM profiling of 31 cancer drugs in 13 cell lines demonstrates the broad applicability of the approach. The resulting 1.8 million dose-response curves are provided as an interactive molecular resource in ProteomicsDB.
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Affiliation(s)
- Jana Zecha
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Florian P. Bayer
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Svenja Wiechmann
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Julia Woortman
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Nicola Berner
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Julian Müller
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Annika Schneider
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Karl Kramer
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Mar Abril-Gil
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Thomas Hopf
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Leonie Reichart
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Lin Chen
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Fynn M. Hansen
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Severin Lechner
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Patroklos Samaras
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Stephan Eckert
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
| | - Ludwig Lautenbacher
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Maria Reinecke
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Firas Hamood
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Polina Prokofeva
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Larsen Vornholz
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Chiara Falcomatà
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
- Technical University of Munich, School of Medicine, Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, 80336 Munich, Germany
| | - Madeleine Dorsch
- West German Cancer Center, University Hospital Essen, Department of Medical Oncology, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Ayla Schröder
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Anton Venhuizen
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Stephanie Wilhelm
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Guillaume Médard
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Gabriele Stoehr
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Jürgen Ruland
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), 81675 Munich, Germany
| | - Barbara M. Grüner
- West German Cancer Center, University Hospital Essen, Department of Medical Oncology, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Dieter Saur
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
- Technical University of Munich, School of Medicine, Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, 80336 Munich, Germany
| | - Maike Buchner
- Technical University of Munich, School of Medicine, Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Benjamin Ruprecht
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Hannes Hahne
- OmicScouts GmbH, Lise-Meitner-Str. 30, 85354 Freising, Germany
| | - Matthew The
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Mathias Wilhelm
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
| | - Bernhard Kuster
- Technical University of Munich, TUM School of Life Sciences, Department of Molecular Life Sciences, 85354 Freising, Germany
- German Cancer Consortium, Partner Site Munich, 80336 Munich, Germany
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7
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Tilak P, Kotnik F, Née G, Seidel J, Sindlinger J, Heinkow P, Eirich J, Schwarzer D, Finkemeier I. Proteome-wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36961081 DOI: 10.1111/tpj.16206] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 05/09/2023]
Abstract
Post-translational modifications (PTMs) of proteins play important roles in the acclimation of plants to environmental stress. Lysine acetylation is a dynamic and reversible PTM, which can be removed by histone deacetylases. Here we investigated the role of lysine acetylation in the response of Arabidopsis leaves to 1 week of salt stress. A quantitative mass spectrometry analysis revealed an increase in lysine acetylation of several proteins from cytosol and plastids, which was accompanied by altered histone deacetylase activities in the salt-treated leaves. While activities of HDA14 and HDA15 were decreased upon salt stress, HDA5 showed a mild and HDA19 a strong increase in activity. Since HDA5 is a cytosolic-nuclear enzyme from the class II histone deacetylase family with yet unknown protein substrates, we performed a lysine acetylome analysis on hda5 mutants and characterized its substrate proteins. Next to histone H2B, the salt stress-responsive transcription factor GT2L and the dehydration-related protein ERD7 were identified as HDA5 substrates. In addition, in protein-protein interaction studies, HDA18 was discovered, among other interacting proteins, to work in a complex together with HDA5. Altogether, this study revealed the substrate proteins of HDA5 and identified new lysine acetylation sites which are hyperacetylated upon salt stress. The identification of specific histone deacetylase substrate proteins, apart from histones, will be important to unravel the acclimation response of Arabidopsis to salt stress and their role in plant physiology.
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Affiliation(s)
- Priyadarshini Tilak
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Florian Kotnik
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Guillaume Née
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Julian Seidel
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Julia Sindlinger
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Paulina Heinkow
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Jürgen Eirich
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry (IFIB), University of Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, DE-48149, Münster, Germany
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8
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Schulte C, Khayenko V, Maric HM. Peptide Microarray-Based Protein Interaction Studies Across Affinity Ranges: Enzyme Stalling, Cross-Linking, Depletion, and Neutralization. Methods Mol Biol 2023; 2578:143-159. [PMID: 36152285 DOI: 10.1007/978-1-0716-2732-7_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
While an ever-increasing number of protein-protein interactions were studied by peptide microarrays with great success, array-based investigations of transiently binding proteins, such as HDACs, and precise binding quantification, remained challenging. Here, we present an updated protocol for the preparation and use of peptide microarrays including the necessary adjustments for simple semi-quantitative and precise measurements across affinity ranges. This procedure describes the mass spectrometric controlled preparation of peptide microarrays in μSPOT format, and their application in binding profiling of recombinant, as well as endogenous, native proteins. We further highlight how cross-linking, blocking, and enzyme stalling can be leveraged to enhance sensitivity and describe how in situ on-chip binding neutralization can enhance the predictive value and robustness of the binding readout. Finally, we included examples for the integration of precise biophysical binding readouts that complement the traditional array-based binding assays.
