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Kostyuk AI, Rapota DD, Morozova KI, Fedotova AA, Jappy D, Semyanov AV, Belousov VV, Brazhe NA, Bilan DS. Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy. Free Radic Biol Med 2024; 217:68-115. [PMID: 38508405 DOI: 10.1016/j.freeradbiomed.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/10/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.
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Affiliation(s)
- Alexander I Kostyuk
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia
| | - Diana D Rapota
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Kseniia I Morozova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna A Fedotova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - David Jappy
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia
| | - Alexey V Semyanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; Sechenov First Moscow State Medical University, Moscow, 119435, Russia; College of Medicine, Jiaxing University, Jiaxing, Zhejiang Province, 314001, China
| | - Vsevolod V Belousov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia; Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia; Life Improvement by Future Technologies (LIFT) Center, Skolkovo, Moscow, 143025, Russia
| | - Nadezda A Brazhe
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Dmitry S Bilan
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia.
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2
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Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
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Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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3
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Li SA, Meng XY, Zhang YJ, Chen CL, Jiao YX, Zhu YQ, Liu PP, Sun W. Progress in pH-Sensitive sensors: essential tools for organelle pH detection, spotlighting mitochondrion and diverse applications. Front Pharmacol 2024; 14:1339518. [PMID: 38269286 PMCID: PMC10806205 DOI: 10.3389/fphar.2023.1339518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
pH-sensitive fluorescent proteins have revolutionized the field of cellular imaging and physiology, offering insight into the dynamic pH changes that underlie fundamental cellular processes. This comprehensive review explores the diverse applications and recent advances in the use of pH-sensitive fluorescent proteins. These remarkable tools enable researchers to visualize and monitor pH variations within subcellular compartments, especially mitochondria, shedding light on organelle-specific pH regulation. They play pivotal roles in visualizing exocytosis and endocytosis events in synaptic transmission, monitoring cell death and apoptosis, and understanding drug effects and disease progression. Recent advancements have led to improved photostability, pH specificity, and subcellular targeting, enhancing their utility. Techniques for multiplexed imaging, three-dimensional visualization, and super-resolution microscopy are expanding the horizon of pH-sensitive protein applications. The future holds promise for their integration into optogenetics and drug discovery. With their ever-evolving capabilities, pH-sensitive fluorescent proteins remain indispensable tools for unravelling cellular dynamics and driving breakthroughs in biological research. This review serves as a comprehensive resource for researchers seeking to harness the potential of pH-sensitive fluorescent proteins.
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Affiliation(s)
- Shu-Ang Li
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiao-Yan Meng
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying-Jie Zhang
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Cai-Li Chen
- Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yu-Xue Jiao
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yong-Qing Zhu
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Pei-Pei Liu
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Sun
- Department of Burn and Repair Reconstruction, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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4
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Schmitt FJ, Mehmood AS, Tüting C, Phan HT, Reisdorf J, Rieder F, Ghane Golmohamadi F, Verma R, Kastritis PL, Laufer J. Effect of Molecular Dynamics and Internal Water Contact on the Photophysical Properties of Red pH-Sensitive Proteins. Biochemistry 2024; 63:82-93. [PMID: 38085825 DOI: 10.1021/acs.biochem.3c00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The pH dependence of the absorption and (time-resolved) fluorescence of two red-shifted fluorescent proteins, mCardinal and mNeptune, was investigated. Decay-associated spectra were measured following fluorescence excitation at 470 nm in PBS buffer with a pH that ranged from 5.5 to 8.0. The fluorescence of both proteins shows two different decay components. mCardinal exhibits an increase in the long-lived fluorescence component with acidification from 1.34 ns at pH 8.0 to 1.62 ns at pH 5.5. An additional fast decay component with 0.64 ns at pH 8.0 up to 1.1 ns at pH 5.5 was found to be blue-shifted compared to the long-lived component. The fluorescence lifetime of mNeptune is insensitive to pH. DAS of mCardinal were simulated assuming a coupled two-level system to describe the 1S state of the chromophore within two different conformations of the protein. MD simulations were conducted to correlate the experimentally observed pH-induced change in the lifetime in mCardinal with its molecular properties. While the chromophores of both protein variants are stabilized by the same number of hydrogen bonds, it was found that the chromophore in mCardinal exhibits more water contacts compared to mNeptune. In mCardinal, interaction between the chromophore and Glu-145 is reduced as compared to mNeptune, but interaction with Thr-147 which is Ser-147 in mNeptune is stronger in mCardinal. Therefore, the dynamics of the excited-state proton transfer (ESPT) might be different in mCardinal and mNeptune. The pH dependency of ESPT is suggested as a key mechanism for pH sensitivity.
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Affiliation(s)
- Franz-Josef Schmitt
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
| | - Amna Shah Mehmood
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06120 Halle, Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Hoang Trong Phan
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
- INM-Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Judith Reisdorf
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
| | - Fabian Rieder
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
| | - Farzin Ghane Golmohamadi
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
| | | | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06120 Halle, Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Jan Laufer
- Institute of Physics, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120 Halle, Saale, Germany
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Shen Y, Wen Y, Sposini S, Vishwanath AA, Abdelfattah AS, Schreiter ER, Lemieux MJ, de Juan-Sanz J, Perrais D, Campbell RE. Rational Engineering of an Improved Genetically Encoded pH Sensor Based on Superecliptic pHluorin. ACS Sens 2023; 8:3014-3022. [PMID: 37481776 DOI: 10.1021/acssensors.3c00484] [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] [Indexed: 07/25/2023]
Abstract
Genetically encoded pH sensors based on fluorescent proteins are valuable tools for the imaging of cellular events that are associated with pH changes, such as exocytosis and endocytosis. Superecliptic pHluorin (SEP) is a pH-sensitive green fluorescent protein (GFP) variant widely used for such applications. Here, we report the rational design, development, structure, and applications of Lime, an improved SEP variant with higher fluorescence brightness and greater pH sensitivity. The X-ray crystal structure of Lime supports the mechanistic rationale that guided the introduction of beneficial mutations. Lime provides substantial improvements relative to SEP for imaging of endocytosis and exocytosis. Furthermore, Lime and its variants are advantageous for a broader range of applications including the detection of synaptic release and neuronal voltage changes.
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Affiliation(s)
- Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yurong Wen
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Silvia Sposini
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux, Bordeaux 33076, France
- Department of Metabolism, Digestion and Reproduction, Institute of Reproductive and Developmental Biology, Imperial College London, London SW7 2BX, United Kingdom
| | - Anjali Amrapali Vishwanath
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, APHP, Häpital de la Pitié Salpêtrière, Sorbonne Université, 75013 Paris, France
| | - Ahmed S Abdelfattah
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virgina 20147, United States
- Department of Neuroscience, Brown University, Providence, Rhode Island 02906, United States
| | - Eric R Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virgina 20147, United States
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jaime de Juan-Sanz
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, APHP, Häpital de la Pitié Salpêtrière, Sorbonne Université, 75013 Paris, France
| | - David Perrais
- CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux, Bordeaux 33076, France
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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6
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FLIM for Evaluation of Difference in Metabolic Status between Native and Differentiated from iPSCs Dermal Papilla Cells. Cells 2022; 11:cells11172730. [PMID: 36078136 PMCID: PMC9454864 DOI: 10.3390/cells11172730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 12/29/2022] Open
Abstract
iPSCs and their derivatives are the most promising cell sources for creating skin equivalents. However, their properties are not fully understood. In addition, new approaches and parameters are needed for studying cells in 3D models without destroying their organization. Thus, the aim of our work was to study and compare the metabolic status and pH of dermal spheroids created from dermal papilla cells differentiated from pluripotent stem cells (iDP) and native dermal papilla cells (hDP) using fluorescence microscopy and fluorescence lifetime imaging microscopy (FLIM). For this purpose, fluorescence intensities of NAD(P)H and FAD, fluorescence lifetimes, and the contributions of NAD(P)H, as well as the fluorescence intensities of SypHer-2 and BCECF were measured. iDP in spheroids were characterized by a more glycolytic phenotype and alkaline intra-cellular pH in comparison with hDP cells. Moreover, the metabolic activity of iDP in spheroids depends on the source of stem cells from which they were obtained. So, less differentiated and condensed spheroids from iDP-iPSDP and iDP-iPSKYOU are characterized by a more glycolytic phenotype compared to dense spheroids from iDP-DYP0730 and iDP-hES. FLIM and fluorescent microscopy in combination with the metabolism and pH are promising tools for minimally invasive and long-term analyses of 3D models based on stem cells.
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7
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Grabarek D, Andruniów T. Quantum chemistry study of the multiphoton absorption in enhanced green fluorescent protein at the single amino acid residue level. Chemphyschem 2022; 23:e202200335. [PMID: 35875840 DOI: 10.1002/cphc.202200335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/17/2022] [Indexed: 11/11/2022]
Abstract
The chromophore (CRO) of fluorescent proteins (FPs) is embedded in a complex environment that is a source of specific interactions with the CRO. Understanding how these interactions influence FPs spectral properties is important for a directed design of novel markers with desired characteristics. In this work, we apply computational chemistry methods to gain insight into one-, two- and three-photon absorption (1PA, 2PA, 3PA) tuning in enhanced green fluorescent protein (EGFP). To achieve this goal, we built EGFP models differing in: i) number and position of hydrogen-bonds (h-bonds) donors to the CRO and ii) the electric field, as approximated by polarizable force field, acting on the CRO. We find that h-bonding to the CRO's phenolate oxygen results in stronger one- and multiphoton absorption. The brighter absorption can be also achieved by creating more positive electric field near the CRO's phenolate moiety. Interestingly, while individual CRO-environment h-bonds usually enhance 1PA and 2PA, it takes a few h-bond donors to enhance 3PA. Clearly, response of the absorption intensity to many-body effects depends on the excitation mechanism. We further employ symmetry-adapted perturbation theory (SAPT) to reveal excellent (2PA) and good (3PA) correlation of multiphoton intensity with electrostatic and induction interaction energies. This points to importance of accounting for mutual CRO-environment polarization in quantitative calculations of absorption spectra in FPs.
