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Verma AK, Noumani A, Yadav AK, Solanki PR. FRET Based Biosensor: Principle Applications Recent Advances and Challenges. Diagnostics (Basel) 2023; 13:diagnostics13081375. [PMID: 37189476 DOI: 10.3390/diagnostics13081375] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 05/17/2023] Open
Abstract
Förster resonance energy transfer (FRET)-based biosensors are being fabricated for specific detection of biomolecules or changes in the microenvironment. FRET is a non-radiative transfer of energy from an excited donor fluorophore molecule to a nearby acceptor fluorophore molecule. In a FRET-based biosensor, the donor and acceptor molecules are typically fluorescent proteins or fluorescent nanomaterials such as quantum dots (QDs) or small molecules that are engineered to be in close proximity to each other. When the biomolecule of interest is present, it can cause a change in the distance between the donor and acceptor, leading to a change in the efficiency of FRET and a corresponding change in the fluorescence intensity of the acceptor. This change in fluorescence can be used to detect and quantify the biomolecule of interest. FRET-based biosensors have a wide range of applications, including in the fields of biochemistry, cell biology, and drug discovery. This review article provides a substantial approach on the FRET-based biosensor, principle, applications such as point-of-need diagnosis, wearable, single molecular FRET (smFRET), hard water, ions, pH, tissue-based sensors, immunosensors, and aptasensor. Recent advances such as artificial intelligence (AI) and Internet of Things (IoT) are used for this type of sensor and challenges.
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Affiliation(s)
- Awadhesh Kumar Verma
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ashab Noumani
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Amit K Yadav
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pratima R Solanki
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
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2
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Contribution of smFRET to Chromatin Research. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Chromatins are structural components of chromosomes and consist of DNA and histone proteins. The structure, dynamics, and function of chromatins are important in regulating genetic processes. Several different experimental and theoretical tools have been employed to understand chromatins better. In this review, we will focus on the literatures engrossed in understanding of chromatins using single-molecule Förster resonance energy transfer (smFRET). smFRET is a single-molecule fluorescence microscopic technique that can furnish information regarding the distance between two points in space. This has been utilized to efficiently unveil the structural details of chromatins.
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3
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Jiménez-Díaz E, Del-Rio D, Fiordelisio T. The Contribution of Cell Imaging to the Study of Anterior Pituitary Function and Its Regulation. Neuroendocrinology 2023; 113:179-192. [PMID: 35231920 DOI: 10.1159/000523860] [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: 07/08/2021] [Accepted: 02/18/2022] [Indexed: 11/19/2022]
Abstract
Advances in the knowledge of the neuroendocrine system are closely related to the development of cellular imaging and labeling techniques. This synergy ranges from the staining techniques that allowed the first characterizations of the anterior pituitary gland, its relationship with the hypothalamus, and the birth of neuroendocrinology; through the development of fluorescence microscopy applications, specific labeling strategies, transgenic systems, and intracellular calcium sensors that enabled the study of processes and dynamics at the cellular and tissue level; until the advent of super-resolution microscopy, miniscopes, optogenetics, fiber photometry, and other imaging methods that allowed high spatiotemporal resolution and long-term three-dimensional cellular activity recordings in living systems in a conscious and freely moving condition. In this review, we briefly summarize the main contributions of cellular imaging techniques that have allowed relevant advances in the field of neuroendocrinology and paradigm shifts that have improved our understanding of the function of the hypothalamic-pituitary axes. The development of these methods and equipment is the result of the integration of knowledge achieved by the integration of several disciplines and effort to solve scientific questions and problems of high impact on health and society that this system entails.
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Affiliation(s)
- Edgar Jiménez-Díaz
- Laboratorio de Neuroendocrinología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio Nacional de Soluciones Biomiméticas para Diagnóstico y Terapia LaNSBioDyT, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Diana Del-Rio
- Laboratorio de Neuroendocrinología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio Nacional de Soluciones Biomiméticas para Diagnóstico y Terapia LaNSBioDyT, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tatiana Fiordelisio
- Laboratorio de Neuroendocrinología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio Nacional de Soluciones Biomiméticas para Diagnóstico y Terapia LaNSBioDyT, Universidad Nacional Autónoma de México, Mexico City, Mexico
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4
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Johnson AA, Crawford TR, Trudeau MC. The N-linker region of hERG1a upregulates hERG1b potassium channels. J Biol Chem 2022; 298:102233. [PMID: 35798139 PMCID: PMC9428852 DOI: 10.1016/j.jbc.2022.102233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 11/29/2022] Open
Abstract
A major physiological role of hERG1 (human Ether-á-go-go-Related Gene 1) potassium channels is to repolarize cardiac action potentials. Two isoforms, hERG1a and hERG1b, associate to form the potassium current IKr in cardiomyocytes. Inherited mutations in hERG1a or hERG1b cause prolonged cardiac repolarization, long QT syndrome, and sudden death arrhythmia. hERG1a subunits assemble with and enhance the number of hERG1b subunits at the plasma membrane, but the mechanism for the increase in hERG1b by hERG1a is not well understood. Here, we report that the hERG1a N-terminal region expressed in trans with hERG1b markedly increased hERG1b currents and increased biotin-labeled hERG1b protein at the membrane surface. hERG1b channels with a deletion of the N-terminal 1b domain did not have a measurable increase in current or biotinylated protein when coexpressed with hERG1a N-terminal regions, indicating that the 1b domain was required for the increase in hERG1b. Using a biochemical pull-down interaction assay and a FRET hybridization experiment, we detected a direct interaction between the hERG1a N-terminal region and the hERG1b N-terminal region. Using engineered deletions and alanine mutagenesis, we identified a short span of amino acids at positions 216 to 220 within the hERG1a "N-linker" region that were necessary for the upregulation of hERG1b. We propose that direct structural interactions between the hERG1a N-linker region and the hERG1b 1b domain increase hERG1b at the plasma membrane. Mechanisms regulating hERG1a and hERG1b are likely critical for cardiac function, may be disrupted by long QT syndrome mutants, and serve as potential targets for therapeutics.
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Affiliation(s)
- Ashley A Johnson
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Taylor R Crawford
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Matthew C Trudeau
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland, USA.
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5
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Ni Z, Gale A, Johnson MS, Sedger LM. Analysis insights for three FRET pairs of chemically unlinked two-molecule FRET cytometry. Cytometry A 2021; 101:387-399. [PMID: 34935263 DOI: 10.1002/cyto.a.24527] [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: 08/26/2021] [Revised: 11/21/2021] [Accepted: 12/06/2021] [Indexed: 11/07/2022]
Abstract
Förster resonance energy transfer (FRET) is the direct energy exchange between two-component fluorescent molecules. FRET methods utilize chemically linked molecules or unlinked fluorescence protein-protein interactions. FRET is therefore a powerful indicator of molecular proximity, but standardized determination of FRET efficiency is challenged when investigating natural (chemically unlinked) interactions. In this paper, we have examined the interactions of tumor necrosis factor receptor-1 (TNFR1) molecules expressed as recombinant fusion proteins of cyan, yellow, or red fluorescent protein (-CFP, -YFP, or -RFP) to evaluate two-molecule chemically unlinked FRET by flow cytometry. We demonstrate three independent FRET pairs CFP→YFP (FRET-1), YFP→RFP (FRET-2) and CFP→RFP (FRET-3), comparing TNFR1+TNFR1 with non-interacting TNFR1+CD27 proteins, on both LSR-II and Fortessa X-20 cytometers. We describe genuine FRET activities reflecting TNFR1 homotypic interactions. FRET events can be visualized during sample acquisition via the use of "spiked" FRET donor cells, together with TNFR1+TNFR1 co-transfected cells, as FRET channel MFI overlays. FRET events are subsequentially indicated by comparing concatenated files of cells expressing either FRET positive events (TNFR1+TNFR1) or FRET negative events (TNFR1+CD27) to generate single-cell scatter plots showing loss of FRET donor brightness. Robust determination of FRET efficiency is then confirmed at the single-cell level by applying matrix calculations based on the measurements of FRET donor, acceptor and FRET fluorescent intensities (I), detector channel emission coefficient (S), fluorescent protein extinction coefficients (ε) and α factor. In this TNFR based system, the mean CFP→YFP FRET-1 efficiency is 0.43 (LSR-II) and 0.41 (Fortessa), the mean YFP→RFP FRET-2 efficiency is 0.30 (LSR-II) and 0.29 (Fortessa), and the mean CFP→RFP FRET-3 efficiency is 0.56 (LSR-II) and 0.54 (Fortessa). This study also embraces multidimensional clustering using t-SNE, Fit-SNE, UMAP, Tri-Map and PaCMAP to further demonstrate FRET. These approaches establish a robust system for standardized detection of chemically unlinked TNFR1 homotypic interactions with three individual FRET pairs.
