1
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Jensen GC, Janis MK, Nguyen HN, David OW, Zastrow ML. Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life. ACS Sens 2024; 9:1622-1643. [PMID: 38587931 PMCID: PMC11073808 DOI: 10.1021/acssensors.3c02695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hazel N Nguyen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Ogonna W David
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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2
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Vakili M, Han H, Schmidt C, Wrona A, Kloos M, de Diego I, Dörner K, Geng T, Kim C, Koua FHM, Melo DVM, Rappas M, Round A, Round E, Sikorski M, Valerio J, Zhou T, Lorenzen K, Schulz J. Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography. J Appl Crystallogr 2023; 56:1038-1045. [PMID: 37555221 PMCID: PMC10405586 DOI: 10.1107/s1600576723004405] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/21/2023] [Indexed: 08/10/2023] Open
Abstract
Time-resolved crystallography enables the visualization of protein molecular motion during a reaction. Although light is often used to initiate reactions in time-resolved crystallography, only a small number of proteins can be activated by light. However, many biological reactions can be triggered by the interaction between proteins and ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D-printed microchannels in conjunction with a micronozzle. The diffusive mixing enables the study of the dynamics of samples in viscous media. The device design allows mixing of the ligands and protein crystals in 2 to 20 s. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within lipidic cubic phase, can be mixed efficiently. The potential of this approach for time-resolved membrane protein crystallography to support the development of new drugs is discussed.
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Affiliation(s)
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Iñaki de Diego
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | - Tian Geng
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Chan Kim
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Mathieu Rappas
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | | | | | - Joana Valerio
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
| | - Tiankun Zhou
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | | | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
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3
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Kumar V, Ozguney B, Vlachou A, Chen Y, Gazit E, Tamamis P. Peptide Self-Assembled Nanocarriers for Cancer Drug Delivery. J Phys Chem B 2023; 127:1857-1871. [PMID: 36812392 PMCID: PMC10848270 DOI: 10.1021/acs.jpcb.2c06751] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/24/2022] [Indexed: 02/24/2023]
Abstract
The design of novel cancer drug nanocarriers is critical in the framework of cancer therapeutics. Nanomaterials are gaining increased interest as cancer drug delivery systems. Self-assembling peptides constitute an emerging novel class of highly attractive nanomaterials with highly promising applications in drug delivery, as they can be used to facilitate drug release and/or stability while reducing side effects. Here, we provide a perspective on peptide self-assembled nanocarriers for cancer drug delivery and highlight the aspects of metal coordination, structure stabilization, and cyclization, as well as minimalism. We review particular challenges in nanomedicine design criteria and, finally, provide future perspectives on addressing a portion of the challenges via self-assembling peptide systems. We consider that the intrinsic advantages of such systems, along with the increasing progress in computational and experimental approaches for their study and design, could possibly lead to novel classes of single or multicomponent systems incorporating such materials for cancer drug delivery.
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Affiliation(s)
- Vijay
Bhooshan Kumar
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Busra Ozguney
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Anastasia Vlachou
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Yu Chen
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ehud Gazit
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department
of Materials Science and Engineering, Iby and Aladar Fleischman Faculty
of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol
School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Phanourios Tamamis
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Department
of Materials Science and Engineering, Texas
A&M University, College
Station, Texas 77843-3003, United States
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4
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Zou W, Nguyen HN, Zastrow ML. Mutant Flavin-Based Fluorescent Protein Sensors for Detecting Intracellular Zinc and Copper in Escherichia coli. ACS Sens 2022; 7:3369-3378. [PMID: 36282086 PMCID: PMC9888404 DOI: 10.1021/acssensors.2c01376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Flavin-based fluorescent proteins (FbFPs) are a class of fluorescent reporters that undergo oxygen-independent fluorophore incorporation, which is an important advantage over green fluorescent proteins (GFPs) and mFruits. A FbFP derived from Chlamydomonas reinhardtii (CreiLOV) is a promising platform for designing new metal sensors. Some FbFPs are intrinsically quenched by metal ions, but the question of where metals bind and how to tune metal affinity has not been addressed. We used site-directed mutagenesis of CreiLOV to probe a hypothesized copper(II) binding site that led to fluorescence quenching. Most mutations changed the fluorescence quenching level, supporting the proposed site. One key mutation introducing a second cysteine residue in place of asparagine (CreiLOVN41C) significantly altered metal affinity and selectivity, yielding a zinc sensor. The fluorescence intensity and lifetime of CreiLOVN41C were reversibly quenched by Zn2+ ions with a biologically relevant affinity (apparent dissociation constant, Kd, of 1 nM). Copper quenching of CreiLOVN41C was retained but with several orders of magnitude higher affinity than CreiLOV (Kd = 0.066 fM for Cu2+, 5.4 fM for Cu+) and partial reversibility. We also show that CreiLOVN41C is an excellent intensity- and lifetime-based zinc sensor in aerobic and anaerobic live bacterial cells. Zn2+-induced fluorescence quenching is reversible over several cycles in Escherichia coli cell suspensions and can be imaged by fluorescence microscopy. CreiLOVN41C is a novel oxygen-independent metal sensor that significantly expands the current fluorescent protein-based toolbox of metal sensors and will allow for studies of anaerobic and low oxygen systems previously precluded by the use of oxygen-dependent GFPs.