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Affiliation(s)
| | - Tadeusz Andruniów
- Wroclaw University of Science and Technology, Chemistry, Wyb. Wyspianskiego, 30-516, Wroclaw, POLAND
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Morioka E, Kasuga Y, Kanda Y, Moritama S, Koizumi H, Yoshikawa T, Miura N, Ikeda M, Higashida H, Holmes TC, Ikeda M. Mitochondrial LETM1 drives ionic and molecular clock rhythms in circadian pacemaker neurons. Cell Rep 2022; 39:110787. [PMID: 35545046 DOI: 10.1016/j.celrep.2022.110787] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/14/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022] Open
Abstract
The mechanisms that generate robust ionic oscillation in circadian pacemaker neurons are under investigation. Here, we demonstrate critical functions of the mitochondrial cation antiporter leucine zipper-EF-hand-containing transmembrane protein 1 (LETM1), which exchanges K+/H+ in Drosophila and Ca2+/H+ in mammals, in circadian pacemaker neurons. Letm1 knockdown in Drosophila pacemaker neurons reduced circadian cytosolic H+ rhythms and prolonged nuclear PERIOD/TIMELESS expression rhythms and locomotor activity rhythms. In rat pacemaker neurons in the hypothalamic suprachiasmatic nucleus (SCN), circadian rhythms in cytosolic Ca2+ and Bmal1 transcription were dampened by Letm1 knockdown. Mitochondrial Ca2+ uptake peaks late during the day were also observed in rat SCN neurons following photolytic elevation of cytosolic Ca2+. Since cation transport by LETM1 is coupled to mitochondrial energy synthesis, we propose that LETM1 integrates metabolic, ionic, and molecular clock rhythms in the central clock system in both invertebrates and vertebrates.
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Affiliation(s)
- Eri Morioka
- Graduate School of Science and Engineering, University of Toyama, Gofuku, Toyama 930-8555, Japan
| | - Yusuke Kasuga
- Graduate School of Science and Engineering, University of Toyama, Gofuku, Toyama 930-8555, Japan
| | - Yuzuki Kanda
- Graduate School of Science and Engineering, University of Toyama, Gofuku, Toyama 930-8555, Japan
| | - Saki Moritama
- Graduate School of Science and Engineering, University of Toyama, Gofuku, Toyama 930-8555, Japan
| | - Hayato Koizumi
- Graduate School of Innovative Life Science, University of Toyama, Gofuku, Toyama 930-8555, Japan
| | - Tomoko Yoshikawa
- Organization for International Education and Exchange, University of Toyama, Toyama 930-8555, Japan
| | - Nobuhiko Miura
- Department of Health Medicine, Yokohama University of Pharmacy, Yokohama, Kanagawa 245-0061, Japan
| | - Masaaki Ikeda
- Department of Physiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Haruhiro Higashida
- Research Center for Child Mental Development, Kanazawa University, Ishikawa 920-8640, Japan
| | - Todd C Holmes
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Masayuki Ikeda
- Graduate School of Innovative Life Science, University of Toyama, Gofuku, Toyama 930-8555, Japan; Organization for International Education and Exchange, University of Toyama, Toyama 930-8555, Japan.
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Wu SY, Shen Y, Shkolnikov I, Campbell RE. Fluorescent Indicators For Biological Imaging of Monatomic Ions. Front Cell Dev Biol 2022; 10:885440. [PMID: 35573682 PMCID: PMC9093666 DOI: 10.3389/fcell.2022.885440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Monatomic ions play critical biological roles including maintaining the cellular osmotic pressure, transmitting signals, and catalyzing redox reactions as cofactors in enzymes. The ability to visualize monatomic ion concentration, and dynamic changes in the concentration, is essential to understanding their many biological functions. A growing number of genetically encodable and synthetic indicators enable the visualization and detection of monatomic ions in biological systems. With this review, we aim to provide a survey of the current landscape of reported indicators. We hope this review will be a useful guide to researchers who are interested in using indicators for biological applications and to tool developers seeking opportunities to create new and improved indicators.
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Affiliation(s)
- Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Irene Shkolnikov
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
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10
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Karsten L, Goett-Zink L, Schmitz J, Hoffrogge R, Grünberger A, Kottke T, Müller KM. Genetically Encoded Ratiometric pH Sensors for the Measurement of Intra- and Extracellular pH and Internalization Rates. BIOSENSORS 2022; 12:bios12050271. [PMID: 35624572 PMCID: PMC9138566 DOI: 10.3390/bios12050271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
Abstract
pH-sensitive fluorescent proteins as genetically encoded pH sensors are promising tools for monitoring intra- and extracellular pH. However, there is a lack of ratiometric pH sensors, which offer a good dynamic range and can be purified and applied extracellularly to investigate uptake. In our study, the bright fluorescent protein CoGFP_V0 was C-terminally fused to the ligand epidermal growth factor (EGF) and retained its dual-excitation and dual-emission properties as a purified protein. The tandem fluorescent variants EGF-CoGFP-mTagBFP2 (pK′ = 6.6) and EGF-CoGFP-mCRISPRed (pK′ = 6.1) revealed high dynamic ranges between pH 4.0 and 7.5. Using live-cell fluorescence microscopy, both pH sensor molecules permitted the conversion of fluorescence intensity ratios to detailed intracellular pH maps, which revealed pH gradients within endocytic vesicles. Additionally, extracellular binding of the pH sensors to cells expressing the EGF receptor (EGFR) enabled the tracking of pH shifts inside cultivation chambers of a microfluidic device. Furthermore, the dual-emission properties of EGF-CoGFP-mCRISPRed upon 488 nm excitation make this pH sensor a valuable tool for ratiometric flow cytometry. This high-throughput method allowed for the determination of internalization rates, which represents a promising kinetic parameter for the in vitro characterization of protein–drug conjugates in cancer therapy.
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Affiliation(s)
- Lennard Karsten
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Lukas Goett-Zink
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Julian Schmitz
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Raimund Hoffrogge
- Cell Culture Technology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany; (J.S.); (A.G.)
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Biophysical Chemistry and Diagnostics, Medical School OWL, Faculty of Chemistry, Bielefeld University, 33615 Bielefeld, Germany; (L.G.-Z.); (T.K.)
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
- Correspondence:
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11
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Grabarek D, Andruniów T. The role of hydrogen bonds and electrostatic interactions in enhancing two-photon absorption in green and yellow fluorescent proteins. Chemphyschem 2022; 23:e202200003. [PMID: 35130370 DOI: 10.1002/cphc.202200003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Indexed: 11/07/2022]
Abstract
The spectral properties of fluorescent proteins (FPs) depend on the protein environment of the chromophore (CRO). A deeper understanding of the CRO - environment interactions in terms of FPs spectral characteristics will allow for a rational design of novel markers with desired properties. Here, we are taking a step towards achieving this important goal. With the time-dependent density functional theory (TDDFT), we calculate one- and two-photon absorption (OPA and TPA) spectra for 5 green FPs (GFPs) and 3 yellow FPs (YFPs) differing in amino acid sequence. The goal is to reveal a role of: (i) electrostatic interactions, (ii) hydrogen-bonds (h-bonds), and (iii) h-bonds together with distant electrostatic field in absorption spectra tuning. Our results point to design hypothesis towards FPs optimised for TPA-based applications. Both h-bonds and electrostatic interactions co-operate in enhancing TPA cross-section (σ TPA ) for the S 0 ->S 1 transition in GFPs. Furthermore, it seems that details of h-bonds network in the CRO's vicinity influences σ TPA response to CRO - environment electrostatic interactions in YFPs. We postulate that engineering FPs with more hydrophilic CRO's environment can lead to greater σ TPA . We also find that removing h-bonds formed with the CRO's phenolate leads to TPA enhancement for transition to higher excited states than S 1 . Particularly Y145 and T203 residues are important in this regard.
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Affiliation(s)
- Dawid Grabarek
- Department of Chemistry, Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Tadeusz Andruniów
- Department of Chemistry, Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
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12
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Linders PTA, Ioannidis M, ter Beest M, van den Bogaart G. Fluorescence Lifetime Imaging of pH along the Secretory Pathway. ACS Chem Biol 2022; 17:240-251. [PMID: 35000377 PMCID: PMC8787756 DOI: 10.1021/acschembio.1c00907] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Many cellular processes
are dependent on correct pH levels, and
this is especially important for the secretory pathway. Defects in
pH homeostasis in distinct organelles cause a wide range of diseases,
including disorders of glycosylation and lysosomal storage diseases.
Ratiometric imaging of the pH-sensitive mutant of green fluorescent
protein, pHLuorin, has allowed for targeted pH measurements in various
organelles, but the required sequential image acquisition is intrinsically
slow and therefore the temporal resolution is unsuitable to follow
the rapid transit of cargo between organelles. Therefore, we applied
fluorescence lifetime imaging microscopy (FLIM) to measure intraorganellar
pH with just a single excitation wavelength. We first validated this
method by confirming the pH in multiple compartments along the secretory
pathway and compared the pH values obtained by the FLIM-based measurements
with those obtained by conventional ratiometric imaging. Then, we
analyzed the dynamic pH changes within cells treated with Bafilomycin
A1, to block the vesicular ATPase, and Brefeldin A, to block endoplasmic
reticulum (ER)–Golgi trafficking. Finally, we followed the
pH changes of newly synthesized molecules of the inflammatory cytokine
tumor necrosis factor-α while they were in transit from the
ER via the Golgi to the plasma membrane. The toolbox we present here
can be applied to measure intracellular pH with high spatial and temporal
resolution and can be used to assess organellar pH in disease models.