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Affiliation(s)
- Zhongran Ni
- School of Life Science, Faculty of Science, University of Technology Sydney
| | - Alex Gale
- School of Life Science, Faculty of Science, University of Technology Sydney
| | - Michael S Johnson
- School of Life Science, Faculty of Science, University of Technology Sydney
| | - Lisa M Sedger
- School of Life Science, Faculty of Science, University of Technology Sydney
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6
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Song Y, Deng X, Shi W, Tang F, Huang W, Gong L, Qin Q. A homogeneous time-resolved fluorometric energy transfer assay for the binding assessment of FcRn with IgG antibodies. J Immunol Methods 2021; 499:113180. [PMID: 34736962 DOI: 10.1016/j.jim.2021.113180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/28/2022]
Abstract
We aimed to develop a homogeneous time-resolved fluorometric energy transfer assay for assessment of human neonatal Fc receptor binding activity with IgG-type antibodies. The assay was configured with FcRn-coupled with Eu cryptate via biotin and streptavidin interaction as donor and IgG1 labeled with d2 as acceptor. Only a single incubation step was involved and no wash step was required. The assay demonstrated good accuracy, precision, linearity and specificity. Our further investigation with a rat pharmacokinetics study revealed that the terminal t1/2 for Trastuzumab and its related three ADCs agreed with the EC50 data. The assay can be applied to various IgGs with modifications to identify antibodies with appropriate binding ability to human FcRn.
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Affiliation(s)
- Yakai Song
- Department of Immunoassay and Immunochemistry, Center for Drug Safety Evaluation and Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203,China
| | - Xiaojie Deng
- Department of Immunoassay and Immunochemistry, Center for Drug Safety Evaluation and Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203,China
| | - Wei Shi
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203, China
| | - Feng Tang
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203, China
| | - Wei Huang
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Center for Biotherapeutics Discovery Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203, China
| | - Likun Gong
- Department of Immunoassay and Immunochemistry, Center for Drug Safety Evaluation and Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203,China.
| | - Qiuping Qin
- Department of Immunoassay and Immunochemistry, Center for Drug Safety Evaluation and Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai 201203,China.
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7
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Velasquez EF, Garcia YA, Ramirez I, Gholkar AA, Torres JZ. CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. Mol Biol Cell 2021; 32:br9. [PMID: 34432510 PMCID: PMC8693966 DOI: 10.1091/mbc.e21-05-0257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The elucidation of a protein’s interaction/association network is important for defining its biological function. Mass spectrometry–based proteomic approaches have emerged as powerful tools for identifying protein–protein interactions (PPIs) and protein–protein associations (PPAs). However, interactome/association experiments are difficult to interpret, considering the complexity and abundance of data that are generated. Although tools have been developed to identify protein interactions/associations quantitatively, there is still a pressing need for easy-to-use tools that allow users to contextualize their results. To address this, we developed CANVS, a computational pipeline that cleans, analyzes, and visualizes mass spectrometry–based interactome/association data. CANVS is wrapped as an interactive Shiny dashboard with simple requirements, allowing users to interface easily with the pipeline, analyze complex experimental data, and create PPI/A networks. The application integrates systems biology databases such as BioGRID and CORUM to contextualize the results. Furthermore, CANVS features a Gene Ontology tool that allows users to identify relevant GO terms in their results and create visual networks with proteins associated with relevant GO terms. Overall, CANVS is an easy-to-use application that benefits all researchers, especially those who lack an established bioinformatic pipeline and are interested in studying interactome/association data.
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Affiliation(s)
- Erick F Velasquez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Yenni A Garcia
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Ivan Ramirez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Ankur A Gholkar
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095.,Molecular Biology Institute, University of California, Los Angeles, CA 90095.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095
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8
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Rooj AK, Cormet-Boyaka E, Clark EB, Qadri YJ, Lee W, Boddu R, Agarwal A, Tambi R, Uddin M, Parpura V, Sorscher EJ, Fuller CM, Berdiev BK. Association of cystic fibrosis transmembrane conductance regulator with epithelial sodium channel subunits carrying Liddle's syndrome mutations. Am J Physiol Lung Cell Mol Physiol 2021; 321:L308-L320. [PMID: 34037494 DOI: 10.1152/ajplung.00298.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The association of the cystic fibrosis transmembrane conductance regulator (CFTR) and epithelial sodium channel (ENaC) in the pathophysiology of cystic fibrosis (CF) is controversial. Previously, we demonstrated a close physical association between wild-type (WT) CFTR and WT ENaC. We have also shown that the F508del CFTR fails to associate with ENaC unless the mutant protein is rescued pharmacologically or by low temperature. In this study, we present the evidence for a direct physical association between WT CFTR and ENaC subunits carrying Liddle's syndrome mutations. We show that all three ENaC subunits bearing Liddle's syndrome mutations (both point mutations and the complete truncation of the carboxy terminus), could be coimmunoprecipitated with WT CFTR. The biochemical studies were complemented by fluorescence lifetime imaging microscopy (FLIM), a distance-dependent approach that monitors protein-protein interactions between fluorescently labeled molecules. Our measurements revealed significantly increased fluorescence resonance energy transfer between CFTR and all tested ENaC combinations as compared with controls (ECFP and EYFP cotransfected cells). Our findings are consistent with the notion that CFTR and ENaC are within reach of each other even in the setting of Liddle's syndrome mutations, suggestive of a direct intermolecular interaction between these two proteins.
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Affiliation(s)
- Arun K Rooj
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | | | - Edlira B Clark
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Yawar J Qadri
- Department of Anesthesiology, The Emory University School of Medicine, Atlanta, Georgia
| | - William Lee
- Department of Neurobiology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Ravindra Boddu
- Department of Medicine, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Anupam Agarwal
- Department of Medicine, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Richa Tambi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Vladimir Parpura
- Department of Neurobiology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Eric J Sorscher
- Department of Pediatrics, The Emory University School of Medicine, Atlanta, Georgia
| | - Cathy M Fuller
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | - Bakhrom K Berdiev
- Department of Cell, Developmental & Integrative Biology, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama.,College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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9
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Rivas S, Hanif K, Chakouri N, Ben-Johny M. Probing ion channel macromolecular interactions using fluorescence resonance energy transfer. Methods Enzymol 2021; 653:319-347. [PMID: 34099178 DOI: 10.1016/bs.mie.2021.01.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ion channels are macromolecular complexes whose functions are exquisitely tuned by interacting proteins. Fluorescence resonance energy transfer (FRET) is a powerful methodology that is adept at quantifying ion channel protein-protein interactions in living cells. For FRET experiments, the interacting partners are tagged with appropriate donor and acceptor fluorescent proteins. If the fluorescently-labeled molecules are in close proximity, then photoexcitation of the donor results in non-radiative energy transfer to the acceptor, and subsequent fluorescence emission of the acceptor. The stoichiometry of ion channel interactions and their relative binding affinities can be deduced by quantifying both the FRET efficiency and the total number of donors and acceptors in a given cell. In this chapter, we discuss general considerations for FRET analysis of biological interactions, various strategies for estimating FRET efficiencies, and detailed protocols for construction of binding curves and determination of stoichiometry. We focus on implementation of FRET assays using a flow cytometer given its amenability for high-throughput data acquisition, enhanced accessibility, and robust analysis. This versatile methodology permits mechanistic dissection of dynamic changes in ion channel interactions.
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Affiliation(s)
- Sharen Rivas
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States
| | | | - Nourdine Chakouri
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States
| | - Manu Ben-Johny
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States.
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10
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Visualization and fluorescence spectroscopy of fingerprints on glass slide using combined 405 nm laser and phase contrast microscope. J Vis (Tokyo) 2021. [DOI: 10.1007/s12650-021-00745-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Emission dynamics of conjugated oligomer (BECV-DHF)/quantum dot perovskite (CsPbBr3) composites in solutions. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2020.125911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Kaur A, Kaur P, Ahuja S. Förster resonance energy transfer (FRET) and applications thereof. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:5532-5550. [PMID: 33210685 DOI: 10.1039/d0ay01961e] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
FRET is a nonradiative process of energy transfer that is based on the dipole-dipole interactions between molecules that are fluorescent. Transfer of energy takes place rapidly from a donor molecule to an acceptor molecule in juxtaposition such as 0 to 10 nm without photonic radiation. FRET has occupied a center stage in biotechnology and biological studies. It is used to gain information on conformation changes in single molecules. The pharmaceutical industry has also developed large fluorescence detection systems with very small sample sizes, at the level of single molecules, using fluorescence correlation spectroscopy.
