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Asadiatouei P, Salem CB, Wanninger S, Ploetz E, Lamb DC. Deep-LASI, single-molecule data analysis software. Biophys J 2024:S0006-3495(24)00133-4. [PMID: 38384132 DOI: 10.1016/j.bpj.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 02/23/2024] Open
Abstract
By avoiding ensemble averaging, single-molecule methods provide novel means of extracting mechanistic insights into function of material and molecules at the nanoscale. However, one of the big limitations is the vast amount of data required for analyzing and extracting the desired information, which is time-consuming and user dependent. Here, we introduce Deep-LASI, a software suite for the manual and automatic analysis of single-molecule traces, interactions, and the underlying kinetics. The software can handle data from one-, two- and three-color fluorescence data, and was particularly designed for the analysis of two- and three-color single-molecule fluorescence resonance energy transfer experiments. The functionalities of the software include: the registration of multiple-channels, trace sorting and categorization, determination of the photobleaching steps, calculation of fluorescence resonance energy transfer correction factors, and kinetic analyses based on hidden Markov modeling or deep neural networks. After a kinetic analysis, the ensuing transition density plots are generated, which can be used for further quantification of the kinetic parameters of the system. Each step in the workflow can be performed manually or with the support of machine learning algorithms. Upon reading in the initial data set, it is also possible to perform the remaining analysis steps automatically without additional supervision. Hence, the time dedicated to the analysis of single-molecule experiments can be reduced from days/weeks to minutes. After a thorough description of the functionalities of the software, we also demonstrate the capabilities of the software via the analysis of a previously published dynamic three-color DNA origami structure fluctuating between three states. With the drastic time reduction in data analysis, new types of experiments become realistically possible that complement our currently available palette of methodologies for investigating the nanoworld.
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Affiliation(s)
- Pooyeh Asadiatouei
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Clemens-Bässem Salem
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Simon Wanninger
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Don C Lamb
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Munich, Germany.
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2
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Wanninger S, Asadiatouei P, Bohlen J, Salem CB, Tinnefeld P, Ploetz E, Lamb DC. Deep-LASI: deep-learning assisted, single-molecule imaging analysis of multi-color DNA origami structures. Nat Commun 2023; 14:6564. [PMID: 37848439 PMCID: PMC10582187 DOI: 10.1038/s41467-023-42272-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023] Open
Abstract
Single-molecule experiments have changed the way we explore the physical world, yet data analysis remains time-consuming and prone to human bias. Here, we introduce Deep-LASI (Deep-Learning Assisted Single-molecule Imaging analysis), a software suite powered by deep neural networks to rapidly analyze single-, two- and three-color single-molecule data, especially from single-molecule Förster Resonance Energy Transfer (smFRET) experiments. Deep-LASI automatically sorts recorded traces, determines FRET correction factors and classifies the state transitions of dynamic traces all in ~20-100 ms per trajectory. We benchmarked Deep-LASI using ground truth simulations as well as experimental data analyzed manually by an expert user and compared the results with a conventional Hidden Markov Model analysis. We illustrate the capabilities of the technique using a highly tunable L-shaped DNA origami structure and use Deep-LASI to perform titrations, analyze protein conformational dynamics and demonstrate its versatility for analyzing both total internal reflection fluorescence microscopy and confocal smFRET data.
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Affiliation(s)
- Simon Wanninger
- Department of Chemistry and Center for NanoScience (CeNS) Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377, Munich, Germany
| | - Pooyeh Asadiatouei
- Department of Chemistry and Center for NanoScience (CeNS) Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377, Munich, Germany
| | - Johann Bohlen
- Department of Chemistry and Center for NanoScience (CeNS) Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377, Munich, Germany
| | - Clemens-Bässem Salem
- Department of Chemistry and Center for NanoScience (CeNS) Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377, Munich, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience (CeNS) Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377, Munich, Germany
| | - Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS) Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377, Munich, Germany.
| | - Don C Lamb
- Department of Chemistry and Center for NanoScience (CeNS) Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377, Munich, Germany.
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3
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Ploetz E, Ambrose B, Barth A, Börner R, Erichson F, Kapanidis AN, Kim HD, Levitus M, Lohman TM, Mazumder A, Rueda DS, Steffen FD, Cordes T, Magennis SW, Lerner E. A new twist on PIFE: photoisomerisation-related fluorescence enhancement. Methods Appl Fluoresc 2023; 12:012001. [PMID: 37726007 PMCID: PMC10570931 DOI: 10.1088/2050-6120/acfb58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/24/2023] [Accepted: 09/19/2023] [Indexed: 09/21/2023]
Abstract
PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate ofcis/transphotoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule. In this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turning PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules.
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Affiliation(s)
- Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Benjamin Ambrose
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, United Kingdom
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, United Kingdom
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Richard Börner
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Felix Erichson
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, United Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, United States of America
| | - Marcia Levitus
- School of Molecular Sciences, Arizona State University, 551 E. University Drive, Tempe, AZ,85287, United States of America
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States of America
| | - Abhishek Mazumder
- CSIR-Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, United Kingdom
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, United Kingdom
| | - Fabio D Steffen
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Großhadernerstr. 2-4, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | - Eitan Lerner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem; Jerusalem 9190401, Israel
- Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem; Jerusalem 9190401, Israel
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4
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Ploetz E, Ambrose B, Barth A, Börner R, Erichson F, Kapanidis AN, Kim HD, Levitus M, Lohman TM, Mazumder A, Rueda DS, Steffen FD, Cordes T, Magennis SW, Lerner E. A new twist on PIFE: photoisomerisation-related fluorescence enhancement. ArXiv 2023:arXiv:2302.12455v2. [PMID: 36866225 PMCID: PMC9980184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate of cis/trans photoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule and, in this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turn PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules.