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Affiliation(s)
- Wenping Zou
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hazel N. Nguyen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L. Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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5
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Metal-Induced Fluorescence Quenching of Photoconvertible Fluorescent Protein DendFP. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092922. [PMID: 35566273 PMCID: PMC9104182 DOI: 10.3390/molecules27092922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 12/29/2022]
Abstract
Sensitive and accurate detection of specific metal ions is important for sensor development and can advance analytical science and support environmental and human medical examinations. Fluorescent proteins (FPs) can be quenched by specific metal ions and spectroscopically show a unique fluorescence-quenching sensitivity, suggesting their potential application as FP-based metal biosensors. Since the characteristics of the fluorescence quenching are difficult to predict, spectroscopic analysis of new FPs is important for the development of FP-based biosensors. Here we reported the spectroscopic and structural analysis of metal-induced fluorescence quenching of the photoconvertible fluorescent protein DendFP. The spectroscopic analysis showed that Fe2+, Fe3+, and Cu2+ significantly reduced the fluorescence emission of DendFP. The metal titration experiments showed that the dissociation constants (Kd) of Fe2+, Fe3+, and Cu2+ for DendFP were 24.59, 41.66, and 137.18 μM, respectively. The tetrameric interface of DendFP, which the metal ions cannot bind to, was analyzed. Structural comparison of the metal-binding sites of DendFP with those of iq-mEmerald and Dronpa suggested that quenchable DendFP has a unique metal-binding site on the β-barrel that does not utilize the histidine pair for metal binding.
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6
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Zhao H, Zastrow ML. Transition Metals Induce Quenching of Monomeric Near-Infrared Fluorescent Proteins. Biochemistry 2022; 61:494-504. [PMID: 35289592 DOI: 10.1021/acs.biochem.1c00705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transition metals such as zinc and copper are essential in numerous life processes, and both deficiency and toxic overload of these metals are associated with various diseases. Fluorescent metal sensors are powerful tools for studying the roles of metal ions in the physiology and pathology of biological systems. Green fluorescent protein (GFP) and its derivatives are highly utilized for protein-based sensor design, but application to anaerobic systems is limited because these proteins require oxygen to become fluorescent. Bacteriophytochrome-based monomeric near-infrared fluorescent proteins (miRFPs) covalently bind a bilin cofactor, which can be added exogenously for anaerobic cells. miRFPs can also have emission wavelengths extending to >700 nm, which is valuable for imaging applications. Here, we evaluated the suitability of miRFP670 and miRFP709 as platforms for single fluorescent protein metal ion sensors. We found that divalent metal ions like Zn2+, Co2+, Ni2+, and Cu2+ can quench from ∼6-20% (Zn2+, Co2+, and Ni2+) and up to nearly 90% (Cu2+) of the fluorescence intensity of pure miRFPs and have similar impacts in live Escherichia coli cells expressing miRFPs. The presence of a 6× histidine tag for purification influences metal quenching, but significant Cu2+-induced quenching and a picomolar binding affinity are retained in the absence of the His6 tag in both cuvettes and live bacterial cells. By comparing the Cu2+ and Cu+-induced quenching results for miRFP670 and miRFP709 and through examining absorption spectra and previously reported crystal structures, we propose a surface metal binding site near the biliverdin IXα chromophore.