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Affiliation(s)
- Amrita Kaur
- Computer Science and Engineering Department, Thapar Institute of Engineering and Technology, Patiala, 147001, India
| | - Pardeep Kaur
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab 140407, India.
| | - Sahil Ahuja
- Computer Science and Engineering Department, Thapar Institute of Engineering and Technology, Patiala, 147001, India
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13
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Yang F, Qu W, Du M, Mai Z, Wang B, Ma Y, Wang X, Chen T. Stoichiometry and regulation network of Bcl-2 family complexes quantified by live-cell FRET assay. Cell Mol Life Sci 2020; 77:2387-2406. [PMID: 31492967 PMCID: PMC11104934 DOI: 10.1007/s00018-019-03286-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/26/2019] [Accepted: 08/23/2019] [Indexed: 01/07/2023]
Abstract
The stoichiometry and affinity of Bcl-2 family complexes are essential information for understanding how their interactome network is orchestrated to regulate mitochondrial permeabilization and apoptosis. Based on over-expression model system, FRET analysis was used to quantify the protein-protein interactions among Bax, Bcl-xL, Bad and tBid in healthy and apoptotic cells. Our data indicate that the stoichiometry and affinity of Bcl-2 complexes are dependent on their membrane environment. Bcl-xL, Bad and tBid can form hetero-trimers in mitochondria. Bcl-xL binds preferentially to Bad, then to tBid and Bax in mitochondria, whilst Bcl-xL displays higher affinity to Bad or tBid than to itself. Strikingly, Bax can bind to Bcl-xL in cytosol. In cytosol of apoptotic cells, Bcl-xL associates with Bax to form hetero-trimer with 1:2 stoichiometry, while Bcl-xL associates with Bad to form hetero-trimer with 2:1 stoichiometry and Bcl-xL associates with tBid to form hetero-dimer. In mitochondria, Bcl-xL associates with Bax/Bad to form hetero-dimer in healthy cells, while Bcl-xL associates with Bad to form hetero-tetramer with 3:1 stoichiometry in apoptotic cells.
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Affiliation(s)
- Fangfang Yang
- MOE Key Laboratory of Laser Life Science and College of Biophotonics, South China Normal University, Guangzhou, China
| | - Wenfeng Qu
- MOE Key Laboratory of Laser Life Science and College of Biophotonics, South China Normal University, Guangzhou, China
| | - Mengyan Du
- MOE Key Laboratory of Laser Life Science and College of Biophotonics, South China Normal University, Guangzhou, China
| | - Zihao Mai
- MOE Key Laboratory of Laser Life Science and College of Biophotonics, South China Normal University, Guangzhou, China
| | - Bin Wang
- MOE Key Laboratory of Laser Life Science and College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yunyun Ma
- MOE Key Laboratory of Laser Life Science and College of Biophotonics, South China Normal University, Guangzhou, China
| | - Xiaoping Wang
- Department of Pain Management, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Tongsheng Chen
- MOE Key Laboratory of Laser Life Science and College of Biophotonics, South China Normal University, Guangzhou, China.
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14
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Ems-McClung SC, Walczak CE. In Vitro FRET- and Fluorescence-Based Assays to Study Protein Conformation and Protein-Protein Interactions in Mitosis. Methods Mol Biol 2020; 2101:93-122. [PMID: 31879900 PMCID: PMC7189611 DOI: 10.1007/978-1-0716-0219-5_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Proper cell division and the equal segregation of genetic material are essential for life. Cell division is mediated by the mitotic spindle, which is composed of microtubules (MTs) and MT-associated proteins that help align and segregate the chromosomes. The localization and characterization of many spindle proteins have been greatly aided by using GFP-tagged proteins in vivo, but these tools typically do not allow for understanding how their activity is regulated biochemically. With the recent explosion of the pallet of GFP-derived fluorescent proteins, fluorescence-based biosensors are becoming useful tools for the quantitative analysis of protein activity and protein-protein interactions. Here, we describe solution-based Förster resonance energy transfer (FRET) and fluorescence assays that can be used to quantify protein-protein interactions and to characterize protein conformations of MT-associated proteins involved in mitosis.
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Affiliation(s)
| | - Claire E Walczak
- Indiana University School of Medicine-Bloomington, Medical Sciences, Bloomington, IN, USA.
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15
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Abstract
Measurement of atomic-scale conformational dynamics in proteins has proved a challenging endeavor, although these movements are pivotal for understanding the mechanisms behind protein function. Herein we describe a fluorescence-based method that enables the measurement of distances between specific domains within a protein and how it might change during protein function. The method is transition metal ion Förster resonance energy transfer (tmFRET) and builds on the principle that the fluorescence emission from a fluorophore can be quenched in a distance-dependent manner by a colored transition metal such as nickel (Ni2+), copper (Cu2+), or cobalt (Co2+). It can be applied to literally any protein where it is possible to perform site-specific incorporation of a fluorescent molecule. This chapter will explain the use and applications of tmFRET in detail using incorporation of the dye with cysteine chemistry on a purified protein sample.
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Affiliation(s)
- Jonas S Mortensen
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, The Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, The Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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16
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Huang SM, Yang F, Cai BY, He QT, Liu Q, Qu CX, Han MJ, Kong W, Jia YL, Li F, Yu X, Sun JP, Wang J. Genetically Encoded Fluorescent Amino Acid for Monitoring Protein Interactions through FRET. Anal Chem 2019; 91:14936-14942. [PMID: 31670502 DOI: 10.1021/acs.analchem.9b03305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Förster resonance energy transfer (FRET) is a well-established method for studying macromolecular interactions and conformational changes within proteins. Such a method normally uses fluorescent proteins or chemical-labeling methods which are often only accessible to surface-exposed residues and risk-disturbing target protein structures. Here, we demonstrate that the genetic incorporation of a synthetic fluorescent amino acid, L-(7-hydroxycoumarin-4-yl) ethylglycine (Cou) and natural endogenous fluorophore Tryptophan (Trp) residues of a protein could serve as an efficient FRET pair to monitor protein interactions, using the signaling transducer β-arrestin-1 as a model system. We used this technology to record the dynamic spectra in both binding and competition experiments of β-arrestin-1, the contribution of each specific phosphate in ternary complex formation, in a rapid and efficient manner. The determined Kd value for the association between the active arrestin and Fab30 is 0.68 μM in the three-component interaction system. Moreover, we were able to determine the contributions of the site 3 phospho-site and the site 6 phospho-site binding, each contributing to the high affinity ternary complex assembly as 2.7 fold and 15.5 fold, respectively, which were never determined before. These results thus highlighted the potential usage of this new method in measurement of the allosteric-induced enhanced affinity with small amount proteins and in a fast manner and in a complex system. Collectively, our newly developed Trp:Cou FRET system based on genetic expansion technology has extended the molecular toolboxes available for biochemical and structural biology studies.
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Affiliation(s)
- Shen-Ming Huang
- Key Laboratory of Molecular Cardiovascular Science, School of Basic Medical Sciences, Ministry of Education , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing , 15 Datun Road , Chaoyang District, Beijing 100101 , China
| | - Fan Yang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology , Shandong University School of Medicine , 44 Wenhua Xi Road , Jinan , Shandong 250012 , China
| | - Bai-Yang Cai
- Key Laboratory of Molecular Cardiovascular Science, School of Basic Medical Sciences, Ministry of Education , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Qing-Tao He
- Institute of Biophysics, Chinese Academy of Sciences, Beijing , 15 Datun Road , Chaoyang District, Beijing 100101 , China.,Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology , Shandong University School of Medicine , 44 Wenhua Xi Road , Jinan , Shandong 250012 , China
| | - Qi Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing , 15 Datun Road , Chaoyang District, Beijing 100101 , China.,Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology , Shandong University School of Medicine , 44 Wenhua Xi Road , Jinan , Shandong 250012 , China
| | - Chang-Xiu Qu
- Key Laboratory of Molecular Cardiovascular Science, School of Basic Medical Sciences, Ministry of Education , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China.,Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology , Shandong University School of Medicine , 44 Wenhua Xi Road , Jinan , Shandong 250012 , China
| | - Ming-Jie Han
- Institute of Biophysics, Chinese Academy of Sciences, Beijing , 15 Datun Road , Chaoyang District, Beijing 100101 , China
| | - Wei Kong
- Key Laboratory of Molecular Cardiovascular Science, School of Basic Medical Sciences, Ministry of Education , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Ying-Li Jia
- Key Laboratory of Molecular Cardiovascular Science, School of Basic Medical Sciences, Ministry of Education , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Fahui Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing , 15 Datun Road , Chaoyang District, Beijing 100101 , China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology , Shandong University School of Medicine , 44 Wenhua Xi Road , Jinan , Shandong 250012 , China
| | - Jin-Peng Sun
- Key Laboratory of Molecular Cardiovascular Science, School of Basic Medical Sciences, Ministry of Education , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China.,Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology , Shandong University School of Medicine , 44 Wenhua Xi Road , Jinan , Shandong 250012 , China
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing , 15 Datun Road , Chaoyang District, Beijing 100101 , China
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17
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Utochnikova V. The use of luminescent spectroscopy to obtain information about the composition and the structure of lanthanide coordination compounds. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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18
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19
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Raghuraman H, Chatterjee S, Das A. Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins. Front Mol Biosci 2019; 6:96. [PMID: 31608290 PMCID: PMC6774292 DOI: 10.3389/fmolb.2019.00096] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.