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Affiliation(s)
- Clemens Schulte
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg, Germany
| | - Vladimir Khayenko
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg, Germany
| | - Hans Michael Maric
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg, Germany.
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9
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Eirich J, Sindlinger J, Schön S, Schwarzer D, Finkemeier I. Peptide CoA conjugates for in situ proteomics profiling of acetyltransferase activities. Methods Enzymol 2023; 684:209-252. [DOI: 10.1016/bs.mie.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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10
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Archibald L, Brown EA, Millard CJ, Watson PJ, Robertson NS, Wang S, Schwabe JWR, Jamieson AG. Hydroxamic Acid-Modified Peptide Library Provides Insights into the Molecular Basis for the Substrate Selectivity of HDAC Corepressor Complexes. ACS Chem Biol 2022; 17:2572-2582. [PMID: 35973051 PMCID: PMC9488896 DOI: 10.1021/acschembio.2c00510] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Targeting the lysine deacetylase activity of class I histone deacetylases (HDACs) is potentially beneficial for the treatment of several diseases including human immunodeficiency virus (HIV) infection, Alzheimer's disease, and various cancers. It is therefore important to understand the function and mechanism of action of these enzymes. Class I HDACs act as catalytic components of seven large, multiprotein corepressor complexes. Different HDAC corepressor complexes have specific, nonredundant roles in the cell. It is likely that their specific functions are at least partly influenced by the substrate specificity of the complexes. To address this, we developed chemical tools to probe the specificity of HDAC complexes. We assessed a library of acetyl-lysine-containing substrate peptides and hydroxamic acid-containing inhibitor peptides against the full range of class I HDAC corepressor complexes. The results suggest that site-specific HDAC corepressor complex activity is driven in part by the recognition of the primary amino acid sequence surrounding a particular lysine position in the histone tail.
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Affiliation(s)
- Lewis
J. Archibald
- School
of Chemistry, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, U.K.
| | - Edward A. Brown
- The
Leicester Institute of Structural and Chemical Biology, Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - Christopher J. Millard
- The
Leicester Institute of Structural and Chemical Biology, Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - Peter J. Watson
- The
Leicester Institute of Structural and Chemical Biology, Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - Naomi S. Robertson
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | - Siyu Wang
- The
Leicester Institute of Structural and Chemical Biology, Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - John W. R. Schwabe
- The
Leicester Institute of Structural and Chemical Biology, Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.,
| | - Andrew G. Jamieson
- School
of Chemistry, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, U.K.,
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11
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Kang W, Liu L, Yu P, Zhang T, Lei C, Nie Z. A switchable Cas12a enabling CRISPR-based direct histone deacetylase activity detection. Biosens Bioelectron 2022; 213:114468. [PMID: 35700604 DOI: 10.1016/j.bios.2022.114468] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 11/02/2022]
Abstract
The efficient and robust signal reporting ability of CRISPR-Cas system exhibits huge value in biosensing, but its applicability for non-nucleic acid analyte detection relies on the coupling of additional recognition modules. To address this limitation, we described a switchable Cas12a and exploited it for CRISPR-based direct analysis of histone deacetylase (HDAC) activity. Starting from the acetylation-mediated inactivation of Cas12a by anti-CRISPR protein AcrVA5, we demonstrated that the acetyl-inactivated Cas12a could be reversibly activated by HDAC-mediated deacetylation based on computational simulations (e.g., deep learning and protein-protein docking analysis) and experimental verifications. By leveraging this switchable Cas12a for both target sensing and signal amplification, we established a sensitive one-pot assay capable of detecting deacetylase sirtuin-1 with sub-nanomolar sensitivity, which is 50 times lower than the standard two-step peptide-based assay. The versability of this assay was validated by the sensitive assessment of cellular HDAC activities in different cell lines with good accuracy, making it a valuable tool for biochemical studies and clinical diagnostics.