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Affiliation(s)
- Peter T. A. Linders
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Melina Ioannidis
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Martin ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
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13
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Tang L, Fang C. Fluorescence Modulation by Ultrafast Chromophore Twisting Events: Developing a Powerful Toolset for Fluorescent-Protein-Based Imaging. J Phys Chem B 2021; 125:13610-13623. [PMID: 34883016 DOI: 10.1021/acs.jpcb.1c08570] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The advancement of modern life sciences has benefited tremendously from the discovery and development of fluorescent proteins (FPs), widely expressed in live cells to track a myriad of cellular events. The chromophores of various FPs can undergo many ultrafast photophysical and/or photochemical processes in the electronic excited state and emit fluorescence with different colors. However, the chromophore becomes essentially nonfluorescent in solution environment due to its intrinsic twisting capability upon photoexcitation. To study "microscopic" torsional events and their effects on "macroscopic" fluorescence, we have developed an integrated ultrafast characterization platform involving femtosecond transient absorption (fs-TA) and wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS). A wide range of naturally occurring, circularly permuted, non-canonical amino-acid-decorated FPs and FP-based optical highlighters with photochromicity, photoconversion, and/or photoswitching capabilities have been recently investigated in great detail. Twisting conformational motions were elucidated to exist in all of these systems but to various extents. The associated different ultrafast pathways can be monitored via frequency changes of characteristic Raman bands during primary events and functional processes. The mapped electronic and structural dynamics information is crucial and has shown great potential and initial success for the rational design of proteins and other photoreceptors with novel functions and fluorescence properties.
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Affiliation(s)
- Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, United States
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331-4003, United States
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14
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Ovechkina VS, Zakian SM, Medvedev SP, Valetdinova KR. Genetically Encoded Fluorescent Biosensors for Biomedical Applications. Biomedicines 2021; 9:biomedicines9111528. [PMID: 34829757 PMCID: PMC8615007 DOI: 10.3390/biomedicines9111528] [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] [Received: 09/13/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
One of the challenges of modern biology and medicine is to visualize biomolecules in their natural environment, in real-time and in a non-invasive fashion, so as to gain insight into their physiological behavior and highlight alterations in pathological settings, which will enable to devise appropriate therapeutic strategies. Genetically encoded fluorescent biosensors constitute a class of imaging agents that enable visualization of biological processes and events directly in situ, preserving the native biological context and providing detailed insight into their localization and dynamics in cells. Real-time monitoring of drug action in a specific cellular compartment, organ, or tissue type; the ability to screen at the single-cell resolution; and the elimination of false-positive results caused by low drug bioavailability that is not detected by in vitro testing methods are a few of the obvious benefits of using genetically encoded fluorescent biosensors in drug screening. This review summarizes results of the studies that have been conducted in the last years toward the fabrication of genetically encoded fluorescent biosensors for biomedical applications with a comprehensive discussion on the challenges, future trends, and potential inputs needed for improving them.
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Affiliation(s)
- Vera S. Ovechkina
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Suren M. Zakian
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, 630055 Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Sergey P. Medvedev
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, 630055 Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Kamila R. Valetdinova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.S.O.); (S.M.Z.); (S.P.M.)
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, 630055 Novosibirsk, Russia
- Correspondence:
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15
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FLIM-Based Intracellular and Extracellular pH Measurements Using Genetically Encoded pH Sensor. BIOSENSORS-BASEL 2021; 11:bios11090340. [PMID: 34562930 PMCID: PMC8468847 DOI: 10.3390/bios11090340] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 02/04/2023]
Abstract
The determination of pH in live cells and tissues is of high importance in physiology and cell biology. In this report, we outline the process of the creation of SypHerExtra, a genetically encoded fluorescent sensor that is capable of measuring extracellular media pH in a mildly alkaline range. SypHerExtra is a protein created by fusing the previously described pH sensor SypHer3s with the neurexin transmembrane domain that targets its expression to the cytoplasmic membrane. We showed that with excitation at 445 nm, the fluorescence lifetime of both SypHer3s and SypHerExtra strongly depend on pH. Using FLIM microscopy in live eukaryotic cells, we demonstrated that SypHerExtra can be successfully used to determine extracellular pH, while SypHer3s can be applied to measure intracellular pH. Thus, these two sensors are suitable for quantitative measurements using the FLIM method, to determine intracellular and extracellular pH in a range from pH 7.5 to 9.5 in different biological systems.
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16
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Zhang Y, Hou D, Wang Z, Cai N, Au C. Nanomaterial-Based Dual-Emission Ratiometric Fluorescent Sensors for Biosensing and Cell Imaging. Polymers (Basel) 2021; 13:2540. [PMID: 34372142 PMCID: PMC8348892 DOI: 10.3390/polym13152540] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/29/2021] [Accepted: 07/29/2021] [Indexed: 12/20/2022] Open
Abstract
Owing to the unique optophysical properties of nanomaterials and their self-calibration characteristics, nanomaterial-based (e.g., polymer dots (Pdots) quantum dots (QDs), silicon nanorods (SiNRs), and gold nanoparticle (AuNPs), etc.) ratiometric fluorescent sensors play an essential role in numerous biosensing and cell imaging applications. The dual-emission ratiometric fluorescence technique has the function of effective internal referencing, thereby avoiding the influence of various analyte-independent confounding factors. The sensitivity and precision of the detection can therefore be greatly improved. In this review, the recent progress in nanomaterial-based dual-emission ratiometric fluorescent biosensors is systematically summarized. First, we introduce two general design approaches for dual-emission ratiometric fluorescent sensors, involving ratiometric fluorescence with changes of one response signal and two reversible signals. Then, some recent typical examples of nanomaterial-based dual-emission ratiometric fluorescent biosensors are illustrated in detail. Finally, probable challenges and future outlooks for dual-emission ratiometric fluorescent nanosensors for biosensing and cell imaging are rationally discussed.
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Affiliation(s)
- Yanan Zhang
- Hubei Key Laboratory for Processing and Application of Catalytic Materials, College of Chemistry and Chemical Engineering, Huanggang Normal University, Huanggang 438000, China; (D.H.); (C.A.)
| | - Dajun Hou
- Hubei Key Laboratory for Processing and Application of Catalytic Materials, College of Chemistry and Chemical Engineering, Huanggang Normal University, Huanggang 438000, China; (D.H.); (C.A.)
| | - Zelong Wang
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory for Novel Reactor and Green Chemistry Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China;
| | - Ning Cai
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory for Novel Reactor and Green Chemistry Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China;
| | - Chaktong Au
- Hubei Key Laboratory for Processing and Application of Catalytic Materials, College of Chemistry and Chemical Engineering, Huanggang Normal University, Huanggang 438000, China; (D.H.); (C.A.)
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17
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Haris U, Kagalwala HN, Kim YL, Lippert AR. Seeking Illumination: The Path to Chemiluminescent 1,2-Dioxetanes for Quantitative Measurements and In Vivo Imaging. Acc Chem Res 2021; 54:2844-2857. [PMID: 34110136 DOI: 10.1021/acs.accounts.1c00185] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chemiluminescence is a fascinating phenomenon that evolved in nature and has been harnessed by chemists in diverse ways to improve life. This Account tells the story of our research group's efforts to formulate and manifest spiroadamantane 1,2-dioxetanes with triggerable chemiluminescence for imaging and monitoring important reactive analytes in living cells, animals, and human clinical samples. Analytes like reactive sulfur, oxygen and nitrogen species, as well as pH and hypoxia can be indicators of cellular function or dysfunction and are often implicated in the causes and effects of disease. We begin with a foundation in binding-based and activity-based fluorescence imaging that has provided transformative tools for understanding biological systems. The intense light sources required for fluorescence excitation, however, introduce autofluorescence and light scattering that reduces sensitivity and complicates in vivo imaging. Our work and the work of our collaborators were the first to demonstrate that spiroadamantane 1,2-dioxetanes had sufficient brightness and biological compatibility for in vivo imaging of enzyme activity and reactive analytes like hydrogen sulfide (H2S) inside of living mice. This launched an era of renewed interest in 1,2-dioxetanes that has resulted in a plethora of new chemiluminescence imaging agents developed by groups around the world. Our own research group focused its efforts on reactive sulfur, oxygen, and nitrogen species, pH, and hypoxia, resulting in a large family of bright chemiluminescent 1,2-dioxetanes validated for cell monitoring and in vivo imaging. These chemiluminescent probes feature low background and high sensitivity that have been proven quite useful for studying signaling, for example, the generation of peroxynitrite (ONOO-) in cellular models of immune function and phagocytosis. This high sensitivity has also enabled real-time quantitative reporting of oxygen-dependent enzyme activity and hypoxia in living cells and tumor xenograft models. We reported some of the first ratiometric chemiluminescent 1,2-dioxetane systems for imaging pH and have introduced a powerful kinetics-based approach for quantification of reactive species like azanone (nitroxyl, HNO) and enzyme activity in living cells. These tools have been applied to untangle complex signaling pathways of peroxynitrite production in radiation therapy and as substrates in a split esterase system to provide an enzyme/substrate pair to rival luciferase/luciferin. Furthermore, we have pushed chemiluminescence toward commercialization and clinical translation by demonstrating the ability to monitor airway hydrogen peroxide in the exhaled breath of asthma patients using transiently produced chemiluminescent 1,2-dioxetanedione intermediates. This body of work shows the powerful possibilities that can emerge when working at the interface of light and chemistry, and we hope that it will inspire future scientists to seek out ever brighter and more illuminating ideas.