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Affiliation(s)
- H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata, India
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20
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Yugandhar K, Gupta S, Yu H. Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review. Comput Struct Biotechnol J 2019; 17:805-811. [PMID: 31316724 PMCID: PMC6611912 DOI: 10.1016/j.csbj.2019.05.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/20/2019] [Accepted: 05/26/2019] [Indexed: 01/06/2023] Open
Abstract
Studying protein-protein interaction networks provide key evidence for the underlying molecular mechanisms. Mass spectrometry-based proteomic approaches have been playing a pivotal role in deciphering these interaction networks, along with precise quantification for individual interactions. In this mini-review we discuss the available techniques and methods for qualitative and quantitative elucidation of protein-protein interaction networks. We then summarize the down-stream computational strategies for identification and quantification of interactions from those techniques. Finally, we highlight the challenges and limitations of current computational pipelines in eliminating false positive interactors, followed by a summary of the innovative algorithms to address these issues, along with the scope for future improvements.
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Affiliation(s)
- Kumar Yugandhar
- Department of Computational Biology, Cornell University, Ithaca, New York 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Shagun Gupta
- Department of Computational Biology, Cornell University, Ithaca, New York 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, New York 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
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21
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FRET events in fluorescent pentapeptides containing aliphatic triazolo amino acid scaffolds: Role of spacer lengths. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Götzke L, Schaper G, März J, Kaden P, Huittinen N, Stumpf T, Kammerlander KK, Brunner E, Hahn P, Mehnert A, Kersting B, Henle T, Lindoy LF, Zanoni G, Weigand JJ. Coordination chemistry of f-block metal ions with ligands bearing bio-relevant functional groups. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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23
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Utochnikova VV, Kalyakina AS, Solodukhin NN, Aslandukov AN. On the Structural Features of Substituted Lanthanide Benzoates. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201801561] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Valentina V. Utochnikova
- Department of Chemistry; M. V. Lomonosov Moscow State University; 119991 Moscow Russian Federation
- SIA Evoled; 1a Puskina iela LV-1020 Riga Latvia
| | - Alena S. Kalyakina
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber Weg 6 76131 Karlsruhe Germany
| | - Nikolay N. Solodukhin
- Department of Chemistry; M. V. Lomonosov Moscow State University; 119991 Moscow Russian Federation
| | - Andrey N. Aslandukov
- Department of Chemistry; M. V. Lomonosov Moscow State University; 119991 Moscow Russian Federation
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24
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Umrao S, S A, Jain V, Chakraborty B, Roy R. Smartphone-based kanamycin sensing with ratiometric FRET. RSC Adv 2019; 9:6143-6151. [PMID: 35517283 PMCID: PMC9060919 DOI: 10.1039/c8ra10035g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/12/2019] [Indexed: 11/21/2022] Open
Abstract
Smartphone-based fluorescence detection is a promising avenue for biosensing that can aid on-site analysis. However, quantitative detection with fluorescence in the field has been limited due to challenges with robust excitation and calibration requirements. Here, we show that ratiometric analysis with Förster resonance energy transfer (FRET) between dye pairs on DNA aptamers can enable rapid and sensitive kanamycin detection. Since our detection scheme relies on ligand binding-induced changes in the aptamer tertiary structure, it is limited only by the kinetics of ligand binding to the aptamer. Our FRET-based kanamycin binding aptamer (KBA) sensor displays two linear ranges of 0.05-5 nM (detection limit of 0.18 nM) and 50-900 nM of kanamycin. The aptamer displays high specificity even in the presence of the 'natural' background from milk. By immobilizing the aptamer in the flow cell, our KBA sensor design is also suitable for repeated kanamycin detection. Finally, we show that the ratiometric FRET-based analysis can be implemented on a cheap custom-built smartphone setup. This smartphone-based FRET aptamer scheme detects kanamycin in a linear range of 50-500 nM with a limit of detection (LOD) of 28 nM.
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Affiliation(s)
- Saurabh Umrao
- Department of Chemical Engineering, Indian Institute of Science Bangalore 560012 India +91-80-2360-8121 +91-80-2293-3115 +91-80-2293-3118
| | - Anusha S
- Department of Chemical Engineering, Indian Institute of Science Bangalore 560012 India +91-80-2360-8121 +91-80-2293-3115 +91-80-2293-3118
| | - Vasundhara Jain
- Department of Chemical Engineering, Indian Institute of Science Bangalore 560012 India +91-80-2360-8121 +91-80-2293-3115 +91-80-2293-3118
| | - Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science Bangalore 560012 India +91-80-2360-8121 +91-80-2293-3115 +91-80-2293-3118
| | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science Bangalore 560012 India +91-80-2360-8121 +91-80-2293-3115 +91-80-2293-3118
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
- Center for Biosystems Science and Engineering, Indian Institute of Science Bangalore 560012 India
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25
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Kim YJ, Kim KO, Lee JJ. d-Glucose recognition based on phenylboronic acid-functionalized polyoligomeric silsesquioxane fluorescent probe. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 95:286-291. [PMID: 30573251 DOI: 10.1016/j.msec.2018.10.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/31/2018] [Accepted: 10/29/2018] [Indexed: 11/26/2022]
Abstract
We report a new strategy to synthesize hybrid fluorescent nanosensors consisting of phenylboronic acid-functionalized POSS (POSS-PBA) and diol-modified 8-anilino-1-naphthalenesulfonic acid (ANSA (a fluorescent dye)) for the detection of the biologically important d-glucose. The probe was characterized by FT-IR and 1H NMR analyses, and the photoluminescence intensity was measured under various conditions to confirm its glucose sensing ability. Our POSS-APBA-dye probe could detect glucose at concentrations of 0-20 mg/mL, with a good linear relationship even at low glucose concentrations of 0-1 mg/mL. The properties of the POSS-APBA-dye probe were evaluated and compared with those of an APBA-dye probe. The glucose sensing ability of our POSS-APBA-dye probe was largely unaffected by the presence of interfering substances. The probe showed high sensing ability in a pH 5 environment and long-term (approximately 40 days) fluorescence stability.
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Affiliation(s)
- Yeon Ju Kim
- Department of Fiber System Engineering, Dankook University, Republic of Korea
| | - Kyu Oh Kim
- Department of Fiber System Engineering, Dankook University, Republic of Korea.
| | - Jung Jin Lee
- Department of Fiber System Engineering, Dankook University, Republic of Korea.
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26
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Dey PC, Das R. Ligand free surface of CdS nanoparticles enhances the energy transfer efficiency on interacting with Eosin Y dye - Helping in the sensing of very low level of chlorpyrifos in water. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 207:156-163. [PMID: 30227346 DOI: 10.1016/j.saa.2018.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 08/10/2018] [Accepted: 09/09/2018] [Indexed: 06/08/2023]
Abstract
With an aim to sense the presence of chlorpyrifos (CP) pesticide in water, fluorescence resonance energy transfer (FRET) between the chemically synthesized ligand free CdS nanocrystals (donor) and Eosin Y dye (acceptor) has been studied in presence and absence of CP in the FRET pair system. This prepared water soluble CdS nanocrystals have been characterized by Transmission Electron microscopy (TEM), which shows that CdS nanocrystals are spherical in shape with an average size of 5 nm approximately. Further, Fourier Transform Infrared Spectroscopic (FTIR) study confirms that these CdS nanocrystals are ligand free stable nanocrystals. It has been observed that this CdS nanocrystals and Eosin Y FRET pair can strongly sense the presence of chlorpyrifos (CP) pesticide in water up to a very low concentration of 10 ppb, which is the sensitivity of detection or detection limit. This FRET pair is found to be very simple and cost effective for the sensing of toxic pesticide CP.
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Affiliation(s)
- Pijush Ch Dey
- Nano-Physics & Nanotechnology Research Lab., Department of Physics, Tripura University (A Central University), Suryamaninagar, Agartala, Tripura 799022, India
| | - Ratan Das
- Nano-Physics & Nanotechnology Research Lab., Department of Physics, Tripura University (A Central University), Suryamaninagar, Agartala, Tripura 799022, India.