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Affiliation(s)
- Haowen Zhao
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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7
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Jiang SD, sheng Y, Wu XJ, Zhu YL, Li PP. Chromophorylation of a Novel Cyanobacteriochrome GAF Domain from Spirulina and Its Response to Copper Ions. J Microbiol Biotechnol 2021; 31:233-239. [PMID: 33203817 PMCID: PMC9705869 DOI: 10.4014/jmb.2009.09048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022]
Abstract
Cyanobacteriochromes (CBCRs) are phytochrome-related photoreceptor proteins in cyanobacteria and cover a wide spectral range from ultraviolet to far-red. A single GAF domain that they contain can bind bilin(s) autocatalytically via heterologous recombination and then fluoresce, with potential applications as biomarkers and biosensors. Here, we report that a novel red/green CBCR GAF domain, SPI1085g2 from Spirulina subsalsa, covalently binds both phycocyanobilin (PCB) and phycoerythrobilin (PEB). The PCB-binding GAF domain exhibited canonical red/green photoconversion with weak fluorescence emission. However, the PEB-binding GAF domain, SPI1085g2-PEB, exhibited an intense orange fluorescence (λabs.max = 520 nm, λfluor.max = 555 nm), with a fluorescence quantum yield close to 1.0. The fluorescence of SPI1085g2-PEB was selectively and instantaneously quenched by copper ions in a concentration-dependent manner and exhibited reversibility upon treatment with the metal chelator EDTA. This study identified a novel PEB-binding cyanobacteriochrome-based fluorescent protein with the highest quantum yield reported to date and suggests its potential as a biosensor for the rapid detection of copper ions.
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Affiliation(s)
- Su-Dan Jiang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 20037, P.R. China
| | - Yi sheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 20037, P.R. China
| | - Xian-Jun Wu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 20037, P.R. China,Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 10037, P.R. China,National Positioning Observation Station of Hung-tse Lake Wetland Ecosystem in Jiangsu Province, Hongze, Jiangsu 22100, P.R. China,Corresponding authors X. Wu Phone: +86-158-5052-0507 E-mail:
| | - Yong-Li Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 20037, P.R. China,Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 10037, P.R. China,National Positioning Observation Station of Hung-tse Lake Wetland Ecosystem in Jiangsu Province, Hongze, Jiangsu 22100, P.R. China
| | - Ping-Ping Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 20037, P.R. China,Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 10037, P.R. China,National Positioning Observation Station of Hung-tse Lake Wetland Ecosystem in Jiangsu Province, Hongze, Jiangsu 22100, P.R. China,P. Li Phone: +86-25-8542-7210 E-mail:
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8
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Kim IJ, Xu Y, Nam KH. Spectroscopic Analysis of Fe Ion-Induced Fluorescence Quenching of the Green Fluorescent Protein ZsGreen. J Fluoresc 2021; 31:307-314. [PMID: 33411229 DOI: 10.1007/s10895-020-02656-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/23/2020] [Indexed: 11/25/2022]
Abstract
The fluorescence of fluorescent proteins (FPs) is quenched when they are exposed to certain transition metals, which makes them promising receptor materials for metal biosensors. In this study, we report the spectroscopic analysis of metal-induced fluorescence quenching of the fluorescent protein ZsGreen from Zoanthus sp. The fluorescence of ZsGreen was reduced to 2%, 1%, and 20% of its original intensity by Fe2+, Fe3+, and Cu2+, respectively. Metal titration experiments indicated that the dissociation constants of Fe2+, Fe3+, and Cu2+ for ZsGreen were 11.5, 16.3, and 68.2 μM, respectively. The maximum binding capacities of ZsGreen for Fe2+, Fe3+, and Cu2+ were 103.3, 102.2, and 82.9, respectively. Reversibility experiments indicated that the fluorescence of ZsGreen, quenched by Fe2+ and Fe3+, could be recovered, but only to about 15% of its original intensity, even at a 50-fold molar excess of EDTA. In contrast, the fluorescence quenched by Cu2+ could be recovered up to 89.47% of its original intensity at a Cu2+: EDTA ratio of 1:5. The homology model of ZsGreen revealed that the protein does not share any metal-binding sites with previously reported FPs, suggesting that ZsGreen contains unprecedented binding sites for fluorescence quenching metal ions.
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Affiliation(s)
- In Jung Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, D-17487, Greifswald, Germany
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Minzu University, Dalian, China
| | - Ki Hyun Nam
- Department of Life Science, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.
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9
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Spectroscopic and Structural Analysis of Cu 2+-Induced Fluorescence Quenching of ZsYellow. BIOSENSORS-BASEL 2020; 10:bios10030029. [PMID: 32210006 PMCID: PMC7146301 DOI: 10.3390/bios10030029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/16/2022]
Abstract
Fluorescent proteins exhibit fluorescence quenching by specific transition metals, suggesting their potential as fluorescent protein-based metal biosensors. Each fluorescent protein exhibits unique spectroscopic properties and mechanisms for fluorescence quenching by metals. Therefore, the metal-induced fluorescence quenching analysis of various new fluorescent proteins would be important step towards the development of such fluorescent protein-based metal biosensors. Here, we first report the spectroscopic and structural analysis of the yellow fluorescent protein ZsYellow, following its metal-induced quenching. Spectroscopic analysis showed that ZsYellow exhibited a high degree of fluorescence quenching by Cu2+. During Cu2+-induced ZsYellow quenching, fluorescence emission was recovered by adding EDTA. The crystal structure of ZsYellow soaked in Cu2+ solution was determined at a 2.6 Å resolution. The electron density map did not indicate the presence of Cu2+ around the chromophore or the β-barrel surface, which resulted in fluorescence quenching without Cu2+ binding to specific site in ZsYellow. Based on these results, we propose the fluorescence quenching to occur in a distance-dependent manner between the metal and the fluorescent protein, when these components get to a closer vicinity at higher metal concentrations. Our results provide useful insights for future development of fluorescent protein-based metal biosensors.