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Affiliation(s)
- Wenyuan Kang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Lin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Peihang Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Tianyi Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China.
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China.
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12
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Paris G, Heidepriem J, Tsouka A, Liu Y, Mattes DS, Pinzón Martín S, Dallabernardina P, Mende M, Lindner C, Wawrzinek R, Rademacher C, Seeberger PH, Breitling F, Bischoff FR, Wolf T, Loeffler FF. Automated Laser-Transfer Synthesis of High-Density Microarrays for Infectious Disease Screening. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2200359. [PMID: 35429012 DOI: 10.1002/adma.202200359] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Laser-induced forward transfer (LIFT) is a rapid laser-patterning technique for high-throughput combinatorial synthesis directly on glass slides. A lack of automation and precision limits LIFT applications to simple proof-of-concept syntheses of fewer than 100 compounds. Here, an automated synthesis instrument is reported that combines laser transfer and robotics for parallel synthesis in a microarray format with up to 10 000 individual reactions cm- 2 . An optimized pipeline for amide bond formation is the basis for preparing complex peptide microarrays with thousands of different sequences in high yield with high reproducibility. The resulting peptide arrays are of higher quality than commercial peptide arrays. More than 4800 15-residue peptides resembling the entire Ebola virus proteome on a microarray are synthesized to study the antibody response of an Ebola virus infection survivor. Known and unknown epitopes that serve now as a basis for Ebola diagnostic development are identified. The versatility and precision of the synthesizer is demonstrated by in situ synthesis of fluorescent molecules via Schiff base reaction and multi-step patterning of precisely definable amounts of fluorophores. This automated laser transfer synthesis approach opens new avenues for high-throughput chemical synthesis and biological screening.
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Affiliation(s)
- Grigori Paris
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Department of System Dynamics and Friction Physics, Institute of Mechanics, Technical University of Berlin, Str. des 17. Juni 135, 10623, Berlin, Germany
| | - Jasmin Heidepriem
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Alexandra Tsouka
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Yuxin Liu
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Daniela S Mattes
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafe, Germany
| | - Sandra Pinzón Martín
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Pietro Dallabernardina
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Marco Mende
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Celina Lindner
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Robert Wawrzinek
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Christoph Rademacher
- Department of Pharmaceutical Sciences, University of Vienna, Althanstr. 14, Vienna, 1090, Austria
- Department of Microbiology and Immunobiology, Max F. Perutz Laboratories GmbH, Dr.-Bohr-Gasse 9, Vienna, 1030, Austria
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Frank Breitling
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafe, Germany
| | - Frank Ralf Bischoff
- Department of Functional Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Timo Wolf
- Infectious Diseases Unit, Department of Medicine, Goethe University Hospital, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Felix F Loeffler
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
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13
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Resolving the deceptive isoform and complex selectivity of HDAC1/2 inhibitors. Cell Chem Biol 2022; 29:1140-1152.e5. [PMID: 35298895 DOI: 10.1016/j.chembiol.2022.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/22/2021] [Accepted: 02/27/2022] [Indexed: 12/18/2022]
Abstract
The histone deacetylase paralogs HDAC1/2/3 and their corepressor complexes serve as epigenetic master regulators of chromatin function. Over the past decades, HDACs have been widely pursued as pharmacological targets, and considerable efforts have been invested in the development of small molecule drugs. Specifically, ortho-aminoanilide-derived inhibitors, including CI-994 and Cpd-60, stand out with their attractive selectivity profiles and have been used extensively as tools to delineate the biological roles of specific HDAC isoforms and complexes. Here, we apply a suite of activity-independent strategies to investigate how dynamic processes that regulate HDAC complexes govern the isoform and complex selectivity of HDAC inhibitors. Importantly, we find that overreliance on static and simplified biochemical activity assays has confounded the determination of the biological selectivity of these ligands. Our data urge a comprehensive reinterpretation of numerous studies utilizing these tool compounds for the interrogation of epigenetic and other cellular processes.
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14
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Bíró L, Buglyó P, Farkas E. Diversity in the Interaction of Amino Acid- and Peptide-Based Hydroxamic Acids with Some Platinum Group Metals in Solution. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030669. [PMID: 35163937 PMCID: PMC8839353 DOI: 10.3390/molecules27030669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
Complexes that incorporate both ligand(s) and metal(s) exhibiting cytotoxic activity can especially be interesting to develop multifunctional drug molecules with desired activities. In this review, the limited number of solution results collected in our laboratory on the complexes of Pd(II) and two other platinum group metals—the half-sandwich type, [(η6-p-cym)Ru(H2O)3]2+, and [(η5-Cp*)Rh(H2O)3]2+—with hydroxamic acid derivatives of three amino acids, two imidazole analogues, and four small peptides are summarized and evaluated. Unlike the limited number of coordination sites of these metal ions (four and three for Pd(II) and the organometallic cations, respectively), the ligands discussed here offer a relatively high number of donor atoms as well as variation in their position within the ligands, resulting in a large versatility of the likely coordination modes. The review, besides presenting the solution equilibrium results, also discusses the main factors, such as (N,N) versus (O,O) chelate; size of chelate; amino-N versus imidazole-N; primary versus secondary hydroxamic function; differences between hydrolytic ability of the metal ions studied; and hydrolysis of the coordinated peptide hydroxamic acids in their Pd(II) complexes, which all determine the coordination modes present in the complexes formed in measurable concentrations in these systems. The options for the quantitative evaluation of metal binding effectivity and selectivity of the various ligands and the comparison with each other by using solution equilibrium data are also discussed.
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15
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Schulte C, Khayenko V, Gupta AJ, Maric HM. Low-cost synthesis of peptide libraries and their use for binding studies via temperature-related intensity change. STAR Protoc 2021; 2:100605. [PMID: 34189471 PMCID: PMC8219886 DOI: 10.1016/j.xpro.2021.100605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Protein-peptide interactions are involved in many fundamental cellular functions and constitute promising drug targets. Here, we provide a detailed protocol for the cost-effective preparation of a cellulose-based solid support for synthesis of nanoscale to micromolar-scale peptide libraries. Their subsequent use for high-throughput protein interaction screening as well as affinity determination in solution provides binding data for thousands of unique peptides with a turnover of 1 to 2 weeks, thereby facilitating in vitro assessment and development of high-affinity binders. For complete details on the use and execution of this protocol, please refer to Schulte et al., (2020).
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Affiliation(s)
- Clemens Schulte
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany.,Biocenter, Department of Biotechnology and Biophysics, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Vladimir Khayenko
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany.,Biocenter, Department of Biotechnology and Biophysics, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Amit Jean Gupta
- Nanotemper Technologies GmbH, Flößergasse 4, 81369 Munich, Germany
| | - Hans Michael Maric
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany.,Biocenter, Department of Biotechnology and Biophysics, University of Wuerzburg, 97074 Wuerzburg, Germany
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16
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Lin W, Gandhi S, Oviedo Lara AR, Thomas AK, Helbig R, Zhang Y. Controlling Surface Wettability for Automated In Situ Array Synthesis and Direct Bioscreening. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2102349. [PMID: 34309086 DOI: 10.1002/adma.202102349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Indexed: 06/13/2023]
Abstract
The in situ synthesis of biomolecules on glass surfaces for direct bioscreening can be a powerful tool in the fields of pharmaceutical sciences, biomaterials, and chemical biology. However, it is still challenging to 1) achieve this conventional multistep combinatorial synthesis on glass surfaces with small feature sizes and high yields and 2) develop a surface which is compatible with solid-phase syntheses, as well as the subsequent bioscreening. This work reports an amphiphilic coating of a glass surface on which small droplets of polar aprotic organic solvents can be deposited with an enhanced contact angle and inhibited motion to permit fully automated multiple rounds of the combinatorial synthesis of small-molecule compounds and peptides. This amphiphilic coating can be switched into a hydrophilic network for protein- and cell-based screening. Employing this in situ synthesis method, chemical space can be probed via array technology with unprecedented speed for various applications, such as lead discovery/optimization in medicinal chemistry and biomaterial development.
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Affiliation(s)
- Weilin Lin
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Shanil Gandhi
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alan Rodrigo Oviedo Lara
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Alvin K Thomas
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Ralf Helbig
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, Hohe Strasse 6, 01069, Dresden, Germany
| | - Yixin Zhang
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
- Cluster of Excellence "Physics of Life", Technische Universität Dresden, 01062, Dresden, Germany
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