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27
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Asanuma H, Murayama K, Kamiya Y, Kashida H. The DNA Duplex as an Aqueous One-Dimensional Soft Crystal Scaffold for Photochemistry. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180278] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroyuki Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Keiji Murayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Yukiko Kamiya
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
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28
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Codding SJ, Trudeau MC. The hERG potassium channel intrinsic ligand regulates N- and C-terminal interactions and channel closure. J Gen Physiol 2018; 151:478-488. [PMID: 30425124 PMCID: PMC6445578 DOI: 10.1085/jgp.201812129] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 10/26/2018] [Indexed: 02/06/2023] Open
Abstract
An intersubunit interaction between the N-terminal PAS domain and C-terminal cyclic nucleotide binding homology domain (CNBHD) regulates slow deactivation in hERG potassium channels. By mutating the intrinsic ligand, Codding and Trudeau disrupt slow deactivation and prevent the PAS-CNBHD interaction. Human ether-à-go-go–related gene (hERG, KCNH2) voltage-activated potassium channels are critical for cardiac excitability. hERG channels have characteristic slow closing (deactivation), which is auto-regulated by a direct interaction between the N-terminal Per-Arnt-Sim (PAS) domain and the C-terminal cyclic nucleotide binding homology domain (CNBHD). hERG channels are not activated by the binding of extrinsic cyclic nucleotide ligands, but rather bind an “intrinsic ligand” that is composed of residues 860–862 within the CNBHD and mimics a cyclic nucleotide. The intrinsic ligand is located at the PAS–CNBHD interface, but its mechanism of action in hERG is not well understood. Here we use whole-cell patch-clamp electrophysiology and FRET spectroscopy to examine how the intrinsic ligand regulates gating. To carry out this work, we coexpress PAS (a PAS domain fused to cyan fluorescent protein) in trans with hERG “core” channels (channels with a deletion of the PAS domain fused to citrine fluorescent protein). The PAS domain in trans with hERG core channels has slow (regulated) deactivation, like that of WT hERG channels, as well as robust FRET, which indicates there is a direct functional and structural interaction of the PAS domain with the channel core. In contrast, PAS in trans with hERG F860A core channels has intermediate deactivation and intermediate FRET, indicating perturbation of the PAS domain interaction with the CNBHD. Furthermore, PAS in trans with hERG L862A core channels, or PAS in trans with hERG F860G,L862G core channels, has fast (nonregulated) deactivation and no measurable FRET, indicating abolition of the PAS and CNBHD interaction. These results indicate that the intrinsic ligand is necessary for the functional and structural interaction between the PAS domain and the CNBHD, which regulates the characteristic slow deactivation gating in hERG channels.
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Affiliation(s)
- Sara J Codding
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD
| | - Matthew C Trudeau
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD
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29
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Pantazis A, Westerberg K, Althoff T, Abramson J, Olcese R. Harnessing photoinduced electron transfer to optically determine protein sub-nanoscale atomic distances. Nat Commun 2018; 9:4738. [PMID: 30413716 PMCID: PMC6226468 DOI: 10.1038/s41467-018-07218-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 10/16/2018] [Indexed: 11/29/2022] Open
Abstract
Proteins possess a complex and dynamic structure, which is influenced by external signals and may change as they perform their biological functions. We present an optical approach, distance-encoding photoinduced electron transfer (DEPET), capable of the simultaneous study of protein structure and function. An alternative to FRET-based methods, DEPET is based on the quenching of small conjugated fluorophores by photoinduced electron transfer: a reaction that requires contact of the excited fluorophore with a suitable electron donor. This property allows DEPET to exhibit exceptional spatial and temporal resolution capabilities in the range pertinent to protein conformational change. We report the first implementation of DEPET on human large-conductance K+ (BK) channels under voltage clamp. We describe conformational rearrangements underpinning BK channel sensitivity to electrical excitation, in conducting channels expressed in living cells. Finally, we validate DEPET in synthetic peptide length standards, to evaluate its accuracy in measuring sub- and near-nanometer intramolecular distances.
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Affiliation(s)
- Antonios Pantazis
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, UCLA, Los Angeles, CA, 90095, USA. .,Division of Neurobiology, Department of Clinical and Experimental Medicine (IKE), Linköping University, Linköping, 581 83, Sweden. .,Wallenberg Center for Molecular Medicine, Linköping University, Linköping, 581 83, Sweden.
| | - Karin Westerberg
- 0000 0001 0657 5612grid.417886.4Amgen, Thousand Oaks, CA 91320 USA
| | - Thorsten Althoff
- 0000 0000 9632 6718grid.19006.3eDepartment of Physiology, UCLA, Los Angeles, CA 90095 USA
| | - Jeff Abramson
- 0000 0000 9632 6718grid.19006.3eDepartment of Physiology, UCLA, Los Angeles, CA 90095 USA
| | - Riccardo Olcese
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, UCLA, Los Angeles, CA, 90095, USA. .,Department of Physiology, UCLA, Los Angeles, CA, 90095, USA.
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30
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Arnett DC, Bailey SK, Johnson CK. Exploring the conformations of nitric oxide synthase with fluorescence. Front Biosci (Landmark Ed) 2018; 23:2133-2145. [PMID: 29772550 DOI: 10.2741/4694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multi-domain oxidoreductases are a family of enzymes that catalyze oxidation-reduction reactions through a series of electron transfers. Efficient electron transfer requires a sequence of protein conformations that position electron donor and acceptor domains in close proximity to each other so that electron transfer can occur efficiently. An example is mammalian nitric oxide synthase (NOS), which consists of an N-terminal oxygenase domain containing heme and a C-terminal reductase domain containing NADPH/FAD and FMN subdomains. We describe the use of time-resolved and single-molecule fluorescence to detect and characterize the conformations and conformational dynamics of the neuronal and endothelial isoforms of NOS. Fluorescence signals are provided by a fluorescent dye attached to the Ca2+-signaling protein calmodulin (CaM), which regulates NOS activity. Time-resolved fluorescence decays reveal the presence of at least four underlying conformational states that are differentiated by the extent of fluorescence quenching. Single-molecule fluorescence displays transitions between conformational states on the time scales of milliseconds to seconds. This review describes the type of information available by analysis of time-resolved and single-molecule fluorescence experiments.
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Affiliation(s)
- David C Arnett
- Department of Chemistry, Northwestern College, 101 7th Street SW, Orange City, IA 51041
| | - Sheila K Bailey
- Department of Chemistry, University of Kansas, 1251 Wescoe Drive, Lawrence, KS 66045
| | - Carey K Johnson
- Department of Chemistry, University of Kansas, 1251 Wescoe Drive, Lawrence, KS 66045,
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31
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Samajdar RN, Manogaran D, Yashonath S, Bhattacharyya AJ. Using porphyrin–amino acid pairs to model the electrochemistry of heme proteins: experimental and theoretical investigations. Phys Chem Chem Phys 2018; 20:10018-10029. [DOI: 10.1039/c8cp00605a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Deconstructing the complex electrochemistry of heme proteins into simpler heme–amino acid interactions.
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Affiliation(s)
- Rudra N. Samajdar
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
| | - Dhivya Manogaran
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
| | - S. Yashonath
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
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32
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Abstract
Most motile bacteria follow spatial gradients of chemical and physical stimuli in their environment. In Escherichia coli and other bacteria, the best characterized chemotaxis is in gradients of amino acids or sugars, but other physiological stimuli such as pH, osmolarity, redox potentials, and temperature are also known to elicit tactic responses. These multiple environmental stimuli are integrated and processed within a highly sophisticated chemotaxis network to generate coordinated chemotaxis behavior, which features high sensitivity, a wide dynamic range, and robustness against variations in background stimulation, protein levels, and temperature. Although early studies relied on behavioral analyses to characterize chemotactic responses in vivo, or on biochemical assays to study the pathway in vitro, we describe here a method to directly measure the intracellular pathway response using Förster resonance energy transfer (FRET). In E. coli, the most commonly used form of the FRET assay relies on the interaction between the phosphorylated response regulator CheY and its phosphatase CheZ to quantify activity of the histidine kinase CheA. We further describe a FRET assay for Bacillus subtilis, which employs CheY and the motor-associated phosphatase FliY as a FRET pair. In particular, we highlight the use of FRET to quantify pathway properties, including signal amplification, dynamic range, and kinetics of adaptation.