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Affiliation(s)
- Uroob Haris
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Husain N. Kagalwala
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Yujin Lisa Kim
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Alexander R. Lippert
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275-0314, United States
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18
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Morikawa TJ, Nishiyama M, Yoshizawa K, Fujita H, Watanabe TM. Glycine insertion modulates the fluorescence properties of Aequorea victoria green fluorescent protein and its variants in their ambient environment. Biophys Physicobiol 2021; 18:145-158. [PMID: 34178565 PMCID: PMC8214926 DOI: 10.2142/biophysico.bppb-v18.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/27/2021] [Indexed: 12/04/2022] Open
Abstract
The green fluorescent protein (GFP) derived from Pacific Ocean jellyfish is an essential tool in biology. GFP-solvent interactions can modulate the fluorescent property of GFP. We previously reported that glycine insertion is an effective mutation in the yellow variant of GFP, yellow fluorescent protein (YFP). Glycine insertion into one of the β-strands comprising the barrel structure distorts its structure, allowing water molecules to invade near the chromophore, enhancing hydrostatic pressure or solution hydrophobicity sensitivity. However, the underlying mechanism of how glycine insertion imparts environmental sensitivity to YFP has not been elucidated yet. To unveil the relationship between fluorescence and β-strand distortion, we investigated the effects of glycine insertion on the dependence of the optical properties of GFP variants named enhanced-GFP (eGFP) and its yellow (eYFP) and cyan (eCFP) variants with respect to pH, temperature, pressure, and hydrophobicity. Our results showed that the quantum yield decreased depending on the number of inserted glycines in all variants, and the dependence on pH, temperature, pressure, and hydrophobicity was altered, indicating the invasion of water molecules into the β-barrel. Peak shifts in the emission spectrum were observed in glycine-inserted eGFP, suggesting a change of the electric state in the excited chromophore. A comparative investigation of the spectral shift among variants under different conditions demonstrated that glycine insertion rearranged the hydrogen bond network between His148 and the chromophore. The present results provide important insights for further understanding the fluorescence mechanism in GFPs and suggest that glycine insertion could be a potent approach for investigating the relationship between water molecules and the intra-protein chromophore.
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Affiliation(s)
- Takamitsu J Morikawa
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Graduate School of Frontier Bioscience, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Kindai University, Higashiosaka, Osaka 577-8502, Japan
| | - Keiko Yoshizawa
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan
| | - Hideaki Fujita
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
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19
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Chebotarev AS, Pochechuev MS, Lanin AA, Kelmanson IV, Kotova DA, Fetisova ES, Panova AS, Bilan DS, Fedotov AB, Belousov VV, Zheltikov AM. Enhanced-contrast two-photon optogenetic pH sensing and pH-resolved brain imaging. JOURNAL OF BIOPHOTONICS 2021; 14:e202000301. [PMID: 33205577 DOI: 10.1002/jbio.202000301] [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: 07/22/2020] [Revised: 10/29/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
We present experiments on cell cultures and brain slices that demonstrate two-photon optogenetic pH sensing and pH-resolved brain imaging using a laser driver whose spectrum is carefully tailored to provide the maximum contrast of a ratiometric two-photon fluorescence readout from a high-brightness genetically encoded yellow-fluorescent-protein-based sensor, SypHer3s. Two spectrally isolated components of this laser field are set to induce two-photon-excited fluorescence (2PEF) by driving SypHer3s through one of two excitation pathways-via either the protonated or deprotonated states of its chromophore. With the spectrum of the laser field accurately adjusted for a maximum contrast of these two 2PEF signals, the ratio of their intensities is shown to provide a remarkably broad dynamic range for pH measurements, enabling high-contrast optogenetic deep-brain pH sensing and pH-resolved 2PEF imaging within a vast class of biological systems, ranging from cell cultures to the living brain.
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Affiliation(s)
- Artem S Chebotarev
- Physics Department, International Laser Center, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Matvei S Pochechuev
- Physics Department, International Laser Center, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Aleksandr A Lanin
- Physics Department, International Laser Center, M.V. Lomonosov Moscow State University, Moscow, Russia
- Russian Quantum Center, Moscow, Russia
- Kazan Quantum Center, A.N. Tupolev Kazan National Research Technical University, Kazan, Russia
| | - Ilya V Kelmanson
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Daria A Kotova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Elena S Fetisova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya S Panova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry S Bilan
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Andrei B Fedotov
- Physics Department, International Laser Center, M.V. Lomonosov Moscow State University, Moscow, Russia
- Russian Quantum Center, Moscow, Russia
- Kazan Quantum Center, A.N. Tupolev Kazan National Research Technical University, Kazan, Russia
- National University of Science and Technology "MISiS,", Moscow, Russia
| | - Vsevolod V Belousov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russia
| | - Aleksei M Zheltikov
- Physics Department, International Laser Center, M.V. Lomonosov Moscow State University, Moscow, Russia
- Russian Quantum Center, Moscow, Russia
- Kazan Quantum Center, A.N. Tupolev Kazan National Research Technical University, Kazan, Russia
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas, USA
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20
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Dos Santos NV, Saponi CF, Ryan TM, Primo FL, Greaves TL, Pereira JFB. Reversible and irreversible fluorescence activity of the Enhanced Green Fluorescent Protein in pH: Insights for the development of pH-biosensors. Int J Biol Macromol 2020; 164:3474-3484. [PMID: 32882278 DOI: 10.1016/j.ijbiomac.2020.08.224] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/09/2020] [Accepted: 08/28/2020] [Indexed: 11/17/2022]
Abstract
Enhanced Green Fluorescent Protein (EGFP) is a biomolecule with intense and natural fluorescence, with biological and medical applications. Although widely used as a biomarker in research, its application as a biosensor is limited by the lack of in-depth knowledge regarding its structure and behavior in adverse conditions. This study is focused on addressing this need by evaluating EGFP activity and structure at different pH using three-dimensional fluorescence, circular dichroism and small-angle X-ray scattering. The focus was on the reversibility of the process to gain insights for the development of biocompatible pH-biosensors. EGFP was highly stable at alkaline pH and quenched from neutral-to-acidic pH. Above pH 6.0, the fluorescence loss was almost completely reversible on return to neutral pH, but only partially reversible from pH 5.0 to 2.0. This work updates the knowledge regarding EGFP behavior in pH by accounting for the recent data on its structure. Hence, it is evident that EGFP presents the required properties for use as natural, biocompatible and environmentally friendly neutral to acidic pH-biosensors.
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Affiliation(s)
- Nathalia Vieira Dos Santos
- Department of Engineering of Bioprocesses and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara-Jaú/Km 01, 14800-903 Araraquara, SP, Brazil; School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Carolina Falaschi Saponi
- Department of Engineering of Bioprocesses and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara-Jaú/Km 01, 14800-903 Araraquara, SP, Brazil; School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Timothy M Ryan
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Fernando L Primo
- Department of Engineering of Bioprocesses and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara-Jaú/Km 01, 14800-903 Araraquara, SP, Brazil
| | - Tamar L Greaves
- School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Jorge F B Pereira
- Department of Engineering of Bioprocesses and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara-Jaú/Km 01, 14800-903 Araraquara, SP, Brazil; Univ Coimbra, CIEPQPF, Department of Chemical Engineering, Rua Sílvio Lima, Pólo II - Pinhal de Marrocos, 3030-790 Coimbra, Portugal.
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21
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Steinegger A, Wolfbeis OS, Borisov SM. Optical Sensing and Imaging of pH Values: Spectroscopies, Materials, and Applications. Chem Rev 2020; 120:12357-12489. [PMID: 33147405 PMCID: PMC7705895 DOI: 10.1021/acs.chemrev.0c00451] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Indexed: 12/13/2022]
Abstract
This is the first comprehensive review on methods and materials for use in optical sensing of pH values and on applications of such sensors. The Review starts with an introduction that contains subsections on the definition of the pH value, a brief look back on optical methods for sensing of pH, on the effects of ionic strength on pH values and pKa values, on the selectivity, sensitivity, precision, dynamic ranges, and temperature dependence of such sensors. Commonly used optical sensing schemes are covered in a next main chapter, with subsections on methods based on absorptiometry, reflectometry, luminescence, refractive index, surface plasmon resonance, photonic crystals, turbidity, mechanical displacement, interferometry, and solvatochromism. This is followed by sections on absorptiometric and luminescent molecular probes for use pH in sensors. Further large sections cover polymeric hosts and supports, and methods for immobilization of indicator dyes. Further and more specific sections summarize the state of the art in materials with dual functionality (indicator and host), nanomaterials, sensors based on upconversion and 2-photon absorption, multiparameter sensors, imaging, and sensors for extreme pH values. A chapter on the many sensing formats has subsections on planar, fiber optic, evanescent wave, refractive index, surface plasmon resonance and holography based sensor designs, and on distributed sensing. Another section summarizes selected applications in areas, such as medicine, biology, oceanography, bioprocess monitoring, corrosion studies, on the use of pH sensors as transducers in biosensors and chemical sensors, and their integration into flow-injection analyzers, microfluidic devices, and lab-on-a-chip systems. An extra section is devoted to current challenges, with subsections on challenges of general nature and those of specific nature. A concluding section gives an outlook on potential future trends and perspectives.
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Affiliation(s)
- Andreas Steinegger
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Otto S. Wolfbeis
- Institute
of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, D-93040 Regensburg, Germany
| | - Sergey M. Borisov
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
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22
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Ryan LS, Gerberich J, Haris U, Nguyen D, Mason RP, Lippert AR. Ratiometric pH Imaging Using a 1,2-Dioxetane Chemiluminescence Resonance Energy Transfer Sensor in Live Animals. ACS Sens 2020; 5:2925-2932. [PMID: 32829636 DOI: 10.1021/acssensors.0c01393] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regulation of physiological pH is integral for proper whole body and cellular function, and disruptions in pH homeostasis can be both a cause and effect of disease. In light of this, many methods have been developed to monitor pH in cells and animals. In this study, we report a chemiluminescence resonance energy transfer (CRET) probe Ratio-pHCL-1, composed of an acrylamide 1,2-dioxetane chemiluminescent scaffold with an appended pH-sensitive carbofluorescein fluorophore. The probe provides an accurate measurement of pH between 6.8 and 8.4, making it a viable tool for measuring pH in biological systems. Further, its ratiometric output is independent of confounding variables. Quantification of pH can be accomplished using both common luminescence spectroscopy and advanced optical imaging methods. Using an IVIS Spectrum, pH can be measured through tissue with Ratio-pHCL-1, which is shown in vitro and calibrated in sacrificed mouse models. Intraperitoneal injections of Ratio-pHCL-1 into live mice show high photon outputs and consistent increases in the flux ratio when measured at pH 6, 7, and 8.
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Affiliation(s)
- Lucas S. Ryan
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Jeni Gerberich
- Prognostic Imaging Research Laboratory (PIRL), Pre-clinical Imaging Section, Department of Radiology, UT Southwestern Medical Center, Dallas, Texas 75390-9058, United States
| | - Uroob Haris
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Daphne Nguyen
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Ralph P. Mason
- Prognostic Imaging Research Laboratory (PIRL), Pre-clinical Imaging Section, Department of Radiology, UT Southwestern Medical Center, Dallas, Texas 75390-9058, United States
| | - Alexander R. Lippert
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275-0314, United States
- Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275-0314, United States
- Center for Global Health Impact (CGHI), Southern Methodist University, Dallas, Texas 75275-0314, United States
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23
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Han Y, Yang W, Luo X, He X, Zhao H, Tang W, Yue T, Li Z. Carbon dots based ratiometric fluorescent sensing platform for food safety. Crit Rev Food Sci Nutr 2020; 62:244-260. [PMID: 32876496 DOI: 10.1080/10408398.2020.1814197] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Food safety has become a major global concern and the rapid detection of food nutritional ingredients and contaminants has aroused much more attention. Nanomaterials-based fluorescent sensing holds great potential in designing highly sensitive and selective detection strategies for food safety analysis. Carbon dots (CDs) possess tremendous prospects in fluorescent sensing food ingredients and contaminants due to their superior properties of chemical and photostability, highly fluorescence with tunability, and no/low-toxicity. Numerous endeavors are demanded to contribute to overcoming the challenge of lower sensitivity and selectivity of the sensors interfered by various components in intricate food matrices to ensure food safety and human health. Nanohybrid CDs based ratiometric fluorescent sensing with self-calibration is regarded as an efficient strategy for the CDs based sensors for the specific recognition of target analyte in the food matrices. This work is devoted to reviewing the development of nanohybrid CDs based ratiometric fluorescent sensing platform and the perspectives of the platform for food safety. The applications of nanohybrid CDs in sensing are summarized and the sensing mechanisms are briefly discussed.
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Affiliation(s)
- Yong Han
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Weixia Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Xueli Luo
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Xie He
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Haiping Zhao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Wenzhi Tang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, Shaanxi, PR China
| | - Zhonghong Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, PR China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, Shaanxi, PR China
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24
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Dos Santos GC, Roldao JC, Shi J, Milián-Medina B, da Silva-Filho LC, Gierschner J. Combined Spectroscopic and TD-DFT Analysis to Elucidate Substituent and Acidochromic Effects in Organic Dyes: A Case Study on Amino- versus Nitro-Substituted 2,4-Diphenylquinolines. Chemphyschem 2020; 21:1797-1804. [PMID: 32602989 DOI: 10.1002/cphc.202000452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/29/2020] [Indexed: 11/09/2022]
Abstract
A combined spectroscopic and TD-DFT case study was performed, to identify a robust method to calculate the complex near UV/Vis absorption spectra of various amino- vs. nitro-substituted 2,4-diphenylquinolines, which vary strongly under neutral and successively acidic conditions. For this, different DFT functionals were tested for geometry optimization and the TD part to calculate the neutral and different protonated species in a fast screening approach, i. e. using single point calculations in an implicit solvent. Offset-corrected M06HF, hitherto only applied to polymers, was identified as a suitable method to reproduce the absorption spectra in a reasonable fashion for all different substitution pattern and all different protonated species at different pH values; moreover, the method properly predicts the energetic ordering of low-lying n-π* and ππ* transitions, which is decisive for the non-/emissive nature of the different compounds. In all, this might provide a valuable tool for computer-aided design of related classes of compounds.
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Affiliation(s)
- Giovanny Carvalho Dos Santos
- Laboratory of Organic Synthesis and Processes (LOSP), São Paulo State University (UNESP), Department of Chemistry, School of Sciences, 17033-360, Bauru, São Paulo, Brazil.,IMDEA Nanociencia, Ciudad Universitaria de Cantoblanco, C/ Faraday 9, 28049, Madrid, Spain
| | - Juan Carlos Roldao
- IMDEA Nanociencia, Ciudad Universitaria de Cantoblanco, C/ Faraday 9, 28049, Madrid, Spain
| | - Junqing Shi
- IMDEA Nanociencia, Ciudad Universitaria de Cantoblanco, C/ Faraday 9, 28049, Madrid, Spain.,Xi'an Institute of Flexible Electronics, Northwestern Polytechnical University Dongda Town, Dongxiang Street 1, 710072, Xi'an, Shaanxi, China
| | - Begoña Milián-Medina
- Department for Physical Chemistry, Faculty of Chemistry, University of Valencia, Avenida Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
| | - Luiz Carlos da Silva-Filho
- Laboratory of Organic Synthesis and Processes (LOSP), São Paulo State University (UNESP), Department of Chemistry, School of Sciences, 17033-360, Bauru, São Paulo, Brazil
| | - Johannes Gierschner
- IMDEA Nanociencia, Ciudad Universitaria de Cantoblanco, C/ Faraday 9, 28049, Madrid, Spain
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25
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FROG/B reporter gives bright insights into redox biology. Proc Natl Acad Sci U S A 2020; 117:19615-19617. [DOI: 10.1073/pnas.2011793117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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Real-time monitoring of the in vivo redox state transition using the ratiometric redox state sensor protein FROG/B. Proc Natl Acad Sci U S A 2020; 117:16019-16026. [PMID: 32576684 DOI: 10.1073/pnas.1918919117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The intracellular redox state is one of the key factors regulating various physiological phenomena in the cell. Monitoring this state is therefore important for understanding physiological homeostasis in cells. Various fluorescent sensor proteins have already been developed to monitor intracellular redox state. We also developed fluorescent redox sensor proteins named Oba-Q and Re-Q, the emissions of which are quenched under oxidized and reduced conditions, respectively. Although these sensors were useful to visualize the redox changes in the cell over time, they have the weakness that their emission signals are directly influenced by their in situ expression levels. To overcome this problem, we developed a redox sensor protein with a single excitation peak and dual variable emission peaks. This sensor protein shows green emission under oxidized conditions and blue emission under reduced conditions. We therefore named this sensor FROG/B, fluorescent protein with redox-dependent change in green/blue. By using this sensor, we successfully measured the changes in intracellular redox potentials in cyanobacterial cells quantitatively caused by light/dark transition just by calculating the ratio of emission between green and blue signals.
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27
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Rhee KY, Chawla R, Lele PP. Protein expression-independent response of intensity-based pH-sensitive fluorophores in Escherichia coli. PLoS One 2020; 15:e0234849. [PMID: 32555627 PMCID: PMC7302705 DOI: 10.1371/journal.pone.0234849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/02/2020] [Indexed: 12/02/2022] Open
Abstract
Fluorescent proteins that modulate their emission intensities when protonated serve as excellent probes of the cytosolic pH. Since the total fluorescence output fluctuates significantly due to variations in the fluorophore levels in cells, eliminating the dependence of the signal on protein concentration is crucial. This is typically accomplished with the aid of ratiometric fluorescent proteins such as pHluorin. However, pHluorin is excited by blue light, which can complicate pH measurements by adversely impacting bacterial physiology. Here, we characterized the response of intensity-based, pH-sensitive fluorescent proteins that excite at longer wavelengths where the blue light effect is diminished. The pH-response was interpreted in terms of an analytical model that assumed two emission states for each fluorophore: a low intensity protonated state and a high intensity deprotonated state. The model suggested a scaling to eliminate the dependence of the signal on the expression levels as well as on the illumination and photon-detection settings. Experiments successfully confirmed the scaling predictions. Thus, the internal pH can be readily determined with intensity-based fluorophores with appropriate calibrations irrespective of the fluorophore concentration and the signal acquisition setup. The framework developed in this work improves the robustness of intensity-based fluorophores for internal pH measurements in E. coli, potentially extending their applications.
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Affiliation(s)
- Kathy Y. Rhee
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Pushkar P. Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
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28
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Kostyuk AI, Kokova AD, Podgorny OV, Kelmanson IV, Fetisova ES, Belousov VV, Bilan DS. Genetically Encoded Tools for Research of Cell Signaling and Metabolism under Brain Hypoxia. Antioxidants (Basel) 2020; 9:E516. [PMID: 32545356 PMCID: PMC7346190 DOI: 10.3390/antiox9060516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/04/2020] [Accepted: 06/06/2020] [Indexed: 02/08/2023] Open
Abstract
Hypoxia is characterized by low oxygen content in the tissues. The central nervous system (CNS) is highly vulnerable to a lack of oxygen. Prolonged hypoxia leads to the death of brain cells, which underlies the development of many pathological conditions. Despite the relevance of the topic, different approaches used to study the molecular mechanisms of hypoxia have many limitations. One promising lead is the use of various genetically encoded tools that allow for the observation of intracellular parameters in living systems. In the first part of this review, we provide the classification of oxygen/hypoxia reporters as well as describe other genetically encoded reporters for various metabolic and redox parameters that could be implemented in hypoxia studies. In the second part, we discuss the advantages and disadvantages of the primary hypoxia model systems and highlight inspiring examples of research in which these experimental settings were combined with genetically encoded reporters.
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Affiliation(s)
- Alexander I. Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Aleksandra D. Kokova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Oleg V. Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Koltzov Institute of Developmental Biology, 119334 Moscow, Russia
| | - Ilya V. Kelmanson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Elena S. Fetisova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.D.K.); (O.V.P.); (I.V.K.); (E.S.F.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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29
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Lin CY, Boxer SG. Mechanism of Color and Photoacidity Tuning for the Protonated Green Fluorescent Protein Chromophore. J Am Chem Soc 2020; 142:11032-11041. [PMID: 32453950 DOI: 10.1021/jacs.0c02796] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The neutral or A state of the green fluorescent protein (GFP) chromophore is a remarkable example of a photoacid naturally embedded in the protein environment and accounts for the large Stokes shift of GFP in response to near UV excitation. Its color tuning mechanism has been largely overlooked, as it is less preferred for imaging applications than the redder anionic or B state. Past studies, based on site-directed mutagenesis or solvatochromism of the isolated chromophore, have concluded that its color tuning range is much narrower than its anionic counterpart. However, as we performed extensive investigation on more GFP mutants, we found that the color of the neutral chromophore can be more sensitive to protein electrostatics than can the anionic counterpart. Electronic Stark spectroscopy reveals a fundamentally different electrostatic color tuning mechanism for the neutral state of the chromophore that demands a three-form model as compared to that of the anionic state, which requires only two forms ( J. Am. Chem. Soc. 2019, 141, 15250-15265). Specifically, an underlying zwitterionic charge-transfer state is required to explain its sensitivity to electrostatics. As the Stokes shift is tightly linked to excited-state proton transfer (ESPT) of the protonated chromophore, we infer design principles of the GFP chromophore as a photoacid through the color tuning mechanisms of both protonation states. The three-form model could also be applied to similar biological and nonbiological dyes and complements the failure of the two-form model for donor-acceptor systems with localized ground-state electronic distributions.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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30
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Chatterjee S, Ahire K, Karuso P. Room-Temperature Dual Fluorescence of a Locked Green Fluorescent Protein Chromophore Analogue. J Am Chem Soc 2019; 142:738-749. [PMID: 31846319 DOI: 10.1021/jacs.9b05096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A structurally locked green fluorescent protein (GFP) chromophore with a phenyl group at C(2) of the imidazolone has been synthesized. Rotation around the exocyclic double bond is hindered, resulting in room-temperature fluorescence. The quantum yield in water is 500 times greater than that of unlocked analogues. Unlike the methyl-substituted analogue, the phenyl analogue exhibits a dual emission (cyan and red) that can be used for ultrasensitive ratiometric measurements and fluorescence microscopy. To explain this dual emission, DFT calculations were carried out along with fluorescence upconversion experiments. The Z-isomer was found to be emissive, while the origin of the dual emission was dependent on the phenyl group in the Z-isomer, which stabilizes the Franck-Condon state, resulting in a cyan fluorescence, while the zwitterionic tautomer fluoresces red. These results bring important new insights into the photophysics of the GFP chromophore and provide a new scaffold capable of dual emission with utility in biotechnology.
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Affiliation(s)
- Soumit Chatterjee
- Department of Molecular Sciences , Macquarie University , Sydney , NSW 2109 , Australia
| | - Ketan Ahire
- Department of Molecular Sciences , Macquarie University , Sydney , NSW 2109 , Australia
| | - Peter Karuso
- Department of Molecular Sciences , Macquarie University , Sydney , NSW 2109 , Australia
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31
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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32
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Kostyuk AI, Panova AS, Bilan DS, Belousov VV. Redox biosensors in a context of multiparameter imaging. Free Radic Biol Med 2018; 128:23-39. [PMID: 29630928 DOI: 10.1016/j.freeradbiomed.2018.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/18/2018] [Accepted: 04/04/2018] [Indexed: 12/22/2022]
Abstract
A wide variety of genetically encoded fluorescent biosensors are available to date. Some of them have already contributed significantly to our understanding of biological processes occurring at cellular and organismal levels. Using such an approach, outstanding success has been achieved in the field of redox biology. The probes allowed researchers to observe, for the first time, the dynamics of important redox parameters in vivo during embryogenesis, aging, the inflammatory response, the pathogenesis of various diseases, and many other processes. Given the differences in the readout and spectra of the probes, they can be used in multiparameter imaging in which several processes are monitored simultaneously in the cell. Intracellular processes form an extensive network of interactions. For example, redox changes are often accompanied by changes in many other biochemical reactions related to cellular metabolism and signaling. Therefore, multiparameter imaging can provide important information concerning the temporal and spatial relationship of various signaling and metabolic processes. In this review, we will describe the main types of genetically encoded biosensors, the most frequently used readout, and their use in multiplexed imaging mode.
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Affiliation(s)
- Alexander I Kostyuk
- Faculty of Biology, Moscow State University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anastasiya S Panova
- Faculty of Biology, Moscow State University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Vsevolod V Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Institute for Cardiovascular Physiology, Georg August University Göttingen, Göttingen D-37073, Germany.
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33
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Genetically encoded fluorescent indicators for live cell pH imaging. Biochim Biophys Acta Gen Subj 2018; 1862:2924-2939. [PMID: 30279147 DOI: 10.1016/j.bbagen.2018.09.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND Intracellular pH underlies most cellular processes. There is emerging evidence of a pH-signaling role in plant cells and microorganisms. Dysregulation of pH is associated with human diseases, such as cancer and Alzheimer's disease. SCOPE OF REVIEW In this review, we attempt to provide a summary of the progress that has been made in the field during the past two decades. First, we present an overview of the current state of the design and applications of fluorescent protein (FP)-based pH indicators. Then, we turn our attention to the development and applications of hybrid pH sensors that combine the capabilities of non-GFP fluorophores with the advantages of genetically encoded tags. Finally, we discuss recent advances in multicolor pH imaging and the applications of genetically encoded pH sensors in multiparameter imaging. MAJOR CONCLUSIONS Genetically encoded pH sensors have proven to be indispensable noninvasive tools for selective targeting to different cellular locations. Although a variety of genetically encoded pH sensors have been designed and applied at the single cell level, there is still much room for improvements and future developments of novel powerful tools for pH imaging. Among the most pressing challenges in this area is the design of brighter redshifted sensors for tissue research and whole animal experiments. GENERAL SIGNIFICANCE The design of precise pH measuring instruments is one of the important goals in cell biochemistry and may give rise to the development of new powerful diagnostic tools for various diseases.
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34
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Lolli G, Raboni S, Pasqualetto E, Benoni R, Campanini B, Ronda L, Mozzarelli A, Bettati S, Battistutta R. Insight into GFPmut2 pH Dependence by Single Crystal Microspectrophotometry and X-ray Crystallography. J Phys Chem B 2018; 122:11326-11337. [PMID: 30179482 DOI: 10.1021/acs.jpcb.8b07260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The fluorescence of Green Fluorescent Protein (wtGFP) and variants has been exploited in distinct applications in cellular and analytical biology. GFPs emission depends on the population of the protonated (A-state) and deprotonated (B-state) forms of the chromophore. Whereas wtGFP is pH-independent, mutants in which Ser65 is replaced by either threonine or alanine (as in GFPmut2) are pH-dependent, with a p Ka around 6. Given the wtGFP pH-independence, only the structure of the protonated form was determined. The deprotonated form was deduced on the basis of the crystal structure of the Ser65Thr mutant at basic pH, assuming that it corresponds to the conformation populated in solution. Here, we present an investigation where structures of the protonated and deprotonated forms of GFPmut2 were determined from crystals grown in either MPD at pH 6 or PEG at pH 8.5, and moved to either higher or lower pH. Both crystal forms of GFPmut2 were titrated monitoring the process via polarized absorption microspectrophotometry in order to precisely correlate the protonation process with the structures. We found that (i) in solution, chromophore titration is not thermodynamically coupled with any residue and Glu222 is always protonated independent of the protonation state of the chromophore; (ii) the lack of coupling is reflected in the structural behavior of the chromophore and Glu222 environments, with only the former showing variations with pH; (iii) titrations of low-pH and high-pH grown crystals exhibit a Hill coefficient of about 0.75, indicating an anticooperative behavior not observed in solution; (iv) structures where pH was changed in the crystal point to Glu222 as the ionizable group responsible for the outset of the anticooperative behavior; and (v) in GFPmut2 the canonical GFP proton wire involving the chromophore is not interrupted at the level of Ser205 and Glu222 at basic pH as in the Ser65Thr mutant. This allows proposing the structure of the deprotonated state of GFPmut2 as an alternative model for the analogous state of wtGFP.
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Affiliation(s)
- Graziano Lolli
- Centro di Biologia Integrata - CIBIO , Università di Trento , 38123 Povo , Trento , Italy
| | - Samanta Raboni
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy
| | - Elisa Pasqualetto
- Dipartimento di Scienze Chimiche , Università degli Studi di Padova and Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , 35131 Padua , Italy
| | - Roberto Benoni
- Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy
| | - Barbara Campanini
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy
| | - Luca Ronda
- Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy.,Istituto di Biofisica , Consiglio Nazionale delle Ricerche , 56124 Pisa , Italy.,Istituto Nazionale Biostrutture e Biosistemi , 00136 Rome , Italy
| | - Stefano Bettati
- Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy.,Istituto Nazionale Biostrutture e Biosistemi , 00136 Rome , Italy
| | - Roberto Battistutta
- Dipartimento di Scienze Chimiche , Università degli Studi di Padova and Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , 35131 Padua , Italy
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Abstract
SIGNIFICANCE Hydrogen peroxide (H2O2) is a key signaling molecule involved in the regulation of both physiological and pathological cellular processes. Genetically encoded HyPer probes are currently among the most effective approaches for monitoring H2O2 dynamics in various biological systems because they can be easily targeted to specific cells and organelles. Since its development in 2006, HyPer has proved to be a robust and powerful tool in redox biology research. Recent Advances: HyPer probes were used in a variety of models to study the role of H2O2 in various redox processes. HyPer has been increasingly used in the past few years for in vivo studies, which has already led to many important discoveries, for example, that H2O2 plays a key role in the regulation of signaling cascades involved in development and aging, inflammation, regeneration, photosynthetic signaling, and other biological processes. CRITICAL ISSUES In this review, we focus on the main achievements in the field of redox biology that have been obtained from in vivo experiments using HyPer probes. FUTURE DIRECTIONS Further in vivo studies of the role of H2O2 largely depend on the development of more suitable versions of HyPer for in vivo models: those having brighter fluorescence and a more stable signal in response to physiological changes in pH. Antioxid. Redox Signal. 29, 569-584.
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Affiliation(s)
- Dmitry S Bilan
- 1 Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia .,2 Pirogov Russian National Research Medical University , Moscow, Russia
| | - Vsevolod V Belousov
- 1 Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia .,2 Pirogov Russian National Research Medical University , Moscow, Russia .,3 Institute for Cardiovascular Physiology, Georg August University Göttingen , Göttingen, Germany
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36
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Walia A, Waadt R, Jones AM. Genetically Encoded Biosensors in Plants: Pathways to Discovery. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:497-524. [PMID: 29719164 DOI: 10.1146/annurev-arplant-042817-040104] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Genetically encoded biosensors that directly interact with a molecule of interest were first introduced more than 20 years ago with fusion proteins that served as fluorescent indicators for calcium ions. Since then, the technology has matured into a diverse array of biosensors that have been deployed to improve our spatiotemporal understanding of molecules whose dynamics have profound influence on plant physiology and development. In this review, we address several types of biosensors with a focus on genetically encoded calcium indicators, which are now the most diverse and advanced group of biosensors. We then consider the discoveries in plant biology made by using biosensors for calcium, pH, reactive oxygen species, redox conditions, primary metabolites, phytohormones, and nutrients. These discoveries were dependent on the engineering, characterization, and optimization required to develop a successful biosensor; they were also dependent on the methodological developments required to express, detect, and analyze the readout of such biosensors.
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Affiliation(s)
- Ankit Walia
- Sainsbury Laboratory, Cambridge University, Cambridge CB2 1LR, United Kingdom;
| | - Rainer Waadt
- Centre for Organismal Studies, Ruprecht-Karls-Universität Heidelberg, Heidelberg 69120, Germany
| | - Alexander M Jones
- Sainsbury Laboratory, Cambridge University, Cambridge CB2 1LR, United Kingdom;
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37
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Steiert F, Petrov EP, Schultz P, Schwille P, Weidemann T. Photophysical Behavior of mNeonGreen, an Evolutionarily Distant Green Fluorescent Protein. Biophys J 2018; 114:2419-2431. [PMID: 29706225 DOI: 10.1016/j.bpj.2018.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 12/31/2022] Open
Abstract
Fluorescent proteins (FPs) feature complex photophysical behavior that must be considered when studying the dynamics of fusion proteins in model systems and live cells. In this work, we characterize mNeonGreen (mNG), a recently introduced FP from the bilaterian Branchiostoma lanceolatum, in comparison to the well-known hydrozoan variants enhanced green fluorescent protein (EGFP) and Aequorea coerulescens GFP by steady-state spectroscopy and fluorescence correlation spectroscopy in solutions of different pH. Blind spectral unmixing of sets of absorption spectra reveals three interconverting electronic states of mNG: a nonfluorescent protonated state, a bright state showing bell-shaped pH dependence, and a similarly bright state dominating at high pH. The gradual population of the acidic form by external protonation is reflected by increased flickering at low pH in fluorescence correlation spectroscopy measurements, albeit with much slower flicker rates and lower amplitudes as compared to Aequorea GFPs. In addition, increased flickering of mNG indicates a second deprotonation step above pH 10 leading to a slight decrease in fluorescence. Thus, mNG is distinguished from Aequorea GFPs by a two-step protonation response with opposite effects that reflects a chemically distinct chromophore environment. Despite the more complex pH dependence, mNG represents a superior FP under a broad range of conditions.
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Affiliation(s)
- Frederik Steiert
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany; Physics Department, Technical University Munich, Garching, Germany
| | - Eugene P Petrov
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany; Faculty of Physics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Peter Schultz
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thomas Weidemann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
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38
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Eguchi Y, Fukumori Y, Taoka A. Measuring magnetosomal pH of the magnetotactic bacterium Magnetospirillum magneticum AMB-1 using pH-sensitive fluorescent proteins. Biosci Biotechnol Biochem 2018; 82:1243-1251. [PMID: 29557302 DOI: 10.1080/09168451.2018.1451739] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Magnetotactic bacteria synthesize uniform-sized and regularly shaped magnetic nanoparticles in their organelles termed magnetosomes. Homeostasis of the magnetosome lumen must be maintained for its role accomplishment. Here, we developed a method to estimate the pH of a single living cell of the magnetotactic bacterium Magnetospirillum magneticum AMB-1 using a pH-sensitive fluorescent protein E2GFP. Using the pH measurement, we estimated that the cytoplasmic pH was approximately 7.6 and periplasmic pH was approximately 7.2. Moreover, we estimated pH in the magnetosome lumen and cytoplasmic surface using fusion proteins of E2GFP and magnetosome-associated proteins. The pH in the magnetosome lumen increased during the exponential growth phase when magnetotactic bacteria actively synthesize magnetite crystals, whereas pH at the magnetosome surface was not affected by the growth stage. This live-cell pH measurement method will help for understanding magnetosome pH homeostasis to reveal molecular mechanisms of magnetite biomineralization in the bacterial organelle.
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Affiliation(s)
- Yukako Eguchi
- a Department of Life Science, Graduate School of Natural Science and Technology , Kanazawa University , Kanazawa , Japan
| | - Yoshihiro Fukumori
- b Faculty of Natural System, Institute of Science and Engineering , Kanazawa University , Kanazawa , Japan
| | - Azuma Taoka
- b Faculty of Natural System, Institute of Science and Engineering , Kanazawa University , Kanazawa , Japan.,c Bio-AFM Frontier Research Center, College of Science and Engineering , Kanazawa University , Kanazawa , Japan
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39
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Disruption of the hydrogen bonding network determines the pH-induced non-fluorescent state of the fluorescent protein ZsYellow by protonation of Glu221. Biochem Biophys Res Commun 2017; 493:562-567. [DOI: 10.1016/j.bbrc.2017.08.152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 08/30/2017] [Indexed: 11/18/2022]
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Ratiometric Matryoshka biosensors from a nested cassette of green- and orange-emitting fluorescent proteins. Nat Commun 2017; 8:431. [PMID: 28874729 PMCID: PMC5585204 DOI: 10.1038/s41467-017-00400-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 06/24/2017] [Indexed: 01/25/2023] Open
Abstract
Sensitivity, dynamic and detection range as well as exclusion of expression and instrumental artifacts are critical for the quantitation of data obtained with fluorescent protein (FP)-based biosensors in vivo. Current biosensors designs are, in general, unable to simultaneously meet all these criteria. Here, we describe a generalizable platform to create dual-FP biosensors with large dynamic ranges by employing a single FP-cassette, named GO-(Green-Orange) Matryoshka. The cassette nests a stable reference FP (large Stokes shift LSSmOrange) within a reporter FP (circularly permuted green FP). GO- Matryoshka yields green and orange fluorescence upon blue excitation. As proof of concept, we converted existing, single-emission biosensors into a series of ratiometric calcium sensors (MatryoshCaMP6s) and ammonium transport activity sensors (AmTryoshka1;3). We additionally identified the internal acid-base equilibrium as a key determinant of the GCaMP dynamic range. Matryoshka technology promises flexibility in the design of a wide spectrum of ratiometric biosensors and expanded in vivo applications.Single fluorescent protein biosensors are susceptible to expression and instrumental artifacts. Here Ast et al. describe a dual fluorescent protein design whereby a reference fluorescent protein is nested within a reporter fluorescent protein to control for such artifacts while preserving sensitivity and dynamic range.
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41
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Kissing S, Saftig P, Haas A. Vacuolar ATPase in phago(lyso)some biology. Int J Med Microbiol 2017; 308:58-67. [PMID: 28867521 DOI: 10.1016/j.ijmm.2017.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/28/2017] [Accepted: 08/23/2017] [Indexed: 12/23/2022] Open
Abstract
Many eukaryotic cells ingest extracellular particles in a process termed phagocytosis which entails the generation of a new intracellular compartment, the phagosome. Phagosomes change their composition over time and this maturation process culminates in their fusion with acidic, hydrolase-rich lysosomes. During the maturation process, degradation and, when applicable, killing of the cargo may ensue. Many of the events that are pathologically relevant depend on strong acidification of phagosomes by the 'vacuolar' ATPase (V-ATPase). This protein complex acidifies the lumen of some intracellular compartments at the expense of ATP hydrolysis. We discuss here the roles and importance of V-ATPase in intracellular trafficking, its distribution, inhibition and activities, its role in the defense against microorganisms and the counteractivities of pathogens.
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Affiliation(s)
- Sandra Kissing
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Paul Saftig
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany.
| | - Albert Haas
- Institut für Zellbiologie, Friedrich-Wilhelms-Universität Bonn, Ulrich-Haberland-Str. 61A, D-53121 Bonn, Germany.
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42
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Slocum JD, Webb LJ. A Double Decarboxylation in Superfolder Green Fluorescent Protein Leads to High Contrast Photoactivation. J Phys Chem Lett 2017; 8:2862-2868. [PMID: 28598160 DOI: 10.1021/acs.jpclett.7b01101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A photoactivatable variant of superfolder green fluorescent protein (GFP) was created by replacing the threonine at position 203 with aspartic acid. Photoactivation by exposure of this mutant to UV light resulted in conversion of the fluorophore from the neutral to the negatively charged form, accompanied by a ∼95-fold increase in fluorescence under 488 nm excitation. Mass spectrometry before and after exposure to UV light revealed a change in mass of 88 Da, attributed to the double decarboxylation of Glu 222 and Asp 203. Kinetics studies and nonlinear power-dependence of the initial rate of photoconversion indicated that the double decarboxylation occurred via a multiphoton absorption process at 254 nm. In addition to providing a photoactivatable GFP with robust folding properties, a detailed mechanistic understanding of this double decarboxylation in GFP will lead to a better understanding of charge transfer in fluorescent proteins.
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Affiliation(s)
- Joshua D Slocum
- Department of Chemistry, Center for Nano and Molecular Science and Technology, and Institute for Cell and Molecular Biology, The University of Texas at Austin , 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
| | - Lauren J Webb
- Department of Chemistry, Center for Nano and Molecular Science and Technology, and Institute for Cell and Molecular Biology, The University of Texas at Austin , 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
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43
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Correlative super-resolution fluorescence and electron microscopy using conventional fluorescent proteins in vacuo. J Struct Biol 2017; 199:120-131. [PMID: 28576556 PMCID: PMC5531056 DOI: 10.1016/j.jsb.2017.05.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 04/27/2017] [Accepted: 05/29/2017] [Indexed: 12/12/2022]
Abstract
Super-resolution light microscopy, correlative light and electron microscopy, and volume electron microscopy are revolutionising the way in which biological samples are examined and understood. Here, we combine these approaches to deliver super-accurate correlation of fluorescent proteins to cellular structures. We show that YFP and GFP have enhanced blinking properties when embedded in acrylic resin and imaged under partial vacuum, enabling in vacuo single molecule localisation microscopy. In conventional section-based correlative microscopy experiments, the specimen must be moved between imaging systems and/or further manipulated for optimal viewing. These steps can introduce undesirable alterations in the specimen, and complicate correlation between imaging modalities. We avoided these issues by using a scanning electron microscope with integrated optical microscope to acquire both localisation and electron microscopy images, which could then be precisely correlated. Collecting data from ultrathin sections also improved the axial resolution and signal-to-noise ratio of the raw localisation microscopy data. Expanding data collection across an array of sections will allow 3-dimensional correlation over unprecedented volumes. The performance of this technique is demonstrated on vaccinia virus (with YFP) and diacylglycerol in cellular membranes (with GFP).
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44
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Rupprecht C, Wingen M, Potzkei J, Gensch T, Jaeger KE, Drepper T. A novel FbFP-based biosensor toolbox for sensitive in vivo determination of intracellular pH. J Biotechnol 2017; 258:25-32. [PMID: 28501596 DOI: 10.1016/j.jbiotec.2017.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 02/07/2023]
Abstract
The intracellular pH is an important modulator of various bio(techno)logical processes such as enzymatic conversion of metabolites or transport across the cell membrane. Changes of intracellular pH due to altered proton distribution can thus cause dysfunction of cellular processes. Consequently, accurate monitoring of intracellular pH allows elucidating the pH-dependency of (patho)physiological and biotechnological processes. In this context, genetically encoded biosensors represent a powerful tool to determine intracellular pH values non-invasively and with high spatiotemporal resolution. We have constructed a toolbox of novel genetically encoded FRET-based pH biosensors (named Fluorescence Biosensors for pH or FluBpH) that utilizes the FMN-binding fluorescent protein EcFbFP as donor domain. In contrast to many fluorescent proteins of the GFP family, EcFbFP exhibits a remarkable tolerance towards acidic pH (pKa∼3.2). To cover the broad range of physiologically relevant pH values, three EYFP variants exhibiting pKa values of 5.7, 6.1 and 7.5 were used as pH-sensing FRET acceptor domains. The resulting biosensors FluBpH 5.7, FluBpH 6.1 and FluBpH 7.5 were calibrated in vitro and in vivo to accurately evaluate their pH indicator properties. To demonstrate the in vivo applicability of FluBpH, changes of intracellular pH were ratiometrically measured in E. coli cells during acid stress.
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Affiliation(s)
- Christian Rupprecht
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Marcus Wingen
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Janko Potzkei
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; GO-Bio Projekt SenseUP, Forschungszentrum Jülich, D-52425 Jülich GmbH, Germany
| | - Thomas Gensch
- Institute of Complex Systems ICS-4: Cellular Biophysics, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany; Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany.
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45
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Abstract
Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques. Finally, we summarize the wide range of sensors in the literature, exploring creative new sensor architectures suitable for different applications.
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Affiliation(s)
- Lynn Sanford
- University of Colorado Boulder, Boulder, CO, United States
| | - Amy Palmer
- University of Colorado Boulder, Boulder, CO, United States.
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46
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Marze NA, Jeliazkov JR, Roy Burman SS, Boyken SE, DiMaio F, Gray JJ. Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35. Proteins 2017; 85:479-486. [PMID: 27667482 PMCID: PMC5710743 DOI: 10.1002/prot.25168] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/01/2016] [Accepted: 09/26/2016] [Indexed: 12/27/2022]
Abstract
The 28th-35th rounds of the Critical Assessment of PRotein Interactions (CAPRI) served as a practical benchmark for our RosettaDock protein-protein docking protocols, highlighting strengths and weaknesses of the approach. We achieved acceptable or better quality models in three out of 11 targets. For the two α-repeat protein-green fluorescent protein (αrep-GFP) complexes, we used a novel ellipsoidal partial-global docking method (Ellipsoidal Dock) to generate models with 2.2 Å/1.5 Å interface RMSD, capturing 49%/42% of the native contacts, for the 7-/5-repeat αrep complexes. For the DNase-immunity protein complex, we used a new predictor of hydrogen-bonding networks, HBNet with Bridging Waters, to place individual water models at the complex interface; models were generated with 1.8 Å interface RMSD and 12% native water contacts recovered. The targets for which RosettaDock failed to create an acceptable model were typically difficult in general, as six had no acceptable models submitted by any CAPRI predictor. The UCH-L5-RPN13 and UCH-L5-INO80G de-ubiquitinating enzyme-inhibitor complexes comprised inhibitors undergoing significant structural changes upon binding, with the partners being highly interwoven in the docked complexes. Our failure to predict the nucleosome-enzyme complex in Target 95 was largely due to tight constraints we placed on our model based on sparse biochemical data suggesting two specific cross-interface interactions, preventing the correct structure from being sampled. While RosettaDock's three successes show that it is a state-of-the-art docking method, the difficulties with highly flexible and multi-domain complexes highlight the need for better flexible docking and domain-assembly methods. Proteins 2017; 85:479-486. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nicholas A. Marze
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Jeliazko R. Jeliazkov
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Shourya S. Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Scott E. Boyken
- Department of Biochemistry, University of Washington, Seattle, Washington
- Institute for Protein Design, University of Washington, Seattle, Washington
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington
- Institute for Protein Design, University of Washington, Seattle, Washington
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
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47
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Barnett LM, Hughes TE, Drobizhev M. Deciphering the molecular mechanism responsible for GCaMP6m's Ca2+-dependent change in fluorescence. PLoS One 2017; 12:e0170934. [PMID: 28182677 PMCID: PMC5300113 DOI: 10.1371/journal.pone.0170934] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/12/2017] [Indexed: 11/19/2022] Open
Abstract
The goal of this work is to determine how GCaMP6m's fluorescence is altered in response to Ca2+-binding. Our detailed spectroscopic study reveals the simplest explanation for how GCaMP6m changes fluorescence in response to Ca2+ is with a four-state model, in which a Ca2+-dependent change of the chromophore protonation state, due to a shift in pKa, is the predominant factor. The pKa shift is quantitatively explained by a change in electrostatic potential around the chromophore due to the conformational changes that occur in the protein when calmodulin binds Ca2+ and interacts with the M13 peptide. The absolute pKa values for the Ca2+-free and Ca2+-saturated states of GCaMP6m are critical to its high signal-to-noise ratio. This mechanism has important implications for further improvements to GCaMP6m and potentially for other similarly designed biosensors.
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Affiliation(s)
- Lauren M. Barnett
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States
| | - Thomas E. Hughes
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States
| | - Mikhail Drobizhev
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, United States
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48
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Abstract
The maintenance of pH in the intracellular compartments is essential for the viability of cells. Several genetically encoded fluorescent pH sensors have been developed for noninvasive in vivo analysis. Here, we describe the methods using PEpHluorin (plant-solubility-modified ecliptic pHluorin) and PRpHluorin (plant-solubility-modified ratiometric pHluorin) as pH sensors for in vivo visualization and quantification organelle pH of in plant secretory pathway.
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Affiliation(s)
- Jinbo Shen
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
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49
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Zagaynova EV, Druzhkova IN, Mishina NM, Ignatova NI, Dudenkova VV, Shirmanova MV. Imaging of Intracellular pH in Tumor Spheroids Using Genetically Encoded Sensor SypHer2. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1035:105-119. [DOI: 10.1007/978-3-319-67358-5_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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50
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Xu X, Qiu L, Yan C, Ma Z, Grinter SZ, Zou X. Performance of MDockPP in CAPRI rounds 28-29 and 31-35 including the prediction of water-mediated interactions. Proteins 2016; 85:424-434. [PMID: 27802576 DOI: 10.1002/prot.25203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/24/2016] [Accepted: 10/24/2016] [Indexed: 01/01/2023]
Abstract
Protein-protein interactions are either through direct contacts between two binding partners or mediated by structural waters. Both direct contacts and water-mediated interactions are crucial to the formation of a protein-protein complex. During the recent CAPRI rounds, a novel parallel searching strategy for predicting water-mediated interactions is introduced into our protein-protein docking method, MDockPP. Briefly, a FFT-based docking algorithm is employed in generating putative binding modes, and an iteratively derived statistical potential-based scoring function, ITScorePP, in conjunction with biological information is used to assess and rank the binding modes. Up to 10 binding modes are selected as the initial protein-protein complex structures for MD simulations in explicit solvent. Water molecules near the interface are clustered based on the snapshots extracted from independent equilibrated trajectories. Then, protein-ligand docking is employed for a parallel search for water molecules near the protein-protein interface. The water molecules generated by ligand docking and the clustered water molecules generated by MD simulations are merged, referred to as the predicted structural water molecules. Here, we report the performance of this protocol for CAPRI rounds 28-29 and 31-35 containing 20 valid docking targets and 11 scoring targets. In the docking experiments, we predicted correct binding modes for nine targets, including one high-accuracy, two medium-accuracy, and six acceptable predictions. Regarding the two targets for the prediction of water-mediated interactions, we achieved models ranked as "excellent" in accordance with the CAPRI evaluation criteria; one of these two targets is considered as a difficult target for structural water prediction. Proteins 2017; 85:424-434. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Xianjin Xu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - Liming Qiu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA
| | - Chengfei Yan
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA.,Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, USA
| | - Zhiwei Ma
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA.,Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, USA
| | - Sam Z Grinter
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA.,Informatics Institute, University of Missouri, Columbia, Missouri, 65211, USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA.,Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, 65211, USA.,Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA.,Informatics Institute, University of Missouri, Columbia, Missouri, 65211, USA
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