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10
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Fischer J, Renn D, Quitterer F, Radhakrishnan A, Liu M, Makki A, Ghorpade S, Rueping M, Arold ST, Groll M, Eppinger J. Robust and Versatile Host Protein for the Design and Evaluation of Artificial Metal Centers. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Johannes Fischer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Dominik Renn
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Felix Quitterer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | | | | | | | | | | | - Stefan T. Arold
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
| | - Michael Groll
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
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11
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Bae JE, Kim IJ, Nam KH. Spectroscopic Analysis of the Cu2+-Induced Fluorescence Quenching of Fluorescent Proteins AmCyan and mOrange2. Mol Biotechnol 2018; 60:485-491. [DOI: 10.1007/s12033-018-0088-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Hao Z, Zhu R, Chen PR. Genetically encoded fluorescent sensors for measuring transition and heavy metals in biological systems. Curr Opin Chem Biol 2017; 43:87-96. [PMID: 29275290 DOI: 10.1016/j.cbpa.2017.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 11/30/2022]
Abstract
Great progress has been made in expanding the repertoire of genetically encoded fluorescent sensors for monitoring intracellular transition metals (TMs). This powerful toolkit permits dynamic and non-invasive detection of TMs with high spatial-temporal resolution, which enables us to better understand the roles of TM homeostasis in both physiological and pathological settings. Here we summarize the recent development of genetically encoded fluorescent sensors for intracellular detection of TMs such as zinc and copper, as well as heavy metals including lead, cadmium, mercury, and arsenic.
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Affiliation(s)
- Ziyang Hao
- Synthetic and Functional Biomolecules Center, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Department of Chemistry, The University of Chicago, Chicago 60637, USA
| | - Rongfeng Zhu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Beijing, China.
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13
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Ross JL. The Dark Matter of Biology. Biophys J 2017; 111:909-16. [PMID: 27602719 PMCID: PMC5018137 DOI: 10.1016/j.bpj.2016.07.037] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/06/2016] [Accepted: 07/26/2016] [Indexed: 02/04/2023] Open
Abstract
The inside of the cell is full of important, yet invisible species of molecules and proteins that interact weakly but couple together to have huge and important effects in many biological processes. Such “dark matter” inside cells remains mostly hidden, because our tools were developed to investigate strongly interacting species and folded proteins. Example dark-matter species include intrinsically disordered proteins, posttranslational states, ion species, and rare, transient, and weak interactions undetectable by biochemical assays. The dark matter of biology is likely to have multiple, vital roles to regulate signaling, rates of reactions, water structure and viscosity, crowding, and other cellular activities. We need to create new tools to image, detect, and understand these dark-matter species if we are to truly understand fundamental physical principles of biology.
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Affiliation(s)
- Jennifer L Ross
- Department of Physics, University of Massachusetts Amherst, Amherst, Massachusetts.