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Affiliation(s)
- Anja Paulick
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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33
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Kim HY, Li T, Jung C, Fu R, Cho DY, Park KS, Park HG. Universally applicable, quantitative PCR method utilizing fluorescent nucleobase analogs. RSC Adv 2018; 8:37391-37395. [PMID: 35557795 PMCID: PMC9089284 DOI: 10.1039/c8ra06675b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/28/2018] [Indexed: 11/21/2022] Open
Abstract
We herein describe a novel quantitative PCR (qPCR) method, which operates in both signal-off and on manners, by utilizing a unique property of fluorescent nucleobase analogs. The first, signal-off method is developed by designing the primers to contain pyrrolo-dC (PdC), one of the most common fluorescent nucleobase analogs. The specially designed single-stranded primer is extended to form double-stranded DNA during PCR and the fluorescence signal from the PdCs incorporated in the primer is accordingly reduced due to its conformation-dependent fluorescence properties. In addition, the second, signal-on method is devised by designing the primers to contain 5′-overhang sequences complementary to the PdC-incorporated DNA probes. At the initial phase, the PdC-incorporated DNA probes are hybridized to the 5′-overhang sequences of the primer, exhibiting the significantly quenched fluorescence signal, but are detached by either hydrolysis or strand displacement reaction during PCR, leading to the highly enhanced fluorescence signal. This method is more advanced than the first one since it produces signal-on fluorescence response and permits the use of a single PdC-incorporated DNA probe for the detection of multiple target nucleic acids, remarkably decreasing the assay cost. With these novel qPCR methods, we successfully quantified target nucleic acids derived from sexually transmitted disease (STD) pathogens with high accuracy. Importantly, the proposed strategies overcome the major drawbacks in the current SYBR Green and TaqMan probe-based qPCR methods such as low specificity and high assay cost. A novel quantitative PCR (qPCR) method was developed by utilizing a unique property of fluorescent nucleobase analogs (PdCs).![]()
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Affiliation(s)
- Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Taihua Li
- College of Biology and the Environment
- Co-Innovation Centre for Sustainable Forestry in Southern China
- Nanjing Forestry University
- Nanjing
- China
| | - Cheulhee Jung
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Rongzhan Fu
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Dae-Yeon Cho
- Labgenomics Clinical Research Institute
- Labgenomics Co. Ltd
- Yong-In
- Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering
- College of Engineering
- Konkuk University
- Seoul 05029
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
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McNally BA, Pendon ZD, Trudeau MC. hERG1a and hERG1b potassium channel subunits directly interact and preferentially form heteromeric channels. J Biol Chem 2017; 292:21548-21557. [PMID: 29089383 DOI: 10.1074/jbc.m117.816488] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/24/2017] [Indexed: 01/20/2023] Open
Abstract
Voltage-activated human ether-á-go-go-related gene (hERG) potassium channels are critical for the repolarization of cardiac action potentials and tune-spike frequency adaptation in neurons. Two isoforms of mammalian ERG1 channel subunits, ERG1a and ERG1b, are the principal subunits that conduct the IKr current in the heart and are also broadly expressed in the nervous system. However, there is little direct evidence that ERG1a and ERG1b form heteromeric channels. Here, using electrophysiology, biochemistry, and fluorescence approaches, we systematically tested for direct interactions between hERG1a and hERG1b subunits. We report 1) that hERG1a dominant-negative subunits suppress hERG1b currents (and vice versa), 2) that disulfide bonds form between single cysteine residues experimentally introduced into an extracellular loop of hERG1a and hERG1b subunits and produce hERG1a-hERG1b dimers, and 3) that hERG1a and hERG1b subunits tagged with fluorescent proteins that are FRET pairs exhibit robust energy transfer at the plasma membrane. Thus, multiple lines of evidence indicated a physical interaction between hERG1a and hERG1b, consistent with them forming heteromeric channels. Moreover, co-expression of variable ratios of hERG1a and hERG1b RNA yielded channels with deactivation kinetics that reached a plateau and were different from those of hERG1b channels, consistent with a preference of hERG1b subunits for hERG1a subunits. Cross-linking studies revealed that an equal input of hERG1a and hERG1b yields more hERG1a-hERG1a or hERG1a-hERG1b dimers than hERG1b-hERG1b dimers, also suggesting that hERG1b preferentially interacts with hERG1a. We conclude that hERG1b preferentially forms heteromeric ion channels with hERG1a at the plasma membrane.
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Affiliation(s)
- Beth A McNally
- From the Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Zeus D Pendon
- From the Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Matthew C Trudeau
- From the Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
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Yao J, Li L, Li P, Yang M. Quantum dots: from fluorescence to chemiluminescence, bioluminescence, electrochemiluminescence, and electrochemistry. NANOSCALE 2017; 9:13364-13383. [PMID: 28880034 DOI: 10.1039/c7nr05233b] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, nanotechnology has become one of the major forces driving basic and applied research. As a novel class of inorganic fluorochromes, research into quantum dots (QDs) has become one of the fastest growing fields of nanotechnology today. QDs are made of a semiconductor material with tunable physical dimensions as well as unique optoelectronic properties, and have attracted multidisciplinary research efforts to further their potential bioanalytical applications. Recently, numerous optical properties of QDs, such as narrow emission band peaks, broad absorption spectra, intense signals, and remarkable resistance to photobleaching, have made them biocompatible and sensitive for biological assays. In this review, we give an overview of these exciting materials and describe their potential, especially in biomolecules analysis, including fluorescence detection, chemiluminescence detection, bioluminescence detection, electrochemiluminescence detection, and electrochemical detection. Finally, conclusions are made, including highlighting some critical challenges remaining and a perspective of how this field can be expected to develop in the future.
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Affiliation(s)
- Jun Yao
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, Sichuan 610500, People's Republic of China.
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Su Q, Feng W, Yang D, Li F. Resonance Energy Transfer in Upconversion Nanoplatforms for Selective Biodetection. Acc Chem Res 2017; 50:32-40. [PMID: 27983801 DOI: 10.1021/acs.accounts.6b00382] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Resonance energy transfer (RET) describes the process that energy is transferred from an excited donor to an acceptor molecule, leading to a reduction in the fluorescence emission intensity of the donor and an increase in that of the acceptor. By this technique, measurements with the good sensitivity can be made about distance within 1 to 10 nm under physiological conditions. For this reason, the RET technique has been widely used in polymer science, biochemistry, and structural biology. Recently, a number of RET systems incorporated with nanoparticles, such as quantum dots, gold nanoparticles, and upconversion nanoparticles, have been developed. These nanocrystals retain their optical superiority and can act as either a donor or a quencher, thereby enhancing the performance of RET systems and providing more opportunities in excitation wavelength selection. Notably, lanthanide-doped upconversion nanophosphors (UCNPs) have attracted considerable attention due to their inherent advantages of large anti-Stoke shifts, long luminescence lifetimes, and absence of autofluorescence under low energy near-infrared (NIR) light excitation. These nanoparticles are promising for the biodetection of various types of analytes. Undoubtedly, the developments of those applications usually rely on resonance energy transfer, which could be regarded as a flexible technology to mediate energy transfer from upconversion phosphor to acceptor for the design of luminescent functional nanoplatforms. Currently, researchers have developed many RET-based upconversion nanosystems (RET-UCNP) that respond to specific changes in the biological environments. Specifically, small organic molecules, biological molecules, metal-organic complexes, or inorganic nanoparticles were carefully selected and bound to the surface of upconversion nanoparticles for the preparation of RET-UCNP nanosystems. Benefiting from the advantage and versatility offered by this technology, the research of RET-based upconversion nanomaterials should have significant implications for advanced biomedical applications. It should be noted that energy transfer in a UCNP based nanosystem is most often related to resonance energy transfer but that reabsorption (and maybe other energy transfer processes) may also play an important role and that more studies regarding the fundamental aspects for energy transfer with UCNPs is necessary. In this Account, we present an overview of recent advances in RET-based upconversion nanocomposites for biodetection with a particular focus on our own work. We have designed a series of upconversion nanoplatforms with remarkably high versatility for different applications. The experience gained from our strategic design and experimental investigations will allow for the construction of next-generation luminescent nanoplatform with marked improvements in their performance. The key aspects of this Account include fundamental principles, design and preparation strategies, biodetection in vitro and in vivo, future opportunities, and challenges of RET-UCNP nanosystems.
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Affiliation(s)
- Qianqian Su
- Department of Chemistry,
State Key Laboratory of Molecular Engineering of Polymers and Institute
of Biomedicine Science, Fudan University, Shanghai 200433, China
| | - Wei Feng
- Department of Chemistry,
State Key Laboratory of Molecular Engineering of Polymers and Institute
of Biomedicine Science, Fudan University, Shanghai 200433, China
| | - Dongpeng Yang
- Department of Chemistry,
State Key Laboratory of Molecular Engineering of Polymers and Institute
of Biomedicine Science, Fudan University, Shanghai 200433, China
| | - Fuyou Li
- Department of Chemistry,
State Key Laboratory of Molecular Engineering of Polymers and Institute
of Biomedicine Science, Fudan University, Shanghai 200433, China
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38
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Ben-Johny M, Yue DN, Yue DT. Detecting stoichiometry of macromolecular complexes in live cells using FRET. Nat Commun 2016; 7:13709. [PMID: 27922011 PMCID: PMC5150656 DOI: 10.1038/ncomms13709] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/25/2016] [Indexed: 11/10/2022] Open
Abstract
The stoichiometry of macromolecular interactions is fundamental to cellular signalling yet challenging to detect from living cells. Fluorescence resonance energy transfer (FRET) is a powerful phenomenon for characterizing close-range interactions whereby a donor fluorophore transfers energy to a closely juxtaposed acceptor. Recognizing that FRET measured from the acceptor's perspective reports a related but distinct quantity versus the donor, we utilize the ratiometric comparison of the two to obtain the stoichiometry of a complex. Applying this principle to the long-standing controversy of calmodulin binding to ion channels, we find a surprising Ca2+-induced switch in calmodulin stoichiometry with Ca2+ channels—one calmodulin binds at basal cytosolic Ca2+ levels while two calmodulins interact following Ca2+ elevation. This feature is curiously absent for the related Na channels, also potently regulated by calmodulin. Overall, our assay adds to a burgeoning toolkit to pursue quantitative biochemistry of dynamic signalling complexes in living cells. Measuring the in vivo stoichiometry of protein-protein interactions is challenging. Here the authors take a FRET-based approach, quantifying stoichiometry based on ratiometric comparison of donor and acceptor fluorescence, and apply their method to report on a Ca2+-induced switch in calmodulin binding to Ca2+ ion channels.
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Affiliation(s)
- Manu Ben-Johny
- Calcium Signals Laboratory, Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Ross Building, Room 713, 720 Rutland Avenue, Baltimore, Maryland 21205, USA
| | - Daniel N Yue
- Calcium Signals Laboratory, Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Ross Building, Room 713, 720 Rutland Avenue, Baltimore, Maryland 21205, USA
| | - David T Yue
- Calcium Signals Laboratory, Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Ross Building, Room 713, 720 Rutland Avenue, Baltimore, Maryland 21205, USA
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Saliba D, Al-Ghoul M. Kinetics of intercalation of fluorescent probes in magnesium-aluminium layered double hydroxide within a multiscale reaction-diffusion framework. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2016.0138. [PMID: 27698034 PMCID: PMC5052724 DOI: 10.1098/rsta.2016.0138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 05/27/2023]
Abstract
We report the synthesis of magnesium-aluminium layered double hydroxide (LDH) using a reaction-diffusion framework (RDF) that exploits the multiscale coupling of molecular diffusion with chemical reactions, nucleation and growth of crystals. In an RDF, the hydroxide anions are allowed to diffuse into an organic gel matrix containing the salt mixture needed for the precipitation of the LDH. The chemical structure and composition of the synthesized magnesium-aluminium LDHs are determined using powder X-ray diffraction (PXRD), thermo-gravimetric analysis, differential scanning calorimetry, solid-state nuclear magnetic resonance (SSNMR), Fourier transform infrared and energy dispersive X-ray spectroscopy. This novel technique also allows the investigation of the mechanism of intercalation of some fluorescent probes, such as the neutral three-dimensional rhodamine B (RhB) and the negatively charged two-dimensional 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS), using in situ steady-state fluorescence spectroscopy. The incorporation of these organic dyes inside the interlayer region of the LDH is confirmed via fluorescence microscopy, solid-state lifetime, SSNMR and PXRD. The activation energies of intercalation of the corresponding molecules (RhB and HPTS) are computed and exhibit dependence on the geometry of the involved probe (two or three dimensions), the charge of the fluorescent molecule (anionic, cationic or neutral) and the cationic ratio of the corresponding LDH.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
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Affiliation(s)
- Daniel Saliba
- Department of Chemistry, American University of Beirut, PO Box 11-0236, Riad El-Solh 1107 2020, Beirut, Lebanon
| | - Mazen Al-Ghoul
- Department of Chemistry, American University of Beirut, PO Box 11-0236, Riad El-Solh 1107 2020, Beirut, Lebanon
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Ozgen H, Baron W, Hoekstra D, Kahya N. Oligodendroglial membrane dynamics in relation to myelin biogenesis. Cell Mol Life Sci 2016; 73:3291-310. [PMID: 27141942 PMCID: PMC4967101 DOI: 10.1007/s00018-016-2228-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
In the central nervous system, oligodendrocytes synthesize a specialized membrane, the myelin membrane, which enwraps the axons in a multilamellar fashion to provide fast action potential conduction and to ensure axonal integrity. When compared to other membranes, the composition of myelin membranes is unique with its relatively high lipid to protein ratio. Their biogenesis is quite complex and requires a tight regulation of sequential events, which are deregulated in demyelinating diseases such as multiple sclerosis. To devise strategies for remedying such defects, it is crucial to understand molecular mechanisms that underlie myelin assembly and dynamics, including the ability of specific lipids to organize proteins and/or mediate protein-protein interactions in healthy versus diseased myelin membranes. The tight regulation of myelin membrane formation has been widely investigated with classical biochemical and cell biological techniques, both in vitro and in vivo. However, our knowledge about myelin membrane dynamics, such as membrane fluidity in conjunction with the movement/diffusion of proteins and lipids in the membrane and the specificity and role of distinct lipid-protein and protein-protein interactions, is limited. Here, we provide an overview of recent findings about the myelin structure in terms of myelin lipids, proteins and membrane microdomains. To give insight into myelin membrane dynamics, we will particularly highlight the application of model membranes and advanced biophysical techniques, i.e., approaches which clearly provide an added value to insight obtained by classical biochemical techniques.
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Affiliation(s)
- Hande Ozgen
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Wia Baron
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
| | - Dick Hoekstra
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Nicoletta Kahya
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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42
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Bag SS, Das SK, Pradhan MK, Jana S. Hybridization accompanying FRET event in labeled natural nucleoside-unnatural nucleoside containing chimeric DNA duplexes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:669-673. [PMID: 27498231 DOI: 10.1016/j.jphotobiol.2016.07.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 07/30/2016] [Indexed: 01/05/2023]
Abstract
Förster resonance energy transfer (FRET) is a highly efficient strategy in illuminating the structures, structural changes and dynamics of DNA, proteins and other biomolecules and thus is being widely utilized in studying such phenomena, in designing molecular/biomolecular probes for monitoring the hybridization event of two single stranded DNA to form duplex, in gene detection and in many other sensory applications in chemistry, biology and material sciences. Moreover, FRET can give information about the positional status of chromophores within the associated biomolecules with much more accuracy than other methods can yield. Toward this end, we want to report here the ability of fluorescent unnatural nucleoside, triazolylphenanthrene ((TPhen)BDo) to show FRET interaction upon hybridization with fluorescently labeled natural nucleosides, (Per)U or (OxoPy)U or (Per)U, forming two stable chimeric DNA duplexes. The pairing selectivity and the thermal duplex stability of the chimeric duplexes are higher than any of the duplexes with natural nucleoside formed. The hybridization results in a Förster resonance energy transfer (FRET) from donor triazolylphenanthrene of (TPhen)BDo to acceptor oxopyrene of (OxoPy)U and/or to perylene chromophore of (Per)U, respectively, in two chimeric DNA duplexes. Therefore, we have established the FRET process in two chimeric DNA duplexes wherein a fluorescently labeled natural nucleoside ((OxoPy)U or (Per)U) paired against an unnatural nucleoside ((TPhen)BDo) without sacrificing the duplex stability and B-DNA conformation. The hybridization accompanying FRET event in these classes of interacting fluorophores is new. Moreover, there is no report of such designed system of chimeric DNA duplex. Our observed phenomenon and the design can potentially be exploited in designing more of such efficient FRET pairs for useful application in the detection and analysis of biomolecular interactions and in material science application.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bio-organic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Suman K Das
- Bio-organic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Manoj Kumar Pradhan
- Bio-organic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Subhashis Jana
- Bio-organic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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43
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Abdelhameed AS, Ajmal MR, Ponnusamy K, Subbarao N, Khan RH. Interaction of the recently approved anticancer drug nintedanib with human acute phase reactant α 1-acid glycoprotein. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.02.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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44
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Hare JE, Goodchild SC, Breit SN, Curmi PMG, Brown LJ. Interaction of Human Chloride Intracellular Channel Protein 1 (CLIC1) with Lipid Bilayers: A Fluorescence Study. Biochemistry 2016; 55:3825-33. [PMID: 27299171 DOI: 10.1021/acs.biochem.6b00080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloride intracellular channel protein 1 (CLIC1) is very unusual as it adopts a soluble glutathione S-transferase-like canonical fold but can also autoinsert into lipid bilayers to form an ion channel. The conversion between these forms involves a large, but reversible, structural rearrangement of the CLIC1 module. The only identified environmental triggers controlling the metamorphic transition of CLIC1 are pH and oxidation. Until now, there have been no high-resolution structural data available for the CLIC1 integral membrane state, and consequently, a limited understanding of how CLIC1 unfolds and refolds across the bilayer to form a membrane protein with ion channel activity exists. Here we show that fluorescence spectroscopy can be used to establish the interaction and position of CLIC1 in a lipid bilayer. Our method employs a fluorescence energy transfer (FRET) approach between CLIC1 and a dansyl-labeled lipid analogue to probe the CLIC1-lipid interface. Under oxidizing conditions, a strong FRET signal between the single tryptophan residue of CLIC1 (Trp35) and the dansyl-lipid analogue was detected. When considering the proportion of CLIC1 interacting with the lipid bilayer, as estimated by fluorescence quenching experiments, the FRET distance between Trp35 and the dansyl moiety on the membrane surface was determined to be ∼15 Å. This FRET-detected interaction provides direct structural evidence that CLIC1 associates with membranes. The results presented support the current model of an oxidation-driven interaction of CLIC1 with lipid bilayers and also propose a membrane anchoring role for Trp35.
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Affiliation(s)
- Joanna E Hare
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Sophia C Goodchild
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds LS29JT, United Kingdom
| | - Samuel N Breit
- St Vincent's Centre for Applied Medical Research, St Vincent's Hospital , Sydney, New South Wales 2010, Australia
| | - Paul M G Curmi
- School of Physics, University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Louise J Brown
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
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Inayathullah M, Rajadas J. Conformational dynamics of a hydrophobic prion fragment (113-127) in different pH and osmolyte solutions. Neuropeptides 2016; 57:9-14. [PMID: 26919915 DOI: 10.1016/j.npep.2016.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 02/09/2016] [Accepted: 02/14/2016] [Indexed: 01/17/2023]
Abstract
Prion diseases are characterized by a conformational change in prion protein from its native state into beta-sheet rich aggregates that are neurotoxic. The central domain that contain a highly conserved hydrophobic region of the protein play an important role in the toxicity. The conformation of the proteins is largely influenced by various solvent environments. Here we report results of study of hydrophobic prion fragment peptide PrP(113-127) under different pH and osmolytes solution conditions. The secondary structure and the folding of PrP(113-127) was determined using circular dichroism and fluorescence spectroscopic methods. The results indicate that PrP(113-127) adopts a random coil conformation in aqueous buffer at neutral pH and that converted into beta sheet on aging. Even though the initial random coil conformation was similar in different pH conditions, the acidic as well as basic pH conditions delays the conformational transition to beta sheet. FRET results indicate that the distance between N and C-terminal regions increased on aging due to unfolding by self-assembly of the peptide into an organized beta sheet structure. Presence of osmolytes, prevented or decelerated the aggregation process of PrP(113-127) peptide.
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Affiliation(s)
- Mohammed Inayathullah
- Biomaterials and Advanced Drug Delivery Laboratory, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Bioorganic and Neurochemistry Laboratory, Central Leather Research Institute, Adyar, Chennai, Tamil Nadu 600020, India; Cardiovascular Pharmacology Division, Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jayakumar Rajadas
- Biomaterials and Advanced Drug Delivery Laboratory, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; Cardiovascular Pharmacology Division, Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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Ajmal MR, Zaidi N, Alam P, Nusrat S, Siddiqi MK, Badr G, Mahmoud MH, Khan RH. Insight into the interaction of antitubercular and anticancer compound clofazimine with human serum albumin: spectroscopy and molecular modelling. J Biomol Struct Dyn 2016; 35:46-57. [DOI: 10.1080/07391102.2015.1132258] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Mohammad Rehan Ajmal
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Nida Zaidi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Parvez Alam
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Saima Nusrat
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | | | - Gamal Badr
- Laboratory of Immunology and Molecular Physiology, Zoology Department, Faculty of Science, Assiut University, 71516 Assiut, Egypt
| | - Mohamed H. Mahmoud
- Deanship of Scientific Research, King Saud University, Riyadh, Saudi Arabia
- Food Science and Nutrition Department, National Research Center, Dokki, Cairo, Egypt
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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Trappl K, Joseph S. Ribosome Induces a Closed to Open Conformational Change in Release Factor 1. J Mol Biol 2016; 428:1333-1344. [PMID: 26827724 DOI: 10.1016/j.jmb.2016.01.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 01/15/2016] [Accepted: 01/22/2016] [Indexed: 11/19/2022]
Abstract
Bacterial translation termination is triggered when a stop codon arrives at the ribosomal A site. Stop codons are recognized by class I release factors (RF1 and RF2 in Escherichia coli), which bind to the ribosome and catalyze the release of the newly synthesized protein. Crystal structures showed that RF1 and RF2 are in an open conformation when bound to the ribosome but are in a closed conformation when not bound to the ribosome. It is not clear whether only the open form of RF1 and RF2 binds to the ribosome. Alternatively, the closed form of RF1 and RF2 may bind to the ribosome and undergo a conformational change to the open state upon binding. We used transition metal ion fluorescence resonance energy transfer experiments to monitor precisely the conformation of RF1 in the absence and presence of the ribosome. Our results indicate that RF1 undergoes a large conformational change from a closed to an open form upon binding to the ribosome. Our results are consistent with the mechanism, in which high termination fidelity is achieved by linking stop codon recognition by RF1 to the change in conformation from closed to open state.
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Affiliation(s)
- Krista Trappl
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0314, USA
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0314, USA.
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Arii Y, Yamaguchi H, Yamasaki M, Fukuoka SI. Detection of an interaction between prion protein and neuregulin I-β1 by fluorescence resonance energy transfer analysis. Biosci Biotechnol Biochem 2016; 80:761-8. [PMID: 26796243 DOI: 10.1080/09168451.2015.1116934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cellular prion protein (PrP) copurifies with neuregulin type I-β1 (NRG I-β1), but no interaction has been detected by a general immunoprecipitation study. We speculate that PrP interacts with NRG I-β1. Here, the interaction of PrP with NRG I-β1 was detected by measuring fluorescence resonance energy transfer (FRET) between enhanced blue (EBFP) and enhanced green (EGFP) fluorescent protein-fusion proteins. Full-length PrP interacted with EGFP in addition to NRG I-β1. From this result, we deduced that PrP interacts with EGFP through its unstructured N-terminal domain. We therefore detected FRET between PrP deleting the N-terminal domain and NRG I-β1. In contrast, the C-terminal domain of PrP interacted with NRG I-β1 and the proteins dissociated completely in the presence of sodium chloride. This interaction occurs at the nanomolar level, which is important for the reaction to be functional in organisms. We concluded that PrP interacted with NRG I-β1 through its C-terminal domain.
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Affiliation(s)
- Yasuhiro Arii
- a Department of Food Science and Nutrition, School of Human Environmental Sciences , Mukogawa Women's University , Nishinomiya , Japan
| | - Hidenori Yamaguchi
- b Biological Science Course, Graduate School of Science and Engineering , Aoyama Gakuin University , Sagamihara , Japan
| | | | - Shin-Ichi Fukuoka
- b Biological Science Course, Graduate School of Science and Engineering , Aoyama Gakuin University , Sagamihara , Japan
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Kundu R. G-Tetraplex-Induced FRET within Telomeric Repeat Sequences Using (Py) A-(Per) A as Energy Donor-Acceptor Pair. Chem Asian J 2015; 11:198-201. [PMID: 26490798 DOI: 10.1002/asia.201500996] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 01/08/2023]
Abstract
G-tetraplex induced fluorescence resonance energy transfer (FRET) within telomeric repeat sequences has been studied using a nucleoside-tethered FRET pair embedded in the human telomeric G-quadruplex forming sequence (5'-A GGG TT(Py) A GGG TT(Per) A GGG TTA GGG-3', Py=pyrene, Per=perylene). Conformational change from a single strand to an anti-parallel G-quadruplex leads to FRET from energy donor ((Py) A) to acceptor ((Per) A). The distance between the FRET donor/acceptor partners was controlled by changing the number of G-quartet spacer units. The FRET efficiency decreases with increase in G-quartet units. Overall findings indicate that this could be further used for the development of FRET-based sensing and measurement techniques.
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Affiliation(s)
- Rajen Kundu
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 790784, South Korea. .,Department of Chemistry and Biochemistry, University of Colorado, Boulder, 80303, USA.
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Deng W, Goldys EM. Chemical sensing with nanoparticles as optical reporters: from noble metal nanoparticles to quantum dots and upconverting nanoparticles. Analyst 2015; 139:5321-34. [PMID: 25170528 DOI: 10.1039/c4an01272k] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A wide variety of biological and medical analyses are based on the use of optical signals to report specific molecular events. Thanks to advances in nanotechnology, various nanostructures have been extensively used as optical reporters in bio- and chemical assays. This review describes recent progress in chemical sensing using noble metal nanoparticles (gold and silver), quantum dots and upconverting nanoparticles. It provides insights into various nanoparticle-based sensing strategies including fluorescence/luminescence resonance energy transfer nanoprobes as well as activatable probes sensitive to specific changes in the biological environment. Finally we list some research challenges to be overcome in order to accelerate the development of applications of nanoparticle bio- and chemical sensors.
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Affiliation(s)
- Wei Deng
- Centre for Nanoscale BioPhotonics, Macquarie University, North Ryde, 2109, NSW, Australia.
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