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Affiliation(s)
- Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Benjamin Ambrose
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, UK, Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, UK
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Richard Börner
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Felix Erichson
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Achillefs N. Kapanidis
- Kavli Institute for Nanoscience Discovery, Department of Biological Physics, The University of Oxford, UK
| | - Harold D. Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
| | - Marcia Levitus
- School of Molecular Sciences, Arizona State University, 551 E. University Drive, Tempe, AZ, 85287, USA
| | - Timothy M. Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Abhishek Mazumder
- Kavli Institute for Nanoscience Discovery, Department of Biological Physics, The University of Oxford, UK
| | - David S. Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, UK, Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, UK
| | - Fabio D. Steffen
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr, 2-4, 82152 Planegg-Martinsried, Germany
| | - Steven W. Magennis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, UK
| | - Eitan Lerner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem; Jerusalem 9190401, Israel, Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem; Jerusalem 9190401, Israel
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5
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Fuchs A, Knechtel F, Wang H, Ji Z, Wuttke S, Yaghi OM, Ploetz E. Water Harvesting at the Single-Crystal Level. J Am Chem Soc 2023. [PMID: 37353221 DOI: 10.1021/jacs.3c02902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2023]
Abstract
Metal-organic frameworks (MOFs) have emerged as a class of porous materials with facile uptake and release of water, turning them into excellent substrates for real-world atmospheric water harvesting applications. The performance of different MOF systems was experimentally characterized at the bulk level by assessing the total amount of water taken up and the release kinetics, leaving the question behind of what the upper limit of the pristine materials actually is. Moreover, recent devices rely on fluidized bed reactors that exploit the harvesting capacities of MOFs at the single-crystal (SC) level. In this publication, we present a novel methodology based on Raman spectroscopy, for acquiring water adsorption isotherms and kinetic curves with a sub-micrometer resolution that provides valuable insights into the material behavior probing the pristine MOF at the SC level. We investigated isolated MOF-801 particles in situ and could dissect contributions of intra- and inter-particle effects on the water harvesting performance of MOF-801 via adsorption-desorption isotherms and kinetic curves. Using spontaneous Raman spectroscopy, we found an almost 20-fold faster uptake for the undisturbed crystalline material. Correlative imaging based on four-wave mixing and coherent anti-Stokes Raman scattering further localized the uptaken water inside MOF-801 and identified inter-particle condensation as the main source for the discrepancies between the performance at the bulk and SC level. Our studies determined an upper limit of around 91.9 L/kgMOF/day for MOF-801.
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Affiliation(s)
- Adrian Fuchs
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Fabian Knechtel
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Haoze Wang
- Department of Chemistry and Kavli Energy Nanoscience Institute, University of California-Berkeley, Berkeley, California 94720, United States
| | - Zhe Ji
- Department of Chemistry and Kavli Energy Nanoscience Institute, University of California-Berkeley, Berkeley, California 94720, United States
| | - Stefan Wuttke
- BCMaterials, Basque Center for Materials, UPV/EHU Science Park, 48940 Leioa, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Omar M Yaghi
- Department of Chemistry and Kavli Energy Nanoscience Institute, University of California-Berkeley, Berkeley, California 94720, United States
- UC Berkeley-KACST Joint Center of Excellence for Nanomaterials for Clean Energy Applications, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
- Bakar Institute of Digital Materials for the Planet, Division of Computing, Data Science, and Society, University of California-Berkeley, Berkeley, California 94720, United States
| | - Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
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6
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Mieskes F, Ploetz E, Wehnekamp F, Rat V, Lamb DC. Multicolor 3D Orbital Tracking. Small 2023; 19:e2204726. [PMID: 36709484 DOI: 10.1002/smll.202204726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Feedback-based single-particle tracking (SPT) is a powerful technique for investigating particle behavior with very high spatiotemporal resolution. The ability to follow different species and their interactions independently adds a new dimension to the information available from SPT. However, only a few approaches have been expanded to multiple colors and no method is currently available that can follow two differently labeled biomolecules in 4 dimensions independently. In this proof-of-concept paper, the new modalities available when performing 3D orbital tracking with a second detection channel are demonstrated. First, dual-color tracking experiments are described studying independently diffusing particles of different types. For interacting particles where their motion is correlated, a second modality is implemented where a particle is tracked in one channel and the position of the second fluorescence species is monitored in the other channel. As a third modality, 3D orbital tracking is performed in one channel while monitoring its spectral signature in a second channel. This last modality is used to successfully readout accurate Förster Resonance Energy Transfer (FRET) values over time while tracking a mobile particle.
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Affiliation(s)
- Frank Mieskes
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377, Munich, Germany
- Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799, Munich, Germany
- Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377, Munich, Germany
- Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799, Munich, Germany
- Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Fabian Wehnekamp
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377, Munich, Germany
- Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799, Munich, Germany
- Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Virgile Rat
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377, Munich, Germany
- Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799, Munich, Germany
- Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Don C Lamb
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377, Munich, Germany
- Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799, Munich, Germany
- Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, Munich, Germany
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7
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Andreo J, Ettlinger R, Zaremba O, Peña Q, Lächelt U, de Luis RF, Freund R, Canossa S, Ploetz E, Zhu W, Diercks CS, Gröger H, Wuttke S. Reticular Nanoscience: Bottom-Up Assembly Nanotechnology. J Am Chem Soc 2022; 144:7531-7550. [PMID: 35389641 DOI: 10.1021/jacs.1c11507] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The chemistry of metal-organic and covalent organic frameworks (MOFs and COFs) is perhaps the most diverse and inclusive among the chemical sciences, and yet it can be radically expanded by blending it with nanotechnology. The result is reticular nanoscience, an area of reticular chemistry that has an immense potential in virtually any technological field. In this perspective, we explore the extension of such an interdisciplinary reach by surveying the explored and unexplored possibilities that framework nanoparticles can offer. We localize these unique nanosized reticular materials at the juncture between the molecular and the macroscopic worlds, and describe the resulting synthetic and analytical chemistry, which is fundamentally different from conventional frameworks. Such differences are mirrored in the properties that reticular nanoparticles exhibit, which we described while referring to the present state-of-the-art and future promising applications in medicine, catalysis, energy-related applications, and sensors. Finally, the bottom-up approach of reticular nanoscience, inspired by nature, is brought to its full extension by introducing the concept of augmented reticular chemistry. Its approach departs from a single-particle scale to reach higher mesoscopic and even macroscopic dimensions, where framework nanoparticles become building units themselves and the resulting supermaterials approach new levels of sophistication of structures and properties.
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Affiliation(s)
- Jacopo Andreo
- Basque Center for Materials, UPV/EHU Science Park, Leioa, 48940, Spain
| | - Romy Ettlinger
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, United Kingdom
| | - Orysia Zaremba
- Basque Center for Materials, UPV/EHU Science Park, Leioa, 48940, Spain
| | - Quim Peña
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular Imaging, RWTH Aachen University, Aachen, 52074, Germany
| | - Ulrich Lächelt
- Division of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, 1090, Austria
| | | | - Ralph Freund
- Institute of Physics, Chair of Solid State and Materials Chemistry, Augsburg University, Augsburg, 86150, Germany
| | - Stefano Canossa
- Department of Nanochemistry, Max Planck Institute for Solid State Research, Stuttgart, 70569, Germany
| | - Evelyn Ploetz
- Department of Chemisrty and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München (LMU), Munich, 81377, Germany
| | - Wei Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, P. R. China
| | - Christian S Diercks
- The Scripps Research Institute, SR202, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Bielefeld, 33615, Germany
| | - Stefan Wuttke
- Basque Center for Materials, UPV/EHU Science Park, Leioa, 48940, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, 48009, Spain
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8
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Veth S, Fuchs A, Özdemir D, Dialer C, Drexler DJ, Knechtel F, Witte G, Hopfner KP, Carell T, Ploetz E. Chemical synthesis of the fluorescent, cyclic dinucleotides cthGAMP. Chembiochem 2022; 23:e202200005. [PMID: 35189023 PMCID: PMC9310808 DOI: 10.1002/cbic.202200005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/12/2022] [Indexed: 11/15/2022]
Abstract
The cGAS‐STING pathway is known for its role in sensing cytosolic DNA introduced by a viral infection, bacterial invasion or tumorigenesis. Free DNA is recognized by the cyclic GMP‐AMP synthase (cGAS) catalyzing the production of 2’,3’‐cyclic guanosine monophosphate‐adenosine monophosphate (2’,3’‐cGAMP) in mammals. This cyclic dinucleotide acts as a second messenger, activating the stimulator of interferon genes (STING) that finally triggers the transcription of interferon genes and inflammatory cytokines. Due to the therapeutic potential of this pathway, both the production and the detection of cGAMP via fluorescent moieties for assay development is of great importance. Here, we introduce the paralleled synthetic access to the intrinsically fluorescent, cyclic dinucleotides 2’3’‐cthGAMP and 3’3’‐cthGAMP based on phosphoramidite and phosphate chemistry, adaptable for large scale synthesis. We examine their binding properties to murine and human STING and confirm biological activity including interferon induction by 2’3’‐cthGAMP in THP‐1 monocytes. Two‐photon imaging revealed successful cellular uptake of 2’3’‐cthGAMP in THP‐1 cells.
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Affiliation(s)
- Simon Veth
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Adrian Fuchs
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Dilara Özdemir
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Clemens Dialer
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - David Jan Drexler
- Ludwig-Maximilians-Universität München Genzentrum: Ludwig-Maximilians-Universitat Munchen Genzentrum, Biochemistry, GERMANY
| | - Fabian Knechtel
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Gregor Witte
- Ludwig-Maximilians-Universität München Genzentrum: Ludwig-Maximilians-Universitat Munchen Genzentrum, Biochemistry, GERMANY
| | - Karl-Peter Hopfner
- Ludwig-Maximilians-Universität München Genzentrum: Ludwig-Maximilians-Universitat Munchen Genzentrum, Biochemistry, GERMANY
| | - Thomas Carell
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Evelyn Ploetz
- Ludwig-Maximilians-Universitat Munchen, Chemistry, Butenandtstr 11, 81377, Muenchen, GERMANY
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9
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Fuchs A, Mannhardt P, Hirschle P, Wang H, Zaytseva I, Ji Z, Yaghi O, Wuttke S, Ploetz E. Single Crystals Heterogeneity Impacts the Intrinsic and Extrinsic Properties of Metal-Organic Frameworks. Adv Mater 2022; 34:e2104530. [PMID: 34806239 DOI: 10.1002/adma.202104530] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/03/2021] [Indexed: 06/13/2023]
Abstract
At present, an enormous characterization gap exists between the study of the crystal structure of a material and its bulk properties. Individual particles falling within this gap cannot be fully characterized in a correlative manner by current methods. The authors address this problem by exploiting the noninvasive nature of optical microscopy and spectroscopy for the correlative analysis of metal-organic framework particles in situ. They probe the intrinsic as well as extrinsic properties in a correlated manner. The authors show that the crystal shape of MIL-88A strongly impacts its optical absorption. Furthermore, the question of how homogeneously water is distributed and adsorbed within one of the most promising materials for harvesting water from humid air, MOF-801, is addressed. The results demonstrate the considerable importance of the particle level and how it can affect the property of the material.
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Affiliation(s)
- Adrian Fuchs
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, 81377, Munich, Germany
| | - Petra Mannhardt
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, 81377, Munich, Germany
| | - Patrick Hirschle
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, 81377, Munich, Germany
| | - Haoze Wang
- Department of Chemistry, University of California-Berkeley, Materials Sciences Division, Lawrence Berkeley National Laboratory, Kavli Energy NanoSciences Institute at Berkeley, and Berkeley Global Science Institute, Berkeley, CA, 94720, USA
| | - Irina Zaytseva
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, 81377, Munich, Germany
| | - Zhe Ji
- Department of Chemistry, University of California-Berkeley, Materials Sciences Division, Lawrence Berkeley National Laboratory, Kavli Energy NanoSciences Institute at Berkeley, and Berkeley Global Science Institute, Berkeley, CA, 94720, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Omar Yaghi
- Department of Chemistry, University of California-Berkeley, Materials Sciences Division, Lawrence Berkeley National Laboratory, Kavli Energy NanoSciences Institute at Berkeley, and Berkeley Global Science Institute, Berkeley, CA, 94720, USA
- UC Berkeley-KACST Joint Center of Excellence for Nanomaterials for Clean Energy Applications, King Abdulaziz City for Science and Technology, Riyadh, 11442, Saudi Arabia
| | - Stefan Wuttke
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, 81377, Munich, Germany
- BCMaterials, Basque Center for Materials, UPV/EHU Science Park, Leioa, 48940, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, 81377, Munich, Germany
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10
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Freund R, Zaremba O, Arnauts G, Ameloot R, Skorupskii G, Dincă M, Bavykina A, Gascon J, Ejsmont A, Goscianska J, Kalmutzki M, Lächelt U, Ploetz E, Diercks CS, Wuttke S. Der derzeitige Stand von MOF‐ und COF‐Anwendungen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106259] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ralph Freund
- Institut für Physik Universität Augsburg Deutschland
| | - Orysia Zaremba
- BCMaterials, Basque Center for Materials, UPV/EHU Science Park Leioa 48940 Spanien
- Department of Chemistry University of California-Berkeley USA
| | - Giel Arnauts
- Center for Membrane Separations, Adsorption, Catalysis, and Spectroscopy (cMACS) KU Leuven Belgien
| | - Rob Ameloot
- Center for Membrane Separations, Adsorption, Catalysis, and Spectroscopy (cMACS) KU Leuven Belgien
| | | | - Mircea Dincă
- Department of Chemistry Massachusetts Institute of Technology Cambridge USA
| | - Anastasiya Bavykina
- King Abdullah University of Science and Technology KAUST Catalysis Center (KCC) Advanced Catalytic Materials Saudi Arabien
| | - Jorge Gascon
- King Abdullah University of Science and Technology KAUST Catalysis Center (KCC) Advanced Catalytic Materials Saudi Arabien
| | | | | | | | - Ulrich Lächelt
- Department für Pharmazie und Center for NanoScience (CeNS) LMU München Deutschland
| | - Evelyn Ploetz
- Department Chemie und Center for NanoScience (CeNS) LMU München Deutschland
| | - Christian S. Diercks
- Materials Sciences Division Lawrence Berkeley National Laboratory Kavli Energy NanoSciences Institute Berkeley CA 94720 USA
| | - Stefan Wuttke
- BCMaterials, Basque Center for Materials, UPV/EHU Science Park Leioa 48940 Spanien
- IKERBASQUE, Basque Foundation for Science Bilbao Spanien
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11
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Freund R, Zaremba O, Arnauts G, Ameloot R, Skorupskii G, Dincă M, Bavykina A, Gascon J, Ejsmont A, Goscianska J, Kalmutzki M, Lächelt U, Ploetz E, Diercks CS, Wuttke S. The Current Status of MOF and COF Applications. Angew Chem Int Ed Engl 2021; 60:23975-24001. [DOI: 10.1002/anie.202106259] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Ralph Freund
- Solid State Chemistry University of Augsburg Germany
| | - Orysia Zaremba
- BCMaterials, Basque Center for Materials UPV/EHU Science Park Leioa 48940 Spain
- Department of Chemistry University of California-Berkeley USA
| | - Giel Arnauts
- Center for Membrane Separations, Adsorption, Catalysis and Spectroscopy (cMACS) KU Leuven Belgium
| | - Rob Ameloot
- Center for Membrane Separations, Adsorption, Catalysis and Spectroscopy (cMACS) KU Leuven Belgium
| | | | - Mircea Dincă
- Department of Chemistry Massachusetts Institute of Technology Cambridge USA
| | - Anastasiya Bavykina
- King Abdullah University of Science and Technology KAUST Catalysis Center (KCC) Advanced Catalytic Materials Saudi Arabia
| | - Jorge Gascon
- King Abdullah University of Science and Technology KAUST Catalysis Center (KCC) Advanced Catalytic Materials Saudi Arabia
| | | | | | | | - Ulrich Lächelt
- Department of Pharmacy and Center for NanoScience (CeNS) LMU Munich Germany
| | - Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS) LMU Munich Germany
| | - Christian S. Diercks
- Materials Sciences Division Lawrence Berkeley National Laboratory Kavli Energy NanoSciences Institute Berkeley CA 94720 USA
| | - Stefan Wuttke
- BCMaterials, Basque Center for Materials UPV/EHU Science Park Leioa 48940 Spain
- IKERBASQUE, Basque Foundation for Science Bilbao Spain
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12
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Krause S, Ploetz E, Bohlen J, Schüler P, Yaadav R, Selbach F, Steiner F, Kamińska I, Tinnefeld P. Graphene-on-Glass Preparation and Cleaning Methods Characterized by Single-Molecule DNA Origami Fluorescent Probes and Raman Spectroscopy. ACS Nano 2021; 15:6430-6438. [PMID: 33834769 DOI: 10.1021/acsnano.0c08383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Graphene exhibits outstanding fluorescence quenching properties that can become useful for biophysics and biosensing applications, but it remains challenging to harness these advantages due to the complex transfer procedure of chemical vapor deposition-grown graphene to glass coverslips and the low yield of usable samples. Here, we screen 10 graphene-on-glass preparation methods and present an optimized protocol. To obtain the required quality for single-molecule and super-resolution imaging on graphene, we introduce a graphene screening method that avoids consuming the investigated sample. We apply DNA origami nanostructures to place fluorescent probes at a defined distance on top of graphene-on-glass coverslips. Subsequent fluorescence lifetime imaging directly reports on the graphene quality, as deviations from the expected fluorescence lifetime indicate imperfections. We compare the DNA origami probes with conventional techniques for graphene characterization, including light microscopy, atomic force microscopy, and Raman spectroscopy. For the latter, we observe a discrepancy between the graphene quality implied by Raman spectra in comparison to the quality probed by fluorescence lifetime quenching measured at the same position. We attribute this discrepancy to the difference in the effective area that is probed by Raman spectroscopy and fluorescence quenching. Moreover, we demonstrate the applicability of already screened and positively evaluated graphene for studying single-molecule conformational dynamics on a second DNA origami structure. Our results constitute the basis for graphene-based biophysics and super-resolution microscopy.
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Affiliation(s)
- Stefan Krause
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Johann Bohlen
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Patrick Schüler
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Renukka Yaadav
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Florian Selbach
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Florian Steiner
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Izabela Kamińska
- Institute of Physical Chemistry of the Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 81377 München, Germany
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13
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Ploetz E, Schuurman-Wolters GK, Zijlstra N, Jager AW, Griffith DA, Guskov A, Gouridis G, Poolman B, Cordes T. Structural and biophysical characterization of the tandem substrate-binding domains of the ABC importer GlnPQ. Open Biol 2021; 11:200406. [PMID: 33823661 PMCID: PMC8025302 DOI: 10.1098/rsob.200406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The ATP-binding cassette transporter GlnPQ is an essential uptake system that transports glutamine, glutamic acid and asparagine in Gram-positive bacteria. It features two extra-cytoplasmic substrate-binding domains (SBDs) that are linked in tandem to the transmembrane domain of the transporter. The two SBDs differ in their ligand specificities, binding affinities and their distance to the transmembrane domain. Here, we elucidate the effects of the tandem arrangement of the domains on the biochemical, biophysical and structural properties of the protein. For this, we determined the crystal structure of the ligand-free tandem SBD1-2 protein from Lactococcus lactis in the absence of the transporter and compared the tandem to the isolated SBDs. We also used isothermal titration calorimetry to determine the ligand-binding affinity of the SBDs and single-molecule Förster resonance energy transfer (smFRET) to relate ligand binding to conformational changes in each of the domains of the tandem. We show that substrate binding and conformational changes are not notably affected by the presence of the adjoining domain in the wild-type protein, and changes only occur when the linker between the domains is shortened. In a proof-of-concept experiment, we combine smFRET with protein-induced fluorescence enhancement (PIFE–FRET) and show that a decrease in SBD linker length is observed as a linear increase in donor-brightness for SBD2 while we can still monitor the conformational states (open/closed) of SBD1. These results demonstrate the feasibility of PIFE–FRET to monitor protein–protein interactions and conformational states simultaneously.
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Affiliation(s)
- Evelyn Ploetz
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Department of Chemistry, Center for Nanosciences (CeNS) and Center for Integrated Proteins Science Munich (CiPSM), Ludwig Maximilians-Universität München, Butenandtstraße 11, 81377 Munich, Germany
| | - Gea K Schuurman-Wolters
- Groningen Biomolecular Science and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Niels Zijlstra
- Physical and Synthetic Biology, Faculty of Biology, Großhaderner Straße 2-4, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Amarins W Jager
- Groningen Biomolecular Science and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Douglas A Griffith
- Physical and Synthetic Biology, Faculty of Biology, Großhaderner Straße 2-4, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Albert Guskov
- Groningen Biomolecular Science and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Moscow Institute of Physics and Technology (MIPT), Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141701, Russian Federation
| | - Giorgos Gouridis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Structural Biology Division, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Nikolaou Plastira 100, Heraklion, Crete, Greece
| | - Bert Poolman
- Groningen Biomolecular Science and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Physical and Synthetic Biology, Faculty of Biology, Großhaderner Straße 2-4, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
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14
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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15
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Cao J, Zaremba OT, Lei Q, Ploetz E, Wuttke S, Zhu W. Artificial Bioaugmentation of Biomacromolecules and Living Organisms for Biomedical Applications. ACS Nano 2021; 15:3900-3926. [PMID: 33656324 DOI: 10.1021/acsnano.0c10144] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The synergistic union of nanomaterials with biomaterials has revolutionized synthetic chemistry, enabling the creation of nanomaterial-based biohybrids with distinct properties for biomedical applications. This class of materials has drawn significant scientific interest from the perspective of functional extension via controllable coupling of synthetic and biomaterial components, resulting in enhancement of the chemical, physical, and biological properties of the obtained biohybrids. In this review, we highlight the forefront materials for the combination with biomacromolecules and living organisms and their advantageous properties as well as recent advances in the rational design and synthesis of artificial biohybrids. We further illustrate the incredible diversity of biomedical applications stemming from artificially bioaugmented characteristics of the nanomaterial-based biohybrids. Eventually, we aim to inspire scientists with the application horizons of the exciting field of synthetic augmented biohybrids.
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Affiliation(s)
- Jiangfan Cao
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Orysia T Zaremba
- Basque Center for Materials, UPV/EHU Science Park, Leioa 48940, Spain
- University of California-Berkeley, Berkeley, California 94720, United States
| | - Qi Lei
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Evelyn Ploetz
- Ludwig-Maximilians-Universität (LMU) Munich, Munich 81377, Germany
| | - Stefan Wuttke
- Basque Center for Materials, UPV/EHU Science Park, Leioa 48940, Spain
- Basque Foundation for Science, Bilbao 48009, Spain
| | - Wei Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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16
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Illes B, Fuchs A, Gegenfurtner F, Ploetz E, Zahler S, Vollmar AM, Engelke H. Spatio-selective activation of nuclear translocation of YAP with light directs invasion of cancer cell spheroids. iScience 2021; 24:102185. [PMID: 33718837 PMCID: PMC7921841 DOI: 10.1016/j.isci.2021.102185] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/14/2021] [Accepted: 02/09/2021] [Indexed: 01/09/2023] Open
Abstract
The mechanical properties of the extracellular matrix strongly influence tumor progression and invasion. Yes-associated protein (YAP) has been shown to be a key regulator of this process translating mechanical cues from the extracellular matrix into intracellular signals. Despite its apparent role in tumor progression and metastasis, it is not clear yet, whether YAP activation can actively trigger the onset of invasion. To address this question, we designed a photo-activatable YAP (optoYAP), which allows for spatiotemporal control of its activation. The activation mechanism of optoYAP is based on optically triggered nuclear translocation of the protein. Activation of optoYAP induces downstream signaling for several hours and leads to increased proliferation in two- and three-dimensional cultures. Applied to cancer spheroids, optoYAP activation induces invasion. Site-selective activation of optoYAP in cancer spheroids strikingly directs invasion into the activated direction. Thus, nuclear translocation of YAP may be enough to trigger the onset of invasion. Photoactivation of nuclear translocation of yes-associated protein (YAP) Photoactivation of YAP induces downstream signaling Site-selective activation of YAP triggers directed invasion of cancer spheroids
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Affiliation(s)
- Bernhard Illes
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377 Munich, Germany
| | - Adrian Fuchs
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377 Munich, Germany
| | - Florian Gegenfurtner
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5, 81377 Munich, Germany
| | - Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377 Munich, Germany
| | - Stefan Zahler
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5, 81377 Munich, Germany
| | - Angelika M Vollmar
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstraße 5, 81377 Munich, Germany
| | - Hanna Engelke
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377 Munich, Germany.,Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Humboldtstr. 46, 8010 Graz, Austria
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17
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Girard EB, Fuchs A, Kaliwoda M, Lasut M, Ploetz E, Schmahl WW, Wörheide G. Sponges as bioindicators for microparticulate pollutants? Environ Pollut 2021; 268:115851. [PMID: 33126031 DOI: 10.1016/j.envpol.2020.115851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/14/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Amongst other threats, the world's oceans are faced with man-made pollution, including an increasing number of microparticulate pollutants. Sponges, aquatic filter-feeding animals, are able to incorporate fine foreign particles, and thus may be a potential bioindicator for microparticulate pollutants. To address this question, 15 coral reef demosponges sampled around Bangka Island (North Sulawesi, Indonesia) were analyzed for the nature of their foreign particle content using traditional histological methods, advanced light microscopy, and Raman spectroscopy. Sampled sponges accumulated and embedded the very fine sediment fraction (<200 μm), absent in the surrounding sand, in the ectosome (outer epithelia) and spongin fibers (skeletal elements), which was confirmed by two-photon microscopy. A total of 34 different particle types were identified, of which degraded man-made products, i.e., polystyrene, particulate cotton, titanium dioxide and blue-pigmented particles, were incorporated by eight specimens at concentrations between 91 and 612 particle/g dry sponge tissue. As sponges can weigh several hundreds of grams, we conservatively extrapolate that sponges can incorporate on average 10,000 microparticulate pollutants in their tissue. The uptake of particles, however, appears independent of the material, which suggests that the fluctuation in material ratios is due to the spatial variation of surrounding microparticles. Therefore, particle-bearing sponges have a strong potential to biomonitor microparticulate pollutants, such as microplastics and other degraded industrial products.
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Affiliation(s)
- Elsa B Girard
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany
| | - Adrian Fuchs
- Department of Chemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Melanie Kaliwoda
- SNSB - Mineralogische Staatssammlung München, 80333, München, Germany
| | - Markus Lasut
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Jalan Kampus Unsrat Bahu, Manado, 95115, Sulawesi Utara, Indonesia
| | - Evelyn Ploetz
- Department of Chemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Wolfgang W Schmahl
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany; SNSB - Mineralogische Staatssammlung München, 80333, München, Germany; GeoBio-Center(LMU), Ludwig-Maximilians-Universität München, 80333, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany; GeoBio-Center(LMU), Ludwig-Maximilians-Universität München, 80333, Munich, Germany; SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, 80333, Munich, Germany.
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18
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Ploetz E, Zimpel A, Cauda V, Bauer D, Lamb DC, Haisch C, Zahler S, Vollmar AM, Wuttke S, Engelke H. Metal-Organic Framework Nanoparticles Induce Pyroptosis in Cells Controlled by the Extracellular pH. Adv Mater 2020; 32:e1907267. [PMID: 32182391 DOI: 10.1002/adma.201907267] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 05/21/2023]
Abstract
Ion homeostasis is essential for cellular survival, and elevated concentrations of specific ions are used to start distinct forms of programmed cell death. However, investigating the influence of certain ions on cells in a controlled way has been hampered due to the tight regulation of ion import by cells. Here, it is shown that lipid-coated iron-based metal-organic framework nanoparticles are able to deliver and release high amounts of iron ions into cells. While high concentrations of iron often trigger ferroptosis, here, the released iron induces pyroptosis, a form of cell death involving the immune system. The iron release occurs only in slightly acidic extracellular environments restricting cell death to cells in acidic microenvironments and allowing for external control. The release mechanism is based on endocytosis facilitated by the lipid-coating followed by degradation of the nanoparticle in the lysosome via cysteine-mediated reduction, which is enhanced in slightly acidic extracellular environment. Thus, a new functionality of hybrid nanoparticles is demonstrated, which uses their nanoarchitecture to facilitate controlled ion delivery into cells. Based on the selectivity for acidic microenvironments, the described nanoparticles may also be used for immunotherapy: the nanoparticles may directly affect the primary tumor and the induced pyroptosis activates the immune system.
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Affiliation(s)
- Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
- Nanosystems Initiative Munich (NIM), LMU Munich, Munich, 81377, Germany
- Center for Integrated Protein Science Munich (CiPSM), LMU Munich, Munich, 81377, Germany
| | - Andreas Zimpel
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
| | - Valentina Cauda
- Department of Applied Science and Technology, Politecnico di Torino, Torino, 10129, Italy
| | - David Bauer
- Department of Chemistry, TU Munich, Munich, 81377, Germany
| | - Don C Lamb
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
- Nanosystems Initiative Munich (NIM), LMU Munich, Munich, 81377, Germany
- Center for Integrated Protein Science Munich (CiPSM), LMU Munich, Munich, 81377, Germany
| | | | - Stefan Zahler
- Department of Pharmacy, LMU Munich, Munich, 81377, Germany
| | | | - Stefan Wuttke
- BCMaterials, Basque Center for Materials, UPV/EHU Science Park, Leioa, 48940, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - Hanna Engelke
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
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19
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Ploetz E, Zimpel A, Cauda V, Bauer D, Lamb DC, Haisch C, Zahler S, Vollmar AM, Wuttke S, Engelke H. Metal-Organic Framework Nanoparticles Induce Pyroptosis in Cells Controlled by the Extracellular pH. Adv Mater 2020; 32:e1907267. [PMID: 32182391 DOI: 10.1002/adfm.201909062] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 05/23/2023]
Abstract
Ion homeostasis is essential for cellular survival, and elevated concentrations of specific ions are used to start distinct forms of programmed cell death. However, investigating the influence of certain ions on cells in a controlled way has been hampered due to the tight regulation of ion import by cells. Here, it is shown that lipid-coated iron-based metal-organic framework nanoparticles are able to deliver and release high amounts of iron ions into cells. While high concentrations of iron often trigger ferroptosis, here, the released iron induces pyroptosis, a form of cell death involving the immune system. The iron release occurs only in slightly acidic extracellular environments restricting cell death to cells in acidic microenvironments and allowing for external control. The release mechanism is based on endocytosis facilitated by the lipid-coating followed by degradation of the nanoparticle in the lysosome via cysteine-mediated reduction, which is enhanced in slightly acidic extracellular environment. Thus, a new functionality of hybrid nanoparticles is demonstrated, which uses their nanoarchitecture to facilitate controlled ion delivery into cells. Based on the selectivity for acidic microenvironments, the described nanoparticles may also be used for immunotherapy: the nanoparticles may directly affect the primary tumor and the induced pyroptosis activates the immune system.
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Affiliation(s)
- Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
- Nanosystems Initiative Munich (NIM), LMU Munich, Munich, 81377, Germany
- Center for Integrated Protein Science Munich (CiPSM), LMU Munich, Munich, 81377, Germany
| | - Andreas Zimpel
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
| | - Valentina Cauda
- Department of Applied Science and Technology, Politecnico di Torino, Torino, 10129, Italy
| | - David Bauer
- Department of Chemistry, TU Munich, Munich, 81377, Germany
| | - Don C Lamb
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
- Nanosystems Initiative Munich (NIM), LMU Munich, Munich, 81377, Germany
- Center for Integrated Protein Science Munich (CiPSM), LMU Munich, Munich, 81377, Germany
| | | | - Stefan Zahler
- Department of Pharmacy, LMU Munich, Munich, 81377, Germany
| | | | - Stefan Wuttke
- BCMaterials, Basque Center for Materials, UPV/EHU Science Park, Leioa, 48940, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - Hanna Engelke
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
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20
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Heiss G, Ploetz E, Voith von Voithenberg L, Viswanathan R, Glaser S, Schluesche P, Madhira S, Meisterernst M, Auble DT, Lamb DC. Conformational changes and catalytic inefficiency associated with Mot1-mediated TBP-DNA dissociation. Nucleic Acids Res 2019; 47:2793-2806. [PMID: 30649478 PMCID: PMC6451094 DOI: 10.1093/nar/gky1322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 12/21/2018] [Accepted: 01/07/2019] [Indexed: 11/12/2022] Open
Abstract
The TATA-box Binding Protein (TBP) plays a central role in regulating gene expression and is the first step in the process of pre-initiation complex (PIC) formation on promoter DNA. The lifetime of TBP at the promoter site is controlled by several cofactors including the Modifier of transcription 1 (Mot1), an essential TBP-associated ATPase. Based on ensemble measurements, Mot1 can use adenosine triphosphate (ATP) hydrolysis to displace TBP from DNA and various models for how this activity is coupled to transcriptional regulation have been proposed. However, the underlying molecular mechanism of Mot1 action is not well understood. In this work, the interaction of Mot1 with the DNA/TBP complex was investigated by single-pair Förster resonance energy transfer (spFRET). Upon Mot1 binding to the DNA/TBP complex, a transition in the DNA/TBP conformation was observed. Hydrolysis of ATP by Mot1 led to a conformational change but was not sufficient to efficiently disrupt the complex. SpFRET measurements of dual-labeled DNA suggest that Mot1's ATPase activity primes incorrectly oriented TBP for dissociation from DNA and additional Mot1 in solution is necessary for TBP unbinding. These findings provide a framework for understanding how the efficiency of Mot1's catalytic activity is tuned to establish a dynamic pool of TBP without interfering with stable and functional TBP-containing complexes.
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Affiliation(s)
- Gregor Heiss
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Evelyn Ploetz
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Lena Voith von Voithenberg
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Ramya Viswanathan
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Samson Glaser
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Peter Schluesche
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Sushi Madhira
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
| | - Michael Meisterernst
- Institut für Molekulare Tumorbiologie, Westfälische Wilhelms-Universität, Münster 48149, Germany
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Don C Lamb
- Department für Chemie, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität, München 81377, Germany
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21
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Ploetz E, Barth A, Voith von Voithenberg L, Agam G, Lamb DC. Elucidating the Molecular Binding Mechanism of the Tata-Binding Protein using Pie-Pife. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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22
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Jazi AA, Ploetz E, Arizki M, Dhandayuthapani B, Waclawska I, Krämer R, Ziegler C, Cordes T. Caging and Photoactivation in Single-Molecule Förster Resonance Energy Transfer Experiments. Biochemistry 2017; 56:2031-2041. [PMID: 28362086 PMCID: PMC5390306 DOI: 10.1021/acs.biochem.6b00916] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Caged
organic fluorophores are established tools for localization-based
super-resolution imaging. Their use relies on reversible deactivation
of standard organic fluorophores by chemical reduction or commercially
available caged dyes with ON switching of the fluorescent signal by
ultraviolet (UV) light. Here, we establish caging of cyanine fluorophores
and caged rhodamine dyes, i.e., chemical deactivation of fluorescence,
for single-molecule Förster resonance energy transfer (smFRET)
experiments with freely diffusing molecules. They allow temporal separation
and sorting of multiple intramolecular donor–acceptor pairs
during solution-based smFRET. We use this “caged FRET”
methodology for the study of complex biochemical species such as multisubunit
proteins or nucleic acids containing more than two fluorescent labels.
Proof-of-principle experiments and a characterization of the uncaging
process in the confocal volume are presented. These reveal that chemical
caging and UV reactivation allow temporal uncoupling of convoluted
fluorescence signals from, e.g., multiple spectrally similar donor
or acceptor molecules on nucleic acids. We also use caging without
UV reactivation to remove unwanted overlabeled species in experiments
with the homotrimeric membrane transporter BetP. We finally outline
further possible applications of the caged FRET methodology, such
as the study of weak biochemical interactions, which are otherwise
impossible with diffusion-based smFRET techniques because of the required
low concentrations of fluorescently labeled biomolecules.
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Affiliation(s)
- Atieh Aminian Jazi
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Institute of Biophysics and Biophysical Chemistry, Universität Regensburg , 95053 Regensburg, Germany
| | - Evelyn Ploetz
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Muhamad Arizki
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | - Izabela Waclawska
- Institute of Biophysics and Biophysical Chemistry, Universität Regensburg , 95053 Regensburg, Germany
| | - Reinhard Krämer
- Institute for Biochemistry, Universität Köln , 50674 Köln, Germany
| | - Christine Ziegler
- Institute of Biophysics and Biophysical Chemistry, Universität Regensburg , 95053 Regensburg, Germany
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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23
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Lerner E, Ploetz E, Hohlbein J, Cordes T, Weiss S. A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET). J Phys Chem B 2016; 120:6401-10. [PMID: 27184889 PMCID: PMC4939467 DOI: 10.1021/acs.jpcb.6b03692] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Single-molecule,
protein-induced fluorescence enhancement (PIFE)
serves as a molecular ruler at molecular distances inaccessible to
other spectroscopic rulers such as Förster-type resonance energy
transfer (FRET) or photoinduced electron transfer. In order to provide
two simultaneous measurements of two distances on different molecular
length scales for the analysis of macromolecular complexes, we and
others recently combined measurements of PIFE and FRET (PIFE-FRET)
on the single molecule level. PIFE relies on steric hindrance of the
fluorophore Cy3, which is covalently attached to a biomolecule of
interest, to rotate out of an excited-state trans isomer to the cis isomer through a 90° intermediate.
In this work, we provide a theoretical framework that accounts for
relevant photophysical and kinetic parameters of PIFE-FRET, show how
this framework allows the extraction of the fold-decrease in isomerization
mobility from experimental data, and show how these results provide
information on changes in the accessible volume of Cy3. The utility
of this model is then demonstrated for experimental results on PIFE-FRET
measurement of different protein–DNA interactions. The proposed
model and extracted parameters could serve as a benchmark to allow
quantitative comparison of PIFE effects in different biological systems.
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Affiliation(s)
- Eitan Lerner
- Department of Chemistry and Biochemistry, University of California Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Evelyn Ploetz
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University and Research , Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.,Microspectroscopy Centre, Wageningen University and Research , Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
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Gouridis G, Schuurman-Wolters GK, Ploetz E, Husada F, Vietrov R, de Boer M, Cordes T, Poolman B. Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ. Nat Struct Mol Biol 2014; 22:57-64. [DOI: 10.1038/nsmb.2929] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/06/2014] [Indexed: 11/09/2022]
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25
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van der Velde JHM, Oelerich J, Huang J, Smit JH, Hiermaier M, Ploetz E, Herrmann A, Roelfes G, Cordes T. The Power of Two: Covalent Coupling of Photostabilizers for Fluorescence Applications. J Phys Chem Lett 2014; 5:3792-3798. [PMID: 26278749 DOI: 10.1021/jz501874f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Fluorescence is a versatile tool for spectroscopic investigations and imaging of dynamic processes and structures across various scientific disciplines. The photophysical performance, that is, signal stability and signal duration, of the employed fluorophores is a major limiting factor. In this Letter, we propose a general concept to covalently link molecules, which are known for their positive effect in photostabilization, to form a combined photostabilizer with new properties. The direct linkage of two (or more) photostabilizers will allow one to obtain combined or synergetic effects in fluorophore stabilization and can simplify the preparation of imaging buffers that would otherwise require a mixture of photostabilizers for optimal performance. This concept was explored by synthesizing a molecule with a reducing and oxidizing moiety that is referred to as internal ROXS or "iROXS". Using single-molecule fluorescence microscopy, inter- and intramolecular healing of iROXS was observed, that is, strongly reduced blinking and increased photostability of the cyanine fluorophore Cy5. Moreover, it is shown that a covalently coupled photostabilizer can replace a mixture of molecules needed to make a functional photostabilizing ROXS buffer and might hence represent the new standard for defined and reproducible imaging conditions in single-molecule experiments. In self-healing fluorophores with intramolecular triplet-state quenching, an unprecedented photostability increase of >100-fold was obtained when using iROXS, which is even competitive with solution-based healing. Control experiments show that the oxidizing part of the iROXS molecule, an aromatic nitro group, dominates the healing process. The suggested synthetic concept and the proof-of-concept experiments represent the starting point for the quest to identify optimal combinations of linked photostabilizers for various fluorescence applications.
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Ploetz E, Visser B, Slingenbergh W, Evers K, Martinez-Martinez D, Pei YT, Feringa BL, De Hosson JTM, Cordes T, van Dorp WF. Selective functionalization of patterned glass surfaces. J Mater Chem B 2014; 2:2606-2615. [DOI: 10.1039/c3tb21763a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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van der Velde JHM, Ploetz E, Hiermaier M, Oelerich J, de Vries JW, Roelfes G, Cordes T. Mechanism of intramolecular photostabilization in self-healing cyanine fluorophores. Chemphyschem 2013; 14:4084-93. [PMID: 24302532 DOI: 10.1002/cphc.201300785] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Indexed: 11/06/2022]
Abstract
Organic fluorophores, which are popular labels for microscopy applications, intrinsically suffer from transient and irreversible excursions to dark-states. An alternative to adding photostabilizers at high concentrations to the imaging buffer relies on the direct linkage to the fluorophore. However, the working principles of this approach are not yet fully understood. In this contribution, we investigate the mechanism of intramolecular photostabilization in self-healing cyanines, in which photodamage is automatically repaired. Experimental evidence is provided to demonstrate that a single photostabilizer, that is, the vitamin E derivative Trolox, efficiently heals the cyanine fluorophore Cy5 in the absence of any photostabilizers in solution. A plausible mechanism is that Trolox interacts with the fluorophore through intramolecular quenching of triplet-related dark-states, which is a mechanism that appears to be common for both triplet-state quenchers (cyclooctatetraene) and redox-active compounds (Trolox, ascorbic acid, methylviologen). Additionally, the influence of solution-additives, such as cysteamine and procatechuic acid, on the self-healing process are studied. The results suggest the potential applicability of self-healing fluorophores in stochastic optical reconstruction microscopy (STORM) with optical super-resolution. The presented data contributes to an improved understanding of the mechanism involved in intramolecular photostabilization and has high relevance for the future development of self-healing fluorophores, including their applications in various research fields.
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Affiliation(s)
- Jasper H M van der Velde
- Molecular Microscopy Research Group & Single-molecule Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands), Fax: (+31) 50-363-9199
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28
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Herzog TT, Ryseck G, Ploetz E, Cordes T. The photochemical ring opening reaction of chromene as seen by transient absorption and fluorescence spectroscopy. Photochem Photobiol Sci 2013; 12:1202-9. [DOI: 10.1039/c3pp50020a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Abstract
In femtosecond stimulated Raman microscopy (FSRM) a spectrally broad pulse (Raman probe) and a spectrally narrow pulse (Raman pump) interact in a sample and thereby generate a Raman spectrum of the focal volume. Here a novel light source for FSRM is presented. It consists of an 8-fs laser (repetition rate of 75 MHz) operating as Raman probe. A Yb(3+) based fiber amplifier generates the Raman pump light at 980 nm. The amplifier is seeded by the spectral wing of the 8-fs laser output which ensures synchronisation of pump and probe pulses. Spectral and temporal characteristics of these pulses are reported and simultaneous recording of broadband Raman spectra relying on these pulses is demonstrated.
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Affiliation(s)
- E Ploetz
- Lehrstuhl für BioMolekulare Optik and Center of Integrated Protein Science Munich Fakultät für Physik, Ludwig-Maximilians-Universität München Oettingenstr 67, D-80538 München, Germany
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