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14
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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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15
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Kim IJ, Kim S, Park J, Eom I, Kim S, Kim JH, Ha SC, Kim YG, Hwang KY, Nam KH. Crystal structures of Dronpa complexed with quenchable metal ions provide insight into metal biosensor development. FEBS Lett 2016; 590:2982-90. [DOI: 10.1002/1873-3468.12316] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/27/2016] [Accepted: 07/11/2016] [Indexed: 11/12/2022]
Affiliation(s)
- In Jung Kim
- Division of Biotechnology; College of Life Sciences & Biotechnology; Korea University; Seoul Korea
| | - Sangsoo Kim
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Jeahyun Park
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Intae Eom
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Sunam Kim
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Jin-Hong Kim
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Sung Chul Ha
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Yeon Gil Kim
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology; College of Life Sciences & Biotechnology; Korea University; Seoul Korea
| | - Ki Hyun Nam
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
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16
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Lei C, Wang Z, Nie Z, Deng H, Hu H, Huang Y, Yao S. Resurfaced fluorescent protein as a sensing platform for label-free detection of copper(II) ion and acetylcholinesterase activity. Anal Chem 2015; 87:1974-80. [PMID: 25560517 DOI: 10.1021/ac504390e] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein engineering by resurfacing is an efficient approach to provide new molecular toolkits for biotechnology and bioanalytical chemistry. H39GFP is a new variant of green fluorescent protein (GFP) containing 39 histidine residues in the primary sequence that was developed by protein resurfacing. Herein, taking H39GFP as the signal reporter, a label-free fluorometric sensor for Cu(2+) sensing was developed based on the unique multivalent metal ion-binding property of H39GFP and fluorescence quenching effect of Cu(2+) by electron transfer. The high affinity of H39GFP with Cu(2+) (Kd, 16.2 nM) leads to rapid detection of Cu(2+) in 5 min with a low detection limit (50 nM). Using acetylthiocholine (ATCh) as the substrate, this H39GFP/Cu(2+) complex-based sensor was further applied for the turn-on fluorescence detection of acetylcholinesterase (AChE) activity. The assay was based on the reaction between Cu(2+) and thiocholine, the hydrolysis product of ATCh by AChE. The proposed sensor is highly sensitive (limit of detection (LOD) = 0.015 mU mL(-1)) and is feasible for screening inhibitors of AChE. Furthermore, the practicability of this method was demonstrated by the detection of pesticide residue (carbaryl) in real food samples. Hence, the successful applications of H39GFP in the detection of metal ion and enzyme activity present the prospect of resurfaced proteins as versatile biosensing platforms.
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Affiliation(s)
- Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University , Changsha 410082, P. R. China
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Choi YA, Keem JO, Kim CY, Yoon HR, Heo WD, Chung BH, Jung Y. A novel copper-chelating strategy for fluorescent proteins to image dynamic copper fluctuations on live cell surfaces. Chem Sci 2014; 6:1301-1307. [PMID: 29560216 PMCID: PMC5811147 DOI: 10.1039/c4sc03027c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/18/2014] [Indexed: 01/08/2023] Open
Abstract
A strong but selective copper-binding tripeptide was employed to develop a highly sensitive and selective copper(ii) protein reporter.
Copper is indispensable in most aerobic organisms although it is toxic if unregulated as illustrated in many neurodegenerative diseases. To elucidate the mechanisms underlying copper release from cells, a membrane-targeting reporter which can compete with extracellular copper-binding molecules is highly desirable. However, engineering a reporter protein to provide both high sensitivity and selectivity for copper(ii) has been challenging, likely due to a lack of proper copper(ii)-chelating strategies within proteins. Here, we report a new genetically encoded fluorescent copper(ii) reporter by employing a copper-binding tripeptide derived from human serum albumin (HSA), which is one of the major copper-binding proteins in extracellular environments. Optimized insertion of the tripeptide into the green fluorescent protein leads to rapid fluorescence quenching (up to >85% change) upon copper-binding, while other metal ions have no effect. Furthermore, the high binding affinity of the reporter enables reliable copper detection even in the presence of competing biomolecules such as HSA and amyloid beta peptides. We also demonstrate that our reporter proteins can be used to visualize dynamic copper fluctuations on living HeLa cell surfaces.
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Affiliation(s)
- Yoon-Aa Choi
- BioNano Health Guard Research Center , 125 Gwahak-ro, Yuseong-gu , Daejeon , 305-806 , Republic of Korea . ; ; Tel: +82-42-860-4442
| | - Joo Oak Keem
- BioNano Health Guard Research Center , 125 Gwahak-ro, Yuseong-gu , Daejeon , 305-806 , Republic of Korea . ; ; Tel: +82-42-860-4442
| | - Cha Yeon Kim
- Graduate School of Nanoscience and Technology , Korea Advanced Institute of Science and Technology (KAIST) , Republic of Korea
| | - Hye Ryeon Yoon
- Department of Chemistry , KAIST , 291 Daehak-ro, Yuseong-gu , Daejeon , 305-701 , Republic of Korea . ; ; Tel: +82-42-350-2817
| | - Won Do Heo
- Department of Biological Sciences , KAIST , Republic of Korea
| | - Bong Hyun Chung
- BioNano Health Guard Research Center , 125 Gwahak-ro, Yuseong-gu , Daejeon , 305-806 , Republic of Korea . ; ; Tel: +82-42-860-4442
| | - Yongwon Jung
- Department of Chemistry , KAIST , 291 Daehak-ro, Yuseong-gu , Daejeon , 305-701 , Republic of Korea . ; ; Tel: +82-42-350-